Year |
Citation |
Score |
2024 |
Haspel N, Jang H, Nussinov R. Allosteric Activation of RhoA Complexed with p115-RhoGEF Deciphered by Conformational Dynamics. Journal of Chemical Information and Modeling. 64: 862-873. PMID 38215280 DOI: 10.1021/acs.jcim.3c01412 |
0.614 |
|
2020 |
Haspel N, Jang H, Nussinov R. Active and Inactive Cdc42 Differ in Their Insert Region Conformational Dynamics. Biophysical Journal. PMID 33347888 DOI: 10.1016/j.bpj.2020.12.007 |
0.647 |
|
2020 |
Zhang M, Jang H, Nussinov R. Structural Features that Distinguish Inactive and Active PI3K Lipid Kinases. Journal of Molecular Biology. PMID 32918948 DOI: 10.1016/J.Jmb.2020.09.002 |
0.308 |
|
2020 |
Dudas B, Merzel F, Jang H, Nussinov R, Perahia D, Balog E. Nucleotide-Specific Autoinhibition of Full-Length K-Ras4B Identified by Extensive Conformational Sampling. Frontiers in Molecular Biosciences. 7: 145. PMID 32754617 DOI: 10.3389/Fmolb.2020.00145 |
0.343 |
|
2020 |
Liao TJ, Jang H, Fushman D, Nussinov R. SOS1 interacts with Grb2 through regions that induce closed nSH3 conformations. The Journal of Chemical Physics. 153: 045106. PMID 32752665 DOI: 10.1063/5.0013926 |
0.391 |
|
2020 |
Younger S, Jang H, Davies HA, Niemiec MJ, Garcia JGN, Nussinov R, Migrino RQ, Madine J, Arce FT. Medin Oligomer Membrane Pore Formation: A Potential Mechanism of Vascular Dysfunction. Biophysical Journal. PMID 32402244 DOI: 10.1016/J.Bpj.2020.04.026 |
0.304 |
|
2020 |
Jang H, Zhang M, Nussinov R. The quaternary assembly of KRas4B with Raf-1 at the membrane. Computational and Structural Biotechnology Journal. 18: 737-748. PMID 32257057 DOI: 10.1016/J.Csbj.2020.03.018 |
0.309 |
|
2020 |
Guven-Maiorov E, Hakouz A, Valjevac S, Keskin O, Tsai CJ, Gursoy A, Nussinov R. HMI-PRED: A Web Server for Structural Prediction of Host-Microbe Interactions Based on Interface Mimicry. Journal of Molecular Biology. PMID 32061934 DOI: 10.1016/J.Jmb.2020.01.025 |
0.325 |
|
2020 |
Liao TJ, Jang H, Nussinov R, Fushman D. High-affinity Interactions of the nSH3/cSH3 Domains of Grb2 with the C-terminal Proline-rich Domain of SOS1. Journal of the American Chemical Society. PMID 31970984 DOI: 10.1021/Jacs.9B10710 |
0.343 |
|
2020 |
Muratcioglu S, Aydin C, Odabasi E, Ozdemir ES, Firat-Karalar EN, Jang H, Tsai CJ, Nussinov R, Kavakli IH, Gursoy A, Keskin O. Oncogenic K-Ras4B dimerization enhances downstream MAPK signaling. Journal of Molecular Biology. PMID 31931009 DOI: 10.1016/J.Jmb.2020.01.002 |
0.305 |
|
2019 |
Guven-Maiorov E, Tsai CJ, Nussinov R. Oncoviruses Can Drive Cancer by Rewiring Signaling Pathways Through Interface Mimicry. Frontiers in Oncology. 9: 1236. PMID 31803618 DOI: 10.3389/Fonc.2019.01236 |
0.343 |
|
2019 |
Zhang M, Li Z, Jang H, Hedman A, Sacks DB, Nussinov R. Ca2+-dependent Switch of Calmodulin Interaction Mode with Tandem IQ motifs in The Scaffolding Protein IQGAP1. Biochemistry. PMID 31724397 DOI: 10.1021/Acs.Biochem.9B00854 |
0.322 |
|
2019 |
Nussinov R, Tsai CJ, Jang H. Dynamic Protein Allosteric Regulation and Disease. Advances in Experimental Medicine and Biology. 1163: 25-43. PMID 31707698 DOI: 10.1007/978-981-13-8719-7_2 |
0.332 |
|
2019 |
Jang H, Banerjee A, Marcus K, Makowski L, Mattos C, Gaponenko V, Nussinov R. The Structural Basis of the Farnesylated and Methylated KRas4B Interaction with Calmodulin. Structure (London, England : 1993). PMID 31495533 DOI: 10.1016/J.Str.2019.08.009 |
0.313 |
|
2019 |
Tsai CJ, Nussinov R. Emerging Allosteric Mechanism of EGFR Activation in Physiological and Pathological Contexts. Biophysical Journal. PMID 31202480 DOI: 10.1016/J.Bpj.2019.05.021 |
0.306 |
|
2019 |
Zhang M, Jang H, Nussinov R. The mechanism of PI3Kα activation at the atomic level. Chemical Science. 10: 3671-3680. PMID 30996962 DOI: 10.1039/C8Sc04498H |
0.313 |
|
2019 |
Nussinov R, Jang H, Tsai CJ, Cheng F. Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers. Plos Computational Biology. 15: e1006658. PMID 30921324 DOI: 10.1371/Journal.Pcbi.1006658 |
0.335 |
|
2019 |
Nussinov R, Tsai CJ, Shehu A, Jang H. Computational Structural Biology: Successes, Future Directions, and Challenges. Molecules (Basel, Switzerland). 24. PMID 30759724 DOI: 10.3390/Molecules24030637 |
0.307 |
|
2019 |
Ozdemir ES, Halakou F, Nussinov R, Gursoy A, Keskin O. Methods for Discovering and Targeting Druggable Protein-Protein Interfaces and Their Application to Repurposing. Methods in Molecular Biology (Clifton, N.J.). 1903: 1-21. PMID 30547433 DOI: 10.1007/978-1-4939-8955-3_1 |
0.312 |
|
2019 |
Guven-Maiorov E, Tsai CJ, Ma B, Nussinov R. Interface-Based Structural Prediction of Novel Host-Pathogen Interactions. Methods in Molecular Biology (Clifton, N.J.). 1851: 317-335. PMID 30298406 DOI: 10.1007/978-1-4939-8736-8_18 |
0.343 |
|
2019 |
Liao T, Jang H, Nussinov R, Fushman D. Abstract 5145: A new discovering motif on SOS1 PR domain clues Grb2-SOS1 association Cancer Research. 79: 5145-5145. DOI: 10.1158/1538-7445.Sabcs18-5145 |
0.361 |
|
2019 |
Liao T, Jang H, Nussinov R, Fushman D. Structure Based Search for Multiple Binding Sites of SOS1 PR Domain Recognizes an Uncovered Motif Favoring GRB2-SOS1 Association Biophysical Journal. 116: 169a. DOI: 10.1016/J.Bpj.2018.11.937 |
0.326 |
|
2018 |
Zhang M, Zheng J, Nussinov R, Ma B. Molecular Recognition between Aβ-Specific Single-Domain Antibody and Aβ Misfolded Aggregates. Antibodies (Basel, Switzerland). 7. PMID 31544877 DOI: 10.3390/Antib7030025 |
0.312 |
|
2018 |
Lei J, Qi R, Tang Y, Wang W, Wei G, Nussinov R, Ma B. Conformational stability and dynamics of the cancer-associated isoform Δ133p53β are modulated by p53 peptides and p53-specific DNA. Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. fj201801973R. PMID 30540922 DOI: 10.1096/Fj.201801973R |
0.338 |
|
2018 |
Ozdemir ES, Nussinov R, Gursoy A, Keskin O. Developments in integrative modeling with dynamical interfaces. Current Opinion in Structural Biology. 56: 11-17. PMID 30439586 DOI: 10.1016/J.Sbi.2018.10.007 |
0.375 |
|
2018 |
Rangarajan S, He Y, Chen Y, Kerzic MC, Ma B, Gowthaman R, Pierce BG, Nussinov R, Mariuzza RA, Orban J. Peptide-MHC (pMHC) binding to a human antiviral T cell receptor induces long-range allosteric communication between pMHC- and CD3-binding sites. The Journal of Biological Chemistry. PMID 30135211 DOI: 10.1074/Jbc.Ra118.003832 |
0.307 |
|
2018 |
Liao TJ, Jang H, Fushman D, Nussinov R. Allosteric KRas4B Can Modulate SOS1 Fast and Slow Ras Activation Cycles. Biophysical Journal. PMID 30097175 DOI: 10.1016/J.Bpj.2018.07.016 |
0.327 |
|
2018 |
Tsai CJ, Nussinov R. Allosteric activation of RAF in the MAPK signaling pathway. Current Opinion in Structural Biology. 53: 100-106. PMID 30059805 DOI: 10.1016/J.Sbi.2018.07.007 |
0.303 |
|
2018 |
Zhang M, Li Z, Wang G, Jang H, Sacks D, Zhang J, Gaponenko V, Nussinov R. Calmodulin (CaM) Activates PI3Kα by Targeting the "Soft" CaM-Binding Motifs in Both the nSH2 and cSH2 Domains of p85α. The Journal of Physical Chemistry. B. PMID 30047727 DOI: 10.1021/Acs.Jpcb.8B05982 |
0.35 |
|
2018 |
Ozdemir ES, Jang H, Gursoy A, Keskin O, Nussinov R. Arl2-Mediated Allosteric Release of Farnesylated KRas4B from Shuttling Factor PDEδ. The Journal of Physical Chemistry. B. PMID 29961325 DOI: 10.1021/Acs.Jpcb.8B04347 |
0.35 |
|
2018 |
Ren B, Hu R, Zhang M, Liu Y, Xu L, Jiang B, Ma J, Ma B, Nussinov R, Zheng J. Experimental and Computational Protocols for Studies of Cross-Seeding Amyloid Assemblies. Methods in Molecular Biology (Clifton, N.J.). 1777: 429-447. PMID 29744852 DOI: 10.1007/978-1-4939-7811-3_27 |
0.311 |
|
2018 |
Qi R, Wei G, Ma B, Nussinov R. Replica Exchange Molecular Dynamics: A Practical Application Protocol with Solutions to Common Problems and a Peptide Aggregation and Self-Assembly Example. Methods in Molecular Biology (Clifton, N.J.). 1777: 101-119. PMID 29744830 DOI: 10.1007/978-1-4939-7811-3_5 |
0.357 |
|
2018 |
Wang G, Zhang M, Jang H, Lu S, Lin S, Chen GQ, Nussinov R, Zhang J, Gaponenko V. Interaction of Calmodulin with the cSH2 Domain of the p85 Regulatory Subunit. Biochemistry. PMID 29494137 DOI: 10.1021/Acs.Biochem.7B01130 |
0.341 |
|
2018 |
Ozdemir ES, Jang H, Gursoy A, Keskin O, Li Z, Sacks DB, Nussinov R. Unraveling the molecular mechanism of interactions of the Rho GTPases Cdc42 and Rac1 with the scaffolding protein IQGAP2. The Journal of Biological Chemistry. PMID 29358323 DOI: 10.1074/Jbc.Ra117.001596 |
0.373 |
|
2018 |
Liao T, Jang H, Fushman D, Nussinov R. Abstract 683: SOS1 allosterically linked conformational changes modulate KRas4B activation Cancer Research. 78: 683-683. DOI: 10.1158/1538-7445.Am2018-683 |
0.306 |
|
2017 |
Zhao J, Zhang B, Zhu J, Nussinov R, Ma B. Structure and energetic basis of overrepresented λ light chain in systemic light chain amyloidosis patients. Biochimica Et Biophysica Acta. PMID 29241665 DOI: 10.1016/J.Bbadis.2017.12.009 |
0.347 |
|
2017 |
Wang M, Zhu D, Zhu J, Nussinov R, Ma B. Local and global anatomy of antibody-protein antigen recognition. Journal of Molecular Recognition : Jmr. PMID 29218757 DOI: 10.1002/Jmr.2693 |
0.319 |
|
2017 |
Zhang M, Jang H, Gaponenko V, Nussinov R. Phosphorylated Calmodulin Promotes PI3K Activation by Binding to the SH2 Domains. Biophysical Journal. 113: 1956-1967. PMID 29117520 DOI: 10.1016/J.Bpj.2017.09.008 |
0.338 |
|
2017 |
Guven-Maiorov E, Tsai CJ, Ma B, Nussinov R. Prediction of Host-Pathogen Interactions for Helicobacter pylori by Interface Mimicry and Implications to Gastric Cancer. Journal of Molecular Biology. PMID 29106933 DOI: 10.1016/J.Jmb.2017.10.023 |
0.304 |
|
2017 |
Nussinov R, Zhang M, Tsai CJ, Jang H. Calmodulin and IQGAP1 activation of PI3Kα and Akt in KRAS, HRAS and NRAS-driven cancers. Biochimica Et Biophysica Acta. PMID 29097261 DOI: 10.1016/J.Bbadis.2017.10.032 |
0.318 |
|
2017 |
Dong X, Sun Y, Wei G, Nussinov R, Ma B. Binding of protofibrillar Aβ trimers to lipid bilayer surface enhances Aβ structural stability and causes membrane thinning. Physical Chemistry Chemical Physics : Pccp. PMID 28979963 DOI: 10.1039/C7Cp05959K |
0.313 |
|
2017 |
Zhao J, Nussinov R, Ma B. Mechanisms of recognition of Aβ monomer, oligomer, and fibril by homologous antibodies. The Journal of Biological Chemistry. PMID 28924036 DOI: 10.1074/Jbc.M117.801514 |
0.354 |
|
2017 |
Liu J, Nussinov R. Energetic redistribution in allostery to execute protein function. Proceedings of the National Academy of Sciences of the United States of America. PMID 28696318 DOI: 10.1073/Pnas.1709071114 |
0.386 |
|
2017 |
Andrabi M, Hutchins AP, Miranda-Saavedra D, Kono H, Nussinov R, Mizuguchi K, Ahmad S. Predicting conformational ensembles and genome-wide transcription factor binding sites from DNA sequences. Scientific Reports. 7: 4071. PMID 28642456 DOI: 10.1038/S41598-017-03199-6 |
0.326 |
|
2017 |
Li N, Jang H, Yuan M, Li W, Yun X, Lee J, Du Q, Nussinov R, Hou J, Lal R, Zhang F. Graphite-Templated Amyloid Nanostructures Formed by A Potential Pentapeptide Inhibitor for Alzheimer's disease: A Combined Study of Real-Time Atomic Force Microscopy and Molecular Dynamics Simulations. Langmuir : the Acs Journal of Surfaces and Colloids. PMID 28605901 DOI: 10.1021/Acs.Langmuir.7B00414 |
0.323 |
|
2017 |
Tuncbag N, Keskin O, Nussinov R, Gursoy A. Prediction of Protein Interactions by Structural Matching: Prediction of PPI Networks and the Effects of Mutations on PPIs that Combines Sequence and Structural Information. Methods in Molecular Biology (Clifton, N.J.). 1558: 255-270. PMID 28150242 DOI: 10.1007/978-1-4939-6783-4_12 |
0.409 |
|
2017 |
Onel M, Sumbul F, Liu J, Nussinov R, Haliloglu T. Cullin Neddylation May Allosterically Tune Polyubiquitin Chain Length and Topology. The Biochemical Journal. PMID 28082425 DOI: 10.1042/Bcj20160748 |
0.358 |
|
2017 |
Xu L, Ma B, Nussinov R, Thompson D. Familial Mutations May Switch Conformational Preferences in α-Synuclein Fibrils. Acs Chemical Neuroscience. PMID 28075555 DOI: 10.1021/Acschemneuro.6B00406 |
0.378 |
|
2017 |
Gan W, Schneidman D, Zhang N, Ma B, Nussinov R. Probing Oligomerized Conformations of Defensin in the Membrane. Methods in Molecular Biology (Clifton, N.J.). 1529: 353-362. PMID 27914061 DOI: 10.1007/978-1-4939-6637-0_18 |
0.358 |
|
2017 |
Haspel N, Zheng J, Aleman C, Zanuy D, Nussinov R. A Protocol for the Design of Protein and Peptide Nanostructure Self-Assemblies Exploiting Synthetic Amino Acids. Methods in Molecular Biology (Clifton, N.J.). 1529: 323-352. PMID 27914060 DOI: 10.1007/978-1-4939-6637-0_17 |
0.661 |
|
2017 |
Zhao J, Nussinov R, Ma B. Allosteric control of antibody-prion recognition through oxidation of a disulfide bond between the CH and CL chains. Protein Engineering, Design & Selection : Peds. 30: 67-76. PMID 27899437 DOI: 10.1093/Protein/Gzw065 |
0.335 |
|
2017 |
Jang H, Banerjee A, Gaponenko V, Nussinov R. Abstract 5229: High affinity interaction of K-Ras4B HVR with calmodulin Cancer Research. 77: 5229-5229. DOI: 10.1158/1538-7445.Am2017-5229 |
0.32 |
|
2016 |
Gong Y, Zhu Y, Zou Y, Ma B, Nussinov R, Zhang Q. Human Neuronal Calcium Sensor-1 Protein Avoids Histidine Residues to Decrease pH Sensitivity. The Journal of Physical Chemistry. B. PMID 28030949 DOI: 10.1021/Acs.Jpcb.6B11094 |
0.354 |
|
2016 |
Ma B, Nussinov R. Protein dynamics: Conformational footprints. Nature Chemical Biology. 12: 890-891. PMID 27755531 DOI: 10.1038/Nchembio.2212 |
0.342 |
|
2016 |
Zhang M, Zheng J, Nussinov R, Ma B. Oncogenic Mutations Differentially Affect Bax Monomer, Dimer, and Oligomeric Pore Formation in the Membrane. Scientific Reports. 6: 33340. PMID 27630059 DOI: 10.1038/Srep33340 |
0.333 |
|
2016 |
Lambrughi M, De Gioia L, Gervasio FL, Lindorff-Larsen K, Nussinov R, Urani C, Bruschi M, Papaleo E. DNA-binding protects p53 from interactions with cofactors involved in transcription-independent functions. Nucleic Acids Research. 44: 9096-9109. PMID 27604871 DOI: 10.1093/Nar/Gkw770 |
0.369 |
|
2016 |
Zhan C, Qi R, Wei G, Guven-Maiorov E, Nussinov R, Ma B. Conformational dynamics of cancer-associated MyD88-TIR domain mutant L252P (L265P) allosterically tilts the landscape toward homo-dimerization. Protein Engineering, Design & Selection : Peds. PMID 27503954 DOI: 10.1093/Protein/Gzw033 |
0.342 |
|
2016 |
Guven-Maiorov E, Tsai CJ, Nussinov R. Pathogen Mimicry of Host Protein-Protein Interfaces Modulates Immune Response. Seminars in Cell & Developmental Biology. PMID 27287306 DOI: 10.1016/J.Semcdb.2016.06.004 |
0.334 |
|
2016 |
Nussinov R. Introduction to Protein Ensembles and Allostery. Chemical Reviews. 116: 6263-6. PMID 27268255 DOI: 10.1021/Acs.Chemrev.6B00283 |
0.343 |
|
2016 |
Ma B, Zhao J, Nussinov R. Conformational selection in amyloid-based immunotherapy: Survey of crystal structures of antibody-amyloid complexes. Biochimica Et Biophysica Acta. PMID 27266343 DOI: 10.1016/J.Bbagen.2016.05.040 |
0.304 |
|
2016 |
Liu J, Nussinov R. Allostery: An Overview of Its History, Concepts, Methods, and Applications. Plos Computational Biology. 12: e1004966. PMID 27253437 DOI: 10.1371/Journal.Pcbi.1004966 |
0.334 |
|
2016 |
Maximova T, Moffatt R, Ma B, Nussinov R, Shehu A. Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics. Plos Computational Biology. 12: e1004619. PMID 27124275 DOI: 10.1371/Journal.Pcbi.1004619 |
0.318 |
|
2016 |
Tuncbag N, Gursoy A, Keskin O, Nussinov R. The potential impact of recent developments in three-dimensional quantitative interaction proteomics on structural biology. Expert Review of Proteomics. 13: 447-9. PMID 27104235 DOI: 10.1080/14789450.2016.1182023 |
0.308 |
|
2016 |
Jang H, Muratcioglu S, Gursoy A, Keskin O, Nussinov R. Membrane-associated Ras dimers are isoform-specific: K-Ras dimers differ from H-Ras dimers. The Biochemical Journal. PMID 27057007 DOI: 10.1042/Bcj20160031 |
0.306 |
|
2016 |
Hewitt WM, Lountos GT, Zlotkowski K, Dahlhauser SD, Saunders LB, Needle D, Tropea JE, Zhan C, Wei G, Ma B, Nussinov R, Waugh DS, Schneekloth JS. Insights Into the Allosteric Inhibition of the SUMO E2 Enzyme Ubc9. Angewandte Chemie (International Ed. in English). PMID 27038327 DOI: 10.1002/Anie.201511351 |
0.316 |
|
2016 |
Zhu Y, Ma B, Qi R, Nussinov R, Zhang Q. Temperature-dependent Conformational Properties of Human Neuronal Calcium Sensor-1 Protein Revealed by All-atom Simulations. The Journal of Physical Chemistry. B. PMID 27007011 DOI: 10.1021/Acs.Jpcb.5B12299 |
0.347 |
|
2016 |
Lei J, Qi R, Wei G, Nussinov R, Ma B. Self-aggregation and coaggregation of the p53 core fragment with its aggregation gatekeeper variant. Physical Chemistry Chemical Physics : Pccp. PMID 26923710 DOI: 10.1039/C5Cp06538K |
0.315 |
|
2016 |
Papaleo E, Saladino G, Lambrughi M, Lindorff-Larsen K, Gervasio FL, Nussinov R. The Role of Protein Loops and Linkers in Conformational Dynamics and Allostery. Chemical Reviews. 116: 6391-423. PMID 26889708 DOI: 10.1021/Acs.Chemrev.5B00623 |
0.4 |
|
2016 |
Xu L, Nussinov R, Ma B. Coupling of the non-amyloid-component (NAC) domain and the KTK(E/Q)GV repeats stabilize the α-synuclein fibrils. European Journal of Medicinal Chemistry. PMID 26873872 DOI: 10.1016/J.Ejmech.2016.01.044 |
0.35 |
|
2016 |
Nussinov R, Udgaonkar JB. Editorial overview: Folding and binding: Dynamic conformational heterogeneity is pivotal to cell life. Current Opinion in Structural Biology. PMID 26873135 DOI: 10.1016/J.Sbi.2016.01.012 |
0.309 |
|
2016 |
Xu L, Zheng J, Margittai M, Nussinov R, Ma B. Hyperphopsphorylation Promotes Tau Aggregation by Modulating Filament Structure and Stability. Acs Chemical Neuroscience. PMID 26854860 DOI: 10.1021/Acschemneuro.5B00294 |
0.334 |
|
2016 |
Zou Y, Sun Y, Zhu Y, Ma B, Nussinov R, Zhang Q. Critical Nucleus Structure and Aggregation Mechanism of the C-terminal Fragment of SOD1 Protein. Acs Chemical Neuroscience. PMID 26815332 DOI: 10.1021/Acschemneuro.5B00242 |
0.348 |
|
2016 |
Lu S, Jang H, Muratcioglu S, Gursoy A, Keskin O, Nussinov R, Zhang J. Ras Conformational Ensembles, Allostery, and Signaling. Chemical Reviews. PMID 26815308 DOI: 10.1021/Acs.Chemrev.5B00542 |
0.317 |
|
2016 |
Wei G, Xi W, Nussinov R, Ma B. Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell. Chemical Reviews. PMID 26807783 DOI: 10.1021/Acs.Chemrev.5B00562 |
0.409 |
|
2016 |
Kumar S, Tsai CJ, Ma B, Nussinov R. Contribution of salt bridges toward protein thermostability. Journal of Biomolecular Structure & Dynamics. 79-85. PMID 22607409 DOI: 10.1080/07391102.2000.10506606 |
0.371 |
|
2016 |
Jang H, Nussinov R. Abstract 1500: How K-Ras4B attaches to the membrane and forms a dimer: A new paradigm Cancer Research. 76: 1500-1500. DOI: 10.1158/1538-7445.Am2016-1500 |
0.324 |
|
2016 |
Ma B, Wei G, Zhen J, Nussinov R. Dancing with Strings: The Conformational Dynamics of VQIXXK Motifs within Tau Protein in Monomer, Fibril and Hyper-Phosphorylated Filament States Biophysical Journal. 110: 553a-554a. DOI: 10.1016/J.Bpj.2015.11.2960 |
0.388 |
|
2016 |
Zhao J, Ma B, Nussinov R. Compilation and Analysis of Enzymes, Engineered Antibodies, and Nanoparticles Designed to Interfere with Amyloid-β Aggregation Israel Journal of Chemistry. 57: 622-633. DOI: 10.1002/Ijch.201600093 |
0.307 |
|
2015 |
Banerjee A, Jang H, Nussinov R, Gaponenko V. The disordered hypervariable region and the folded catalytic domain of oncogenic K-Ras4B partner in phospholipid binding. Current Opinion in Structural Biology. 36: 10-17. PMID 26709496 DOI: 10.1016/J.Sbi.2015.11.010 |
0.329 |
|
2015 |
Chavan TS, Jang H, Khavrutskii L, Abraham SJ, Banerjee A, Freed BC, Johannessen L, Tarasov SG, Gaponenko V, Nussinov R, Tarasova NI. High-Affinity Interaction of the K-Ras4B Hypervariable Region with the Ras Active Site. Biophysical Journal. 109: 2602-13. PMID 26682817 DOI: 10.1016/J.Bpj.2015.09.034 |
0.351 |
|
2015 |
Xu L, Nussinov R, Ma B. Allosteric stabilization of the amyloid-β peptide hairpin by the fluctuating N-terminal. Chemical Communications (Cambridge, England). PMID 26666686 DOI: 10.1039/C5Cc08107F |
0.334 |
|
2015 |
Datta SA, Clark PK, Fan L, Ma B, Harvin DP, Sowder RC, Nussinov R, Wang YX, Rein A. DIMERIZATION OF THE SP-1 REGION OF HIV-1 GAG INDUCES A HELICAL CONFORMATION AND ASSOCIATION INTO HELICAL BUNDLES: IMPLICATIONS FOR PARTICLE ASSEMBLY. Journal of Virology. PMID 26637452 DOI: 10.1128/Jvi.02061-15 |
0.304 |
|
2015 |
Nussinov R, Tsai CJ. Tandem Domains with Tuned Interactions Are a Powerful Biological Design Principle. Plos Biology. 13: e1002306. PMID 26618518 DOI: 10.1371/Journal.Pbio.1002306 |
0.399 |
|
2015 |
Shehu A, Nussinov R. Computational Methods for Exploration and Analysis of Macromolecular Structure and Dynamics. Plos Computational Biology. 11: e1004585. PMID 26505479 DOI: 10.1371/Journal.Pcbi.1004585 |
0.407 |
|
2015 |
Lu S, Banerjee A, Jang H, Zhang J, Gaponenko V, Nussinov R. GTP Binding and Oncogenic Mutations May Attenuate Hypervariable Region (HVR)-Catalytic Domain Interactions in Small GTPase KRAS4B, Exposing the Effector Binding Site. The Journal of Biological Chemistry. PMID 26453300 DOI: 10.1074/Jbc.M115.664755 |
0.326 |
|
2015 |
Zhu Y, Yang S, Qi R, Zou Y, Ma B, Nussinov R, Zhang Q. Effects of the C-Terminal Tail on the Conformational Dynamics of Human Neuronal Calcium Sensor-1 Protein. The Journal of Physical Chemistry. B. PMID 26447771 DOI: 10.1021/Acs.Jpcb.5B07962 |
0.368 |
|
2015 |
Clausen R, Ma B, Nussinov R, Shehu A. Mapping the Conformation Space of Wildtype and Mutant H-Ras with a Memetic, Cellular, and Multiscale Evolutionary Algorithm. Plos Computational Biology. 11: e1004470. PMID 26325505 DOI: 10.1371/Journal.Pcbi.1004470 |
0.383 |
|
2015 |
Muratcioglu S, Presman DM, Pooley JR, Grøntved L, Hager GL, Nussinov R, Keskin O, Gursoy A. Structural Modeling of GR Interactions with the SWI/SNF Chromatin Remodeling Complex and C/EBP. Biophysical Journal. 109: 1227-39. PMID 26278180 DOI: 10.1016/J.Bpj.2015.06.044 |
0.381 |
|
2015 |
Guven-Maiorov E, Keskin O, Gursoy A, Nussinov R. A Structural View of Negative Regulation of the Toll-like Receptor-Mediated Inflammatory Pathway. Biophysical Journal. 109: 1214-26. PMID 26276688 DOI: 10.1016/J.Bpj.2015.06.048 |
0.357 |
|
2015 |
Zhou P, Zhang N, Nussinov R, Ma B. Defining the Domain Arrangement of the Mammalian Target of Rapamycin Complex Component Rictor Protein. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 26176550 DOI: 10.1089/Cmb.2015.0103 |
0.361 |
|
2015 |
Muratcioglu S, Chavan TS, Freed BC, Jang H, Khavrutskii L, Freed RN, Dyba MA, Stefanisko K, Tarasov SG, Gursoy A, Keskin O, Tarasova NI, Gaponenko V, Nussinov R. GTP-Dependent K-Ras Dimerization. Structure (London, England : 1993). 23: 1325-35. PMID 26051715 DOI: 10.7490/F1000Research.1110253.1 |
0.316 |
|
2015 |
Xu L, Shan S, Chen Y, Wang X, Nussinov R, Ma B. Coupling of Zinc-Binding and Secondary Structure in Nonfibrillar Aβ40 Peptide Oligomerization. Journal of Chemical Information and Modeling. 55: 1218-30. PMID 26017140 DOI: 10.1021/Acs.Jcim.5B00063 |
0.317 |
|
2015 |
Nussinov R. Advancements and challenges in computational biology. Plos Computational Biology. 11: e1004053. PMID 25569585 DOI: 10.1371/Journal.Pcbi.1004053 |
0.317 |
|
2015 |
Miller Y, Ma B, Nussinov R. Polymorphism in self-assembly of peptide-based β-hairpin contributes to network morphology and hydrogel mechanical rigidity. The Journal of Physical Chemistry. B. 119: 482-90. PMID 25545881 DOI: 10.1021/Jp511485N |
0.345 |
|
2015 |
Nussinov R, Tsai CJ. Allostery without a conformational change? Revisiting the paradigm. Current Opinion in Structural Biology. 30: 17-24. PMID 25500675 DOI: 10.1016/J.Sbi.2014.11.005 |
0.357 |
|
2015 |
Cronin M, Coolbaugh MJ, Nellis D, Zhu J, Wood DW, Nussinov R, Ma B. Dynamics differentiate between active and inactive inteins. European Journal of Medicinal Chemistry. 91: 51-62. PMID 25087201 DOI: 10.1016/J.Ejmech.2014.07.094 |
0.373 |
|
2015 |
Nussinov R, Jang H, Tsai CJ. Oligomerization and nanocluster organization render specificity. Biological Reviews of the Cambridge Philosophical Society. 90: 587-98. PMID 24917483 DOI: 10.1111/Brv.12124 |
0.322 |
|
2015 |
Qi R, Luo Y, Wei G, Nussinov R, Ma B. Aβ "stretching-and-Packing" Cross-Seeding Mechanism Can Trigger Tau Protein Aggregation Journal of Physical Chemistry Letters. 6: 3276-3282. DOI: 10.1021/Acs.Jpclett.5B01447 |
0.339 |
|
2015 |
Jang H, Lu S, Chakrabarti M, Khavrutskii L, Tarasova NI, Gaponenko V, Nussinov R. Nucleotide-Dependent Membrane Interaction and Dimerization of K-Ras4B Biophysical Journal. 108: 93a-94a. DOI: 10.1016/J.Bpj.2014.11.542 |
0.338 |
|
2015 |
Xu L, Margittai M, Nussinov R, Ma B. Simulation of the Distribution of Disordered Tau Proteins Around Its Amyloid Fibrils Core Biophysical Journal. 108: 62a. DOI: 10.1016/J.Bpj.2014.11.371 |
0.333 |
|
2015 |
Lu S, Huang W, Wang Q, Shen Q, Li S, Nussinov R, Zhang J. The Structural Basis of ATP as an Allosteric Modulator Biophysical Journal. 108: 5-8. DOI: 10.1016/J.Bpj.2014.11.2894 |
0.312 |
|
2015 |
Chakrabarti M, Lu S, Jang H, Khavrutskii L, Tarasova NI, Gaponenko V, Nussinov R. Elucidating the Functional Significance of the C-Terminal Hypervariable Region (HVR) in K-Ras4A Biophysical Journal. 108: 210a-211a. DOI: 10.1016/J.Bpj.2014.11.1165 |
0.336 |
|
2014 |
Szalay KZ, Nussinov R, Csermely P. Attractor Structures of Signaling Networks: Consequences of Different Conformational Barcode Dynamics and Their Relations to Network-Based Drug Design. Molecular Informatics. 33: 463-8. PMID 27485984 DOI: 10.1002/Minf.201400029 |
0.348 |
|
2014 |
Nussinov R, Tsai CJ, Liu J. Principles of allosteric interactions in cell signaling. Journal of the American Chemical Society. 136: 17692-701. PMID 25474128 DOI: 10.1021/Ja510028C |
0.334 |
|
2014 |
Ma B, Kolb S, Diprima M, Karna M, Tosato G, Yang Q, Huang Q, Nussinov R. Investigation of the interactions between the EphB2 receptor and SNEW peptide variants. Growth Factors (Chur, Switzerland). 32: 236-46. PMID 25410963 DOI: 10.3109/08977194.2014.985786 |
0.33 |
|
2014 |
Lu S, Huang W, Wang Q, Shen Q, Li S, Nussinov R, Zhang J. The structural basis of ATP as an allosteric modulator. Plos Computational Biology. 10: e1003831. PMID 25211773 DOI: 10.1371/Journal.Pcbi.1003831 |
0.309 |
|
2014 |
Luo Y, Ma B, Nussinov R, Wei G. Structural Insight into Tau Protein's Paradox of Intrinsically Disordered Behavior, Self-Acetylation Activity, and Aggregation. The Journal of Physical Chemistry Letters. 5: 3026-3031. PMID 25206938 DOI: 10.1021/Jz501457F |
0.353 |
|
2014 |
Cui Q, Nussinov R. Making biomolecular simulations accessible in the post-Nobel Prize era. Plos Computational Biology. 10: e1003786. PMID 25122142 DOI: 10.1371/Journal.Pcbi.1003786 |
0.332 |
|
2014 |
Sudha G, Nussinov R, Srinivasan N. An overview of recent advances in structural bioinformatics of protein-protein interactions and a guide to their principles. Progress in Biophysics and Molecular Biology. 116: 141-50. PMID 25077409 DOI: 10.1016/J.Pbiomolbio.2014.07.004 |
0.414 |
|
2014 |
Nussinov R, Jang H. Dynamic multiprotein assemblies shape the spatial structure of cell signaling Progress in Biophysics and Molecular Biology. 116: 158-164. PMID 25046855 DOI: 10.1016/J.Pbiomolbio.2014.07.002 |
0.357 |
|
2014 |
Dai D, Huang Q, Nussinov R, Ma B. Promiscuous and specific recognition among ephrins and Eph receptors. Biochimica Et Biophysica Acta. 1844: 1729-40. PMID 25017878 DOI: 10.1016/J.Bbapap.2014.07.002 |
0.332 |
|
2014 |
Gillman AL, Jang H, Lee J, Ramachandran S, Kagan BL, Nussinov R, Teran Arce F. Activity and architecture of pyroglutamate-modified amyloid-β (AβpE3-42) pores. The Journal of Physical Chemistry. B. 118: 7335-44. PMID 24922585 DOI: 10.1021/Jp5040954 |
0.313 |
|
2014 |
Baspinar A, Cukuroglu E, Nussinov R, Keskin O, Gursoy A. PRISM: a web server and repository for prediction of protein-protein interactions and modeling their 3D complexes. Nucleic Acids Research. 42: W285-9. PMID 24829450 DOI: 10.1093/Nar/Gku397 |
0.343 |
|
2014 |
Guven-Maiorov E, Acuner-Ozbabacan SE, Keskin O, Gursoy A, Nussinov R. Structural pathways of cytokines may illuminate their roles in regulation of cancer development and immunotherapy. Cancers. 6: 663-83. PMID 24670367 DOI: 10.3390/Cancers6020663 |
0.389 |
|
2014 |
Jang H, Arce FT, Ramachandran S, Kagan BL, Lal R, Nussinov R. Disordered amyloidogenic peptides may insert into the membrane and assemble into common cyclic structural motifs. Chemical Society Reviews. 43: 6750-64. PMID 24566672 DOI: 10.1039/C3Cs60459D |
0.332 |
|
2014 |
Acuner Ozbabacan SE, Gursoy A, Nussinov R, Keskin O. The structural pathway of interleukin 1 (IL-1) initiated signaling reveals mechanisms of oncogenic mutations and SNPs in inflammation and cancer. Plos Computational Biology. 10: e1003470. PMID 24550720 DOI: 10.1371/Journal.Pcbi.1003470 |
0.367 |
|
2014 |
Tsai CJ, Nussinov R. A unified view of "how allostery works". Plos Computational Biology. 10: e1003394. PMID 24516370 DOI: 10.1371/Journal.Pcbi.1003394 |
0.331 |
|
2014 |
Nussinov R, Tsai CJ. Free energy diagrams for protein function. Chemistry & Biology. 21: 311-8. PMID 24508196 DOI: 10.1016/J.Chembiol.2013.12.015 |
0.356 |
|
2014 |
Cukuroglu E, Gursoy A, Nussinov R, Keskin O. Non-redundant unique interface structures as templates for modeling protein interactions. Plos One. 9: e86738. PMID 24475173 DOI: 10.1371/Journal.Pone.0086738 |
0.415 |
|
2014 |
Meyer V, Dinkel PD, Luo Y, Yu X, Wei G, Zheng J, Eaton GR, Ma B, Nussinov R, Eaton SS, Margittai M. Single mutations in tau modulate the populations of fibril conformers through seed selection. Angewandte Chemie (International Ed. in English). 53: 1590-3. PMID 24453187 DOI: 10.1002/Anie.201308473 |
0.334 |
|
2014 |
Tsai CJ, Nussinov R. The free energy landscape in translational science: how can somatic mutations result in constitutive oncogenic activation? Physical Chemistry Chemical Physics : Pccp. 16: 6332-41. PMID 24445437 DOI: 10.1039/C3Cp54253J |
0.347 |
|
2014 |
Kuzu G, Keskin O, Nussinov R, Gursoy A. Modeling protein assemblies in the proteome. Molecular & Cellular Proteomics : McP. 13: 887-96. PMID 24445405 DOI: 10.1074/Mcp.M113.031294 |
0.38 |
|
2014 |
Nussinov R. The significance of the 2013 Nobel Prize in Chemistry and the challenges ahead. Plos Computational Biology. 10: e1003423. PMID 24391489 DOI: 10.1371/Journal.Pcbi.1003423 |
0.372 |
|
2014 |
Nussinov R, Ma B, Tsai CJ. Multiple conformational selection and induced fit events take place in allosteric propagation. Biophysical Chemistry. 186: 22-30. PMID 24239303 DOI: 10.1016/J.Bpc.2013.10.002 |
0.315 |
|
2014 |
Ma B, Nussinov R. Druggable orthosteric and allosteric hot spots to target protein-protein interactions. Current Pharmaceutical Design. 20: 1293-301. PMID 23713780 DOI: 10.2174/13816128113199990073 |
0.389 |
|
2014 |
Engin HB, Gursoy A, Nussinov R, Keskin O. Network-based strategies can help mono- and poly-pharmacology drug discovery: a systems biology view. Current Pharmaceutical Design. 20: 1201-7. PMID 23713773 DOI: 10.2174/13816128113199990066 |
0.302 |
|
2014 |
Chavan TS, Jang H, Khavrutskii L, Freed BC, Johannessen L, Tarasov SG, Abraham SJ, Gaponenko V, Nussinov R, Tarasova N. Abstract 3224: High affinity interaction of K-Ras4B hypervariable region with Ras active site Cancer Research. 74: 3224-3224. DOI: 10.1158/1538-7445.Am2014-3224 |
0.351 |
|
2014 |
Murase SK, Haspel N, Del Valle LJ, Perpète EA, Michaux C, Nussinov R, Puiggalí J, Alemán C. Molecular characterization of l-phenylalanine terminated poly(l-lactide) conjugates Rsc Advances. 4: 23231-23241. DOI: 10.1039/C4Ra01534G |
0.644 |
|
2013 |
Gupta K, Jang H, Harlen K, Puri A, Nussinov R, Schneider JP, Blumenthal R. Mechanism of membrane permeation induced by synthetic β-hairpin peptides. Biophysical Journal. 105: 2093-103. PMID 24209854 DOI: 10.1016/J.Bpj.2013.09.040 |
0.323 |
|
2013 |
Nussinov R, Ma B, Tsai CJ, Csermely P. Allosteric conformational barcodes direct signaling in the cell. Structure (London, England : 1993). 21: 1509-21. PMID 24010710 DOI: 10.1016/J.Str.2013.06.002 |
0.341 |
|
2013 |
Jang H, Arce FT, Ramachandran S, Kagan BL, Lal R, Nussinov R. Familial Alzheimer's disease Osaka mutant (ΔE22) β-barrels suggest an explanation for the different Aβ1-40/42 preferred conformational states observed by experiment. The Journal of Physical Chemistry. B. 117: 11518-29. PMID 24000923 DOI: 10.1021/Jp405389N |
0.355 |
|
2013 |
Guven Maiorov E, Keskin O, Gursoy A, Nussinov R. The structural network of inflammation and cancer: merits and challenges. Seminars in Cancer Biology. 23: 243-51. PMID 23712403 DOI: 10.1016/J.Semcancer.2013.05.003 |
0.347 |
|
2013 |
Kuzu G, Gursoy A, Nussinov R, Keskin O. Exploiting conformational ensembles in modeling protein-protein interactions on the proteome scale. Journal of Proteome Research. 12: 2641-53. PMID 23590674 DOI: 10.1021/Pr400006K |
0.405 |
|
2013 |
Ma B, Nussinov R. Structured crowding and its effects on enzyme catalysis. Topics in Current Chemistry. 337: 123-37. PMID 23571857 DOI: 10.1007/128_2012_316 |
0.38 |
|
2013 |
Luo Y, Dinkel P, Yu X, Margittai M, Zheng J, Nussinov R, Wei G, Ma B. Molecular insights into the reversible formation of tau protein fibrils. Chemical Communications (Cambridge, England). 49: 3582-4. PMID 23527380 DOI: 10.1039/C3Cc00241A |
0.301 |
|
2013 |
Zanuy D, Kotla R, Nussinov R, Teesalu T, Sugahara KN, Alemán C, Haspel N. Sequence dependence of C-end rule peptides in binding and activation of neuropilin-1 receptor. Journal of Structural Biology. 182: 78-86. PMID 23462097 DOI: 10.1016/J.Jsb.2013.02.006 |
0.663 |
|
2013 |
Nussinov R, Tsai CJ, Ma B. The underappreciated role of allostery in the cellular network. Annual Review of Biophysics. 42: 169-89. PMID 23451894 DOI: 10.1146/Annurev-Biophys-083012-130257 |
0.385 |
|
2013 |
Xu Y, Wang H, Nussinov R, Ma B. Protein charge and mass contribute to the spatio-temporal dynamics of protein-protein interactions in a minimal proteome. Proteomics. 13: 1339-51. PMID 23420643 DOI: 10.1002/Pmic.201100540 |
0.349 |
|
2013 |
Szilágyi A, Nussinov R, Csermely P. Allo-network drugs: extension of the allosteric drug concept to protein- protein interaction and signaling networks. Current Topics in Medicinal Chemistry. 13: 64-77. PMID 23409766 DOI: 10.2174/1568026611313010007 |
0.308 |
|
2013 |
Csermely P, Nussinov R, Szilágyi A. From allosteric drugs to allo-network drugs: state of the art and trends of design, synthesis and computational methods. Current Topics in Medicinal Chemistry. 13: 2-4. PMID 23409761 DOI: 10.2174/1568026611313010002 |
0.319 |
|
2013 |
Nussinov R, Ma B, Tsai CJ. A broad view of scaffolding suggests that scaffolding proteins can actively control regulation and signaling of multienzyme complexes through allostery. Biochimica Et Biophysica Acta. 1834: 820-9. PMID 23291467 DOI: 10.1016/J.Bbapap.2012.12.014 |
0.352 |
|
2013 |
Zanuy D, Sayago FJ, Revilla-López G, Ballano G, Agemy L, Kotamraju VR, Jiménez AI, Cativiela C, Nussinov R, Sawvel AM, Stucky G, Ruoslahti E, Alemán C. Engineering strategy to improve peptide analogs: from structure-based computational design to tumor homing. Journal of Computer-Aided Molecular Design. 27: 31-43. PMID 23239171 DOI: 10.1007/S10822-012-9623-5 |
0.327 |
|
2012 |
Liu J, Nussinov R. The role of allostery in the ubiquitin-proteasome system. Critical Reviews in Biochemistry and Molecular Biology. 48: 89-97. PMID 23234564 DOI: 10.3109/10409238.2012.742856 |
0.314 |
|
2012 |
Haspel N, Laurent AD, Zanuy D, Nussinov R, Alemán C, Puiggalí J, Revilla-López G. Conformational exploration of two peptides and their hybrid polymer conjugates: potentialities as self-aggregating materials. The Journal of Physical Chemistry. B. 116: 13941-52. PMID 23157485 DOI: 10.1021/Jp3043363 |
0.649 |
|
2012 |
Nussinov R, Tsai CJ, Xin F, Radivojac P. Allosteric post-translational modification codes. Trends in Biochemical Sciences. 37: 447-55. PMID 22884395 DOI: 10.1016/J.Tibs.2012.07.001 |
0.339 |
|
2012 |
Engin HB, Keskin O, Nussinov R, Gursoy A. A strategy based on protein-protein interface motifs may help in identifying drug off-targets. Journal of Chemical Information and Modeling. 52: 2273-86. PMID 22817115 DOI: 10.1021/Ci300072Q |
0.324 |
|
2012 |
Papp D, Lenti K, Módos D, Fazekas D, Dúl Z, Türei D, Földvári-Nagy L, Nussinov R, Csermely P, Korcsmáros T. The NRF2-related interactome and regulome contain multifunctional proteins and fine-tuned autoregulatory loops. Febs Letters. 586: 1795-802. PMID 22641035 DOI: 10.1016/J.Febslet.2012.05.016 |
0.307 |
|
2012 |
Kuzu G, Keskin O, Gursoy A, Nussinov R. Constructing structural networks of signaling pathways on the proteome scale. Current Opinion in Structural Biology. 22: 367-77. PMID 22575757 DOI: 10.1016/J.Sbi.2012.04.004 |
0.384 |
|
2012 |
Xu Y, Ma B, Nussinov R. Structural and functional consequences of phosphate-arsenate substitutions in selected nucleotides: DNA, RNA, and ATP. The Journal of Physical Chemistry. B. 116: 4801-11. PMID 22480264 DOI: 10.1021/Jp300307U |
0.328 |
|
2012 |
Korkmaz EN, Nussinov R, Haliloğlu T. Conformational control of the binding of the transactivation domain of the MLL protein and c-Myb to the KIX domain of CREB. Plos Computational Biology. 8: e1002420. PMID 22438798 DOI: 10.1371/Journal.Pcbi.1002420 |
0.357 |
|
2012 |
Connelly L, Jang H, Arce FT, Ramachandran S, Kagan BL, Nussinov R, Lal R. Effects of point substitutions on the structure of toxic Alzheimer's β-amyloid channels: atomic force microscopy and molecular dynamics simulations. Biochemistry. 51: 3031-8. PMID 22413858 DOI: 10.1021/Bi300257E |
0.358 |
|
2012 |
Acuner Ozbabacan SE, Keskin O, Nussinov R, Gursoy A. Enriching the human apoptosis pathway by predicting the structures of protein-protein complexes. Journal of Structural Biology. 179: 338-46. PMID 22349545 DOI: 10.1016/J.Jsb.2012.02.002 |
0.371 |
|
2012 |
Nussinov R, Tsai CJ. The different ways through which specificity works in orthosteric and allosteric drugs. Current Pharmaceutical Design. 18: 1311-6. PMID 22316155 DOI: 10.2174/138161212799436377 |
0.343 |
|
2012 |
Nussinov R, Ma B. Protein dynamics and conformational selection in bidirectional signal transduction. Bmc Biology. 10: 2. PMID 22277130 DOI: 10.1186/1741-7007-10-2 |
0.364 |
|
2012 |
Tuncbag N, Keskin O, Nussinov R, Gursoy A. Fast and accurate modeling of protein-protein interactions by combining template-interface-based docking with flexible refinement. Proteins. 80: 1239-49. PMID 22275112 DOI: 10.1002/Prot.24022 |
0.406 |
|
2012 |
Capone R, Jang H, Kotler SA, Kagan BL, Nussinov R, Lal R. Probing structural features of Alzheimer's amyloid-β pores in bilayers using site-specific amino acid substitutions. Biochemistry. 51: 776-85. PMID 22242635 DOI: 10.1021/Bi2017427 |
0.327 |
|
2012 |
Connelly L, Jang H, Arce FT, Capone R, Kotler SA, Ramachandran S, Kagan BL, Nussinov R, Lal R. Atomic force microscopy and MD simulations reveal pore-like structures of all-D-enantiomer of Alzheimer's β-amyloid peptide: relevance to the ion channel mechanism of AD pathology. The Journal of Physical Chemistry. B. 116: 1728-35. PMID 22217000 DOI: 10.1021/Jp2108126 |
0.316 |
|
2012 |
Kuzu G, Keskin O, Gursoy A, Nussinov R. Expanding the conformational selection paradigm in protein-ligand docking. Methods in Molecular Biology (Clifton, N.J.). 819: 59-74. PMID 22183530 DOI: 10.1007/978-1-61779-465-0_5 |
0.41 |
|
2012 |
Nussinov R. Allosteric modulators can restore function in an amino acid neurotransmitter receptor by slightly altering intra-molecular communication pathways. British Journal of Pharmacology. 165: 2110-2. PMID 22122331 DOI: 10.1111/J.1476-5381.2011.01793.X |
0.316 |
|
2012 |
Kagan BL, Jang H, Capone R, Teran Arce F, Ramachandran S, Lal R, Nussinov R. Antimicrobial properties of amyloid peptides. Molecular Pharmaceutics. 9: 708-17. PMID 22081976 DOI: 10.1021/Mp200419B |
0.306 |
|
2012 |
Csermely P, Sandhu KS, Hazai E, Hoksza Z, Kiss HJ, Miozzo F, Veres DV, Piazza F, Nussinov R. Disordered proteins and network disorder in network descriptions of protein structure, dynamics and function: hypotheses and a comprehensive review. Current Protein & Peptide Science. 13: 19-33. PMID 22044146 DOI: 10.2174/138920312799277992 |
0.341 |
|
2012 |
Connelly LS, Teran Arce F, Jang H, Capone R, Kotler S, Kagan B, Nussinov R, Lal R. Alzheimer's β-Amyloid All-D-Enantiomers and Native All-L-Enantiomers Exhibit Similar Pore Structures in Lipid Bilayers: Atomic Force Microscopy Biophysical Journal. 102: 588a-589a. DOI: 10.1016/J.Bpj.2011.11.3207 |
0.323 |
|
2012 |
Jang H, Capone R, Kotler SA, Teran Arce F, Connelly L, Ramachandran S, Kagan BL, Lal R, Nussinov R. Modeling Alzheimer's Ion Channel Structures in Lipid Bilayers Formed by D- and L-Enantiomers of Beta-Amyloid (1-42) Peptide Biophysical Journal. 102: 440a. DOI: 10.1016/J.Bpj.2011.11.2410 |
0.314 |
|
2011 |
Ma B, Nussinov R. Selective molecular recognition in amyloid growth and transmission and cross-species barriers. Journal of Molecular Biology. 421: 172-84. PMID 22119878 DOI: 10.1016/J.Jmb.2011.11.023 |
0.33 |
|
2011 |
Liu J, Nussinov R. Flexible cullins in cullin-RING E3 ligases allosterically regulate ubiquitination. The Journal of Biological Chemistry. 286: 40934-42. PMID 21937436 DOI: 10.1074/Jbc.M111.277236 |
0.378 |
|
2011 |
Arce FT, Jang H, Ramachandran S, Landon PB, Nussinov R, Lal R. Polymorphism of amyloid β peptide in different environments: implications for membrane insertion and pore formation. Soft Matter. 7: 5267-5273. PMID 21918653 DOI: 10.1039/C1Sm05162H |
0.355 |
|
2011 |
Tsai CJ, Nussinov R. Gene-specific transcription activation via long-range allosteric shape-shifting. The Biochemical Journal. 439: 15-25. PMID 21916844 DOI: 10.1042/Bj20110972 |
0.321 |
|
2011 |
Tuncbag N, Gursoy A, Nussinov R, Keskin O. Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM. Nature Protocols. 6: 1341-54. PMID 21886100 DOI: 10.1038/Nprot.2011.367 |
0.414 |
|
2011 |
Ma B, Nussinov R. Polymorphic triple beta-sheet structures contribute to amide hydrogen/deuterium (H/D) exchange protection in the Alzheimer amyloid beta42 peptide. The Journal of Biological Chemistry. 286: 34244-53. PMID 21832091 DOI: 10.1074/Jbc.M111.241141 |
0.347 |
|
2011 |
Tsai CJ, Nussinov R. A unified convention for biological assemblies with helical symmetry. Acta Crystallographica. Section D, Biological Crystallography. 67: 716-28. PMID 21795813 DOI: 10.1107/S0907444911024024 |
0.318 |
|
2011 |
Nussinov R. How do dynamic cellular signals travel long distances? Molecular Biosystems. 8: 22-6. PMID 21766126 DOI: 10.1039/C1Mb05205E |
0.316 |
|
2011 |
Ma B, Tsai CJ, Haliloğlu T, Nussinov R. Dynamic allostery: linkers are not merely flexible. Structure (London, England : 1993). 19: 907-17. PMID 21742258 DOI: 10.1016/J.Str.2011.06.002 |
0.398 |
|
2011 |
Mashiach-Farkash E, Nussinov R, Wolfson HJ. SymmRef: a flexible refinement method for symmetric multimers. Proteins. 79: 2607-23. PMID 21721046 DOI: 10.1002/Prot.23082 |
0.349 |
|
2011 |
Pan Y, Nussinov R. The role of response elements organization in transcription factor selectivity: the IFN-β enhanceosome example. Plos Computational Biology. 7: e1002077. PMID 21698143 DOI: 10.1371/Journal.Pcbi.1002077 |
0.351 |
|
2011 |
Miller Y, Ma B, Nussinov R. Synergistic interactions between repeats in tau protein and Aβ amyloids may be responsible for accelerated aggregation via polymorphic states. Biochemistry. 50: 5172-81. PMID 21506544 DOI: 10.1021/Bi200400U |
0.314 |
|
2011 |
Revilla-López G, Rodríguez-Ropero F, Curcó D, Torras J, Isabel Calaza M, Zanuy D, Jiménez AI, Cativiela C, Nussinov R, Alemán C. Integrating the intrinsic conformational preferences of noncoded α-amino acids modified at the peptide bond into the noncoded amino acids database. Proteins. 79: 1841-52. PMID 21491493 DOI: 10.1002/Prot.23009 |
0.311 |
|
2011 |
Jang H, Arce FT, Mustata M, Ramachandran S, Capone R, Nussinov R, Lal R. Antimicrobial protegrin-1 forms amyloid-like fibrils with rapid kinetics suggesting a functional link. Biophysical Journal. 100: 1775-83. PMID 21463591 DOI: 10.1016/J.Bpj.2011.01.072 |
0.331 |
|
2011 |
Kifer I, Nussinov R, Wolfson HJ. Protein structure prediction using a docking-based hierarchical folding scheme. Proteins. 79: 1759-73. PMID 21445943 DOI: 10.1002/Prot.22999 |
0.392 |
|
2011 |
Yuan P, Liang K, Ma B, Zheng N, Nussinov R, Huang J. Multiple-targeting and conformational selection in the estrogen receptor: computation and experiment. Chemical Biology & Drug Design. 78: 137-49. PMID 21443691 DOI: 10.1111/J.1747-0285.2011.01119.X |
0.308 |
|
2011 |
Miller Y, Ma B, Nussinov R. The unique Alzheimer's β-amyloid triangular fibril has a cavity along the fibril axis under physiological conditions. Journal of the American Chemical Society. 133: 2742-8. PMID 21299220 DOI: 10.1021/Ja1100273 |
0.321 |
|
2011 |
Kifer I, Nussinov R, Wolfson HJ. GOSSIP: a method for fast and accurate global alignment of protein structures. Bioinformatics (Oxford, England). 27: 925-32. PMID 21296751 DOI: 10.1093/Bioinformatics/Btr044 |
0.357 |
|
2011 |
Revilla-López G, Torras J, Nussinov R, Alemán C, Zanuy D. Exploring the energy landscape of a molecular engineered analog of a tumor-homing peptide. Physical Chemistry Chemical Physics : Pccp. 13: 9986-94. PMID 21258721 DOI: 10.1039/C0Cp02572K |
0.342 |
|
2011 |
Haspel N, Zanuy D, Nussinov R, Teesalu T, Ruoslahti E, Aleman C. Binding of a C-end rule peptide to the neuropilin-1 receptor: a molecular modeling approach. Biochemistry. 50: 1755-62. PMID 21247217 DOI: 10.1021/Bi101662J |
0.665 |
|
2011 |
Buch I, Tsai CJ, Wolfson HJ, Nussinov R. Symmetry-based self-assembled nanotubes constructed using native protein structures: the key role of flexible linkers. Protein and Peptide Letters. 18: 362-72. PMID 21222638 DOI: 10.2174/092986611794653996 |
0.389 |
|
2011 |
Miller Y, Ma B, Nussinov R. Alzheimer Aβ Amyloid Annular Fibrils: Insight Into Polymorphism Biophysical Journal. 100: 531a. DOI: 10.1016/J.Bpj.2010.12.3100 |
0.32 |
|
2011 |
Tuncbag N, Gursoy A, Nussinov R, Keskin O. Prediction of Protein-Protein Interactions at Genome Scale Biophysical Journal. 100: 386a. DOI: 10.1016/J.Bpj.2010.12.2296 |
0.395 |
|
2011 |
Pan Y, Nussinov r. P53-Response Element Complex Organization is Dominated by Lys120 Interactions with Variant Nucleotides Biophysical Journal. 100: 374a-375a. DOI: 10.1016/J.Bpj.2010.12.2232 |
0.304 |
|
2011 |
Liu J, Nussinov R. Molecular Dynamics Simulations Reveal Distinct Conformational Changes of Three Cullins in Cullin-Ring E3 Ubiquitin Ligases Biophysical Journal. 100: 310a. DOI: 10.1016/J.Bpj.2010.12.1893 |
0.368 |
|
2011 |
Jang H, Arce FT, Ramachandran S, Capone R, Lal R, Nussinov R. Transmembrane β-Barrel Topology Model for Alzheimer's β-Amyloid (Aβ) Ion Channels Biophysical Journal. 100: 201a. DOI: 10.1016/J.Bpj.2010.12.1312 |
0.304 |
|
2010 |
Jang H, Arce FT, Ramachandran S, Capone R, Lal R, Nussinov R. β-Barrel topology of Alzheimer's β-amyloid ion channels. Journal of Molecular Biology. 404: 917-34. PMID 20970427 DOI: 10.1016/J.Jmb.2010.10.025 |
0.317 |
|
2010 |
Revilla-López G, Jiménez AI, Cativiela C, Nussinov R, Alemán C, Zanuy D. Conformational profile of a proline-arginine hybrid. Journal of Chemical Information and Modeling. 50: 1781-9. PMID 20886854 DOI: 10.1021/Ci100135F |
0.33 |
|
2010 |
Kar G, Keskin O, Gursoy A, Nussinov R. Allostery and population shift in drug discovery. Current Opinion in Pharmacology. 10: 715-22. PMID 20884293 DOI: 10.1016/J.Coph.2010.09.002 |
0.341 |
|
2010 |
Ma B, Nussinov R. Polymorphic C-terminal beta-sheet interactions determine the formation of fibril or amyloid beta-derived diffusible ligand-like globulomer for the Alzheimer Abeta42 dodecamer. The Journal of Biological Chemistry. 285: 37102-10. PMID 20847046 DOI: 10.1074/Jbc.M110.133488 |
0.318 |
|
2010 |
Ma B, Nussinov R. Enzyme dynamics point to stepwise conformational selection in catalysis. Current Opinion in Chemical Biology. 14: 652-9. PMID 20822947 DOI: 10.1016/J.Cbpa.2010.08.012 |
0.313 |
|
2010 |
Curcó D, Zanuy D, Nussinov R, Alemán C. A simulation strategy for the atomistic modeling of flexible molecules covalently tethered to rigid surfaces: application to peptides. Journal of Computational Chemistry. 32: 607-19. PMID 20806264 DOI: 10.1002/Jcc.21647 |
0.333 |
|
2010 |
Pan Y, Nussinov R. Lysine120 interactions with p53 response elements can allosterically direct p53 organization. Plos Computational Biology. 6. PMID 20700496 DOI: 10.1371/Journal.Pcbi.1000878 |
0.307 |
|
2010 |
Zen A, Micheletti C, Keskin O, Nussinov R. Comparing interfacial dynamics in protein-protein complexes: an elastic network approach. Bmc Structural Biology. 10: 26. PMID 20691107 DOI: 10.1186/1472-6807-10-26 |
0.388 |
|
2010 |
Liu J, Nussinov R. Rbx1 flexible linker facilitates cullin-RING ligase function before neddylation and after deneddylation. Biophysical Journal. 99: 736-44. PMID 20682250 DOI: 10.1016/J.Bpj.2010.05.021 |
0.32 |
|
2010 |
Mashiach E, Schneidman-Duhovny D, Peri A, Shavit Y, Nussinov R, Wolfson HJ. An integrated suite of fast docking algorithms Proteins: Structure, Function and Bioinformatics. 78: 3197-3204. PMID 20607855 DOI: 10.1002/Prot.22790 |
0.328 |
|
2010 |
Csermely P, Palotai R, Nussinov R. Induced fit, conformational selection and independent dynamic segments: an extended view of binding events. Trends in Biochemical Sciences. 35: 539-46. PMID 20541943 DOI: 10.1016/J.Tibs.2010.04.009 |
0.385 |
|
2010 |
Mashiach E, Nussinov R, Wolfson HJ. FiberDock: a web server for flexible induced-fit backbone refinement in molecular docking. Nucleic Acids Research. 38: W457-61. PMID 20460459 DOI: 10.1093/Nar/Gkq373 |
0.41 |
|
2010 |
Revilla-López G, Torras J, Curcó D, Casanovas J, Calaza MI, Zanuy D, Jiménez AI, Cativiela C, Nussinov R, Grodzinski P, Alemán C. NCAD, a database integrating the intrinsic conformational preferences of non-coded amino acids. The Journal of Physical Chemistry. B. 114: 7413-22. PMID 20455555 DOI: 10.1021/Jp102092M |
0.323 |
|
2010 |
Miller Y, Ma B, Nussinov R. Zinc ions promote alzheimer aβ aggregation via population shift of polymorphic states Proceedings of the National Academy of Sciences of the United States of America. 107: 9490-9495. PMID 20448202 DOI: 10.1073/Pnas.0913114107 |
0.307 |
|
2010 |
Yu X, Wang J, Yang JC, Wang Q, Cheng SZ, Nussinov R, Zheng J. Atomic-scale simulations confirm that soluble beta-sheet-rich peptide self-assemblies provide amyloid mimics presenting similar conformational properties. Biophysical Journal. 98: 27-36. PMID 20085717 DOI: 10.1016/J.Bpj.2009.10.003 |
0.361 |
|
2010 |
Liu J, Nussinov R. Molecular dynamics reveal the essential role of linker motions in the function of cullin-RING E3 ligases. Journal of Molecular Biology. 396: 1508-23. PMID 20083119 DOI: 10.1016/J.Jmb.2010.01.022 |
0.362 |
|
2010 |
Mashiach E, Nussinov R, Wolfson HJ. FiberDock: Flexible induced-fit backbone refinement in molecular docking. Proteins. 78: 1503-19. PMID 20077569 DOI: 10.1002/Prot.22668 |
0.356 |
|
2010 |
Pan Y, Tsai CJ, Ma B, Nussinov R. Mechanisms of transcription factor selectivity. Trends in Genetics : Tig. 26: 75-83. PMID 20074831 DOI: 10.1016/J.Tig.2009.12.003 |
0.311 |
|
2010 |
Pan Y, Nussinov R. Preferred drifting along the DNA major groove and cooperative anchoring of the p53 core domain: mechanisms and scenarios. Journal of Molecular Recognition : Jmr. 23: 232-40. PMID 19856322 DOI: 10.1002/Jmr.990 |
0.31 |
|
2010 |
Ozbabacan SEA, Gursoy A, Keskin O, Nussinov R. Conformational ensembles, signal transduction and residue hot spots: Application to drug discovery Current Opinion in Drug Discovery & Development. 13: 527-537. DOI: 10.5072/Zenodo.38298 |
0.384 |
|
2010 |
Arce FMT, Jang H, Nussinov R, Lal R. Real-Time Afm Imaging of Surface-Induced Oligomerization of the Non-Amyloidogenic P3 Peptide: Implications for Membrane Insertion and Ion Channel Formation Biophysical Journal. 98: 110a. DOI: 10.1016/J.Bpj.2009.12.611 |
0.308 |
|
2010 |
Miller Y, Ma B, Nussinov R. Polymorphism in Alzheimer Aβ Amyloid Organization: Insight into Aβ Aggregation Biophysical Journal. 98: 457a. DOI: 10.1016/J.Bpj.2009.12.2484 |
0.326 |
|
2010 |
Liu J, Nussinov R. Conformational Control of Ubiquitination in the Cullin-Ring E3 Ligase Machinery Biophysical Journal. 98: 26a-27a. DOI: 10.1016/J.Bpj.2009.12.158 |
0.364 |
|
2009 |
Pan Y, Tsai CJ, Ma B, Nussinov R. How do transcription factors select specific binding sites in the genome? Nature Structural & Molecular Biology. 16: 1118-20. PMID 19888307 DOI: 10.1038/Nsmb1109-1118 |
0.308 |
|
2009 |
Boehr DD, Nussinov R, Wright PE. The role of dynamic conformational ensembles in biomolecular recognition. Nature Chemical Biology. 5: 789-96. PMID 19841628 DOI: 10.1038/Nchembio.232 |
0.409 |
|
2009 |
Tsai CJ, Ma B, Nussinov R. Protein-protein interaction networks: how can a hub protein bind so many different partners? Trends in Biochemical Sciences. 34: 594-600. PMID 19837592 DOI: 10.1016/J.Tibs.2009.07.007 |
0.377 |
|
2009 |
Liu J, Nussinov R. The mechanism of ubiquitination in the cullin-RING E3 ligase machinery: conformational control of substrate orientation. Plos Computational Biology. 5: e1000527. PMID 19798438 DOI: 10.1371/Journal.Pcbi.1000527 |
0.349 |
|
2009 |
Alemán C, Jiménez AI, Cativiela C, Nussinov R, Casanovas J. Conformational preferences of 1-amino-2-phenylcyclohexanecarboxylic acid, a phenylalanine cyclohexane analogue. The Journal of Organic Chemistry. 74: 7834-43. PMID 19772338 DOI: 10.1021/Jo901594E |
0.314 |
|
2009 |
Miller Y, Ma B, Nussinov R. Polymorphism of Alzheimer's Aβ17-42 (p3) oligomers: The importance of the turn location and its conformation Biophysical Journal. 97: 1168-1177. PMID 19686665 DOI: 10.1016/J.Bpj.2009.05.042 |
0.326 |
|
2009 |
del Sol A, Tsai CJ, Ma B, Nussinov R. The origin of allosteric functional modulation: multiple pre-existing pathways. Structure (London, England : 1993). 17: 1042-50. PMID 19679084 DOI: 10.1016/J.Str.2009.06.008 |
0.394 |
|
2009 |
Tuncbag N, Kar G, Gursoy A, Keskin O, Nussinov R. Towards inferring time dimensionality in protein-protein interaction networks by integrating structures: the p53 example. Molecular Biosystems. 5: 1770-8. PMID 19585003 DOI: 10.1039/B905661K |
0.354 |
|
2009 |
Zanuy D, Ballano G, Jiménez AI, Casanovas J, Haspel N, Cativiela C, Curcó D, Nussinov R, Alemán C. Protein segments with conformationally restricted amino acids can control supramolecular organization at the nanoscale. Journal of Chemical Information and Modeling. 49: 1623-9. PMID 19548653 DOI: 10.1021/Ci9001487 |
0.602 |
|
2009 |
Zanuy D, Flores-Ortega A, Jiménez AI, Calaza MI, Cativiela C, Nussinov R, Ruoslahti E, Alemán C. In silico molecular engineering for a targeted replacement in a tumor-homing peptide. The Journal of Physical Chemistry. B. 113: 7879-89. PMID 19432404 DOI: 10.1021/Jp9006119 |
0.354 |
|
2009 |
Ma B, Nussinov R. Amplification of signaling via cellular allosteric relay and protein disorder. Proceedings of the National Academy of Sciences of the United States of America. 106: 6887-8. PMID 19416924 DOI: 10.1073/Pnas.0903024106 |
0.371 |
|
2009 |
Carbonell P, Nussinov R, del Sol A. Energetic determinants of protein binding specificity: insights into protein interaction networks. Proteomics. 9: 1744-53. PMID 19253304 DOI: 10.1002/Pmic.200800425 |
0.382 |
|
2009 |
Tuncbag N, Kar G, Keskin O, Gursoy A, Nussinov R. A survey of available tools and web servers for analysis of protein-protein interactions and interfaces. Briefings in Bioinformatics. 10: 217-32. PMID 19240123 DOI: 10.1093/Bib/Bbp001 |
0.334 |
|
2009 |
Revilla-López G, Torras J, Jiménez AI, Cativiela C, Nussinov R, Alemán C. Side-chain to backbone interactions dictate the conformational preferences of a cyclopentane arginine analogue. The Journal of Organic Chemistry. 74: 2403-12. PMID 19236034 DOI: 10.1021/Jo802704H |
0.323 |
|
2009 |
Ma B, Nussinov R. Regulating highly dynamic unstructured proteins and their coding mRNAs Genome Biology. 10: 204. PMID 19226433 DOI: 10.1186/Gb-2009-10-1-204 |
0.317 |
|
2009 |
Tsai CJ, Del Sol A, Nussinov R. Protein allostery, signal transmission and dynamics: a classification scheme of allosteric mechanisms. Molecular Biosystems. 5: 207-16. PMID 19225609 DOI: 10.1039/B819720B |
0.321 |
|
2009 |
Buch I, Brooks BR, Wolfson HJ, Nussinov R. Computational validation of protein nanotubes. Nano Letters. 9: 1096-102. PMID 19199488 DOI: 10.1021/Nl803521J |
0.357 |
|
2009 |
Tsai CJ, Ma B, Nussinov R. Intra-molecular chaperone: the role of the N-terminal in conformational selection and kinetic control. Physical Biology. 6: 013001. PMID 19193974 DOI: 10.1088/1478-3975/6/1/013001 |
0.381 |
|
2009 |
Zanuy D, Curcó D, Nussinov R, Alemán C. Influence of the dye presence on the conformational preferences of CREKA, a tumor homing linear pentapeptide. Biopolymers. 92: 83-93. PMID 19051312 DOI: 10.1002/Bip.21122 |
0.356 |
|
2009 |
Andrusier N, Mashiach E, Nussinov R, Wolfson HJ. Principles of flexible protein-protein docking. Proteins. 73: 271-89. PMID 18655061 DOI: 10.1002/Prot.22170 |
0.369 |
|
2009 |
Kifer I, Nussinov R, Wolfson HJ. Constructing templates for protein structure prediction by simulation of protein folding pathways. Proteins. 73: 380-94. PMID 18433063 DOI: 10.1002/Prot.22073 |
0.398 |
|
2009 |
Nussinov R. Allosteric effects and regulation of signaling: the ubiquitin E3 ligases Biophysical Journal. 96: 3a. DOI: 10.1016/J.Bpj.2008.12.906 |
0.355 |
|
2009 |
Tuncbag N, Keskin O, Nussinov R, Gursoy A. Large Scale Prediction of Computational Hot Spots in Protein Interfaces Biophysical Journal. 96: 650a-651a. DOI: 10.1016/J.Bpj.2008.12.3436 |
0.353 |
|
2009 |
Kar G, Gursoy A, Nussinov R, Keskin O. Combining Protein-protein Interaction Networks with Structures Biophysical Journal. 96: 649a. DOI: 10.1016/J.Bpj.2008.12.3430 |
0.359 |
|
2009 |
Nussinov R, Pan Y. P53 Induced Dna Bending Biophysical Journal. 96: 577a. DOI: 10.1016/J.Bpj.2008.12.3018 |
0.308 |
|
2009 |
Liu J, Nussinov R. Searching For the Hinge of E3 Ubiquitin Ligase Machinery with MD Simulations Biophysical Journal. 96: 365a. DOI: 10.1016/J.Bpj.2008.12.1963 |
0.359 |
|
2009 |
Ma J, Wang J, Tsai C, Nussinov R, Ma B. Diameters of single-walled carbon nanotubes (SWCNTs) and related nanochemistry and nanobiology Frontiers of Materials Science in China. 4: 17-28. DOI: 10.1007/S11706-010-0001-8 |
0.331 |
|
2008 |
Emekli U, Gunasekaran K, Nussinov R, Haliloglu T. What can we learn from highly connected beta-rich structures for structural interface design? Methods in Molecular Biology (Clifton, N.J.). 474: 235-53. PMID 19031068 DOI: 10.1007/978-1-59745-480-3_12 |
0.388 |
|
2008 |
Buch I, Tsai CJ, Wolfson HJ, Nussinov R. Self-assembly of fused homo-oligomers to create nanotubes. Methods in Molecular Biology (Clifton, N.J.). 474: 117-31. PMID 19031064 DOI: 10.1007/978-1-59745-480-3_8 |
0.304 |
|
2008 |
Gursoy A, Keskin O, Nussinov R. Topological properties of protein interaction networks from a structural perspective. Biochemical Society Transactions. 36: 1398-403. PMID 19021563 DOI: 10.1042/Bst0361398 |
0.341 |
|
2008 |
Shulman-Peleg A, Nussinov R, Wolfson HJ. RsiteDB: a database of protein binding pockets that interact with RNA nucleotide bases. Nucleic Acids Research. 37: D369-73. PMID 18953028 DOI: 10.1093/Nar/Gkn759 |
0.35 |
|
2008 |
Flores-Ortega A, Casanovas J, Nussinov R, Alemán C. Conformational preferences of beta- and gamma-aminated proline analogues. The Journal of Physical Chemistry. B. 112: 14045-55. PMID 18842022 DOI: 10.1021/Jp807638P |
0.315 |
|
2008 |
Ballano G, Zanuy D, Jiménez AI, Cativiela C, Nussinov R, Alemán C. Structural analysis of a beta-helical protein motif stabilized by targeted replacements with conformationally constrained amino acids. The Journal of Physical Chemistry. B. 112: 13101-15. PMID 18811190 DOI: 10.1021/Jp8032116 |
0.368 |
|
2008 |
Ahmad S, Keskin O, Sarai A, Nussinov R. Protein-DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins. Nucleic Acids Research. 36: 5922-32. PMID 18801847 DOI: 10.1093/Nar/Gkn573 |
0.387 |
|
2008 |
Tsai CJ, Sauna ZE, Kimchi-Sarfaty C, Ambudkar SV, Gottesman MM, Nussinov R. Synonymous mutations and ribosome stalling can lead to altered folding pathways and distinct minima. Journal of Molecular Biology. 383: 281-91. PMID 18722384 DOI: 10.1016/J.Jmb.2008.08.012 |
0.375 |
|
2008 |
Dror O, Schneidman-Duhovny D, Shulman-Peleg A, Nussinov R, Wolfson HJ, Sharan R. Structural similarity of genetically interacting proteins. Bmc Systems Biology. 2: 69. PMID 18671848 DOI: 10.1186/1752-0509-2-69 |
0.305 |
|
2008 |
Schneidman-Duhovny D, Dror O, Inbar Y, Nussinov R, Wolfson HJ. Deterministic pharmacophore detection via multiple flexible alignment of drug-like molecules. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 15: 737-54. PMID 18662104 DOI: 10.1089/Cmb.2007.0130 |
0.304 |
|
2008 |
Tuncbag N, Gursoy A, Guney E, Nussinov R, Keskin O. Architectures and functional coverage of protein-protein interfaces. Journal of Molecular Biology. 381: 785-802. PMID 18620705 DOI: 10.1016/J.Jmb.2008.04.071 |
0.341 |
|
2008 |
Keskin O, Nussinov R, Gursoy A. PRISM: protein-protein interaction prediction by structural matching. Methods in Molecular Biology (Clifton, N.J.). 484: 505-21. PMID 18592198 DOI: 10.1007/978-1-59745-398-1_30 |
0.383 |
|
2008 |
Zanuy D, Flores-Ortega A, Casanovas J, Curcó D, Nussinov R, Alemán C. The energy landscape of a selective tumor-homing pentapeptide. The Journal of Physical Chemistry. B. 112: 8692-700. PMID 18588341 DOI: 10.1021/Jp711477K |
0.337 |
|
2008 |
Shulman-Peleg A, Shatsky M, Nussinov R, Wolfson HJ. MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions. Nucleic Acids Research. 36: W260-4. PMID 18467424 DOI: 10.1093/Nar/Gkn185 |
0.401 |
|
2008 |
Zheng J, Jang H, Ma B, Nussinov R. Annular structures as intermediates in fibril formation of Alzheimer Abeta17-42. The Journal of Physical Chemistry. B. 112: 6856-65. PMID 18457440 DOI: 10.1021/Jp711335B |
0.366 |
|
2008 |
Shulman-Peleg A, Shatsky M, Nussinov R, Wolfson HJ. Prediction of interacting single-stranded RNA bases by protein-binding patterns. Journal of Molecular Biology. 379: 299-316. PMID 18452949 DOI: 10.1016/J.Jmb.2008.03.043 |
0.377 |
|
2008 |
Schneidman-Duhovny D, Dror O, Inbar Y, Nussinov R, Wolfson HJ. PharmaGist: a webserver for ligand-based pharmacophore detection. Nucleic Acids Research. 36: W223-8. PMID 18424800 DOI: 10.1093/Nar/Gkn187 |
0.323 |
|
2008 |
Mashiach E, Schneidman-Duhovny D, Andrusier N, Nussinov R, Wolfson HJ. FireDock: a web server for fast interaction refinement in molecular docking. Nucleic Acids Research. 36: W229-32. PMID 18424796 DOI: 10.1093/Nar/Gkn186 |
0.38 |
|
2008 |
Yaffe E, Fishelovitch D, Wolfson HJ, Halperin D, Nussinov R. MolAxis: efficient and accurate identification of channels in macromolecules. Proteins. 73: 72-86. PMID 18393395 DOI: 10.1002/Prot.22052 |
0.302 |
|
2008 |
Keskin O, Gursoy A, Ma B, Nussinov R. Principles of protein-protein interactions: what are the preferred ways for proteins to interact? Chemical Reviews. 108: 1225-44. PMID 18355092 DOI: 10.1021/Cr040409X |
0.347 |
|
2008 |
Tsai CJ, del Sol A, Nussinov R. Allostery: absence of a change in shape does not imply that allostery is not at play. Journal of Molecular Biology. 378: 1-11. PMID 18353365 DOI: 10.1016/J.Jmb.2008.02.034 |
0.315 |
|
2008 |
Yogurtcu ON, Erdemli SB, Nussinov R, Turkay M, Keskin O. Restricted mobility of conserved residues in protein-protein interfaces in molecular simulations. Biophysical Journal. 94: 3475-85. PMID 18227135 DOI: 10.1529/Biophysj.107.114835 |
0.39 |
|
2008 |
Zheng J, Jang H, Nussinov R. Beta2-microglobulin amyloid fragment organization and morphology and its comparison to Abeta suggests that amyloid aggregation pathways are sequence specific. Biochemistry. 47: 2497-509. PMID 18215070 DOI: 10.1021/Bi7019194 |
0.331 |
|
2008 |
Rodríguez-Ropero F, Zanuy D, Casanovas J, Nussinov R, Alemán C. Application of 1-aminocyclohexane carboxylic acid to protein nanostructure computer design. Journal of Chemical Information and Modeling. 48: 333-43. PMID 18201062 DOI: 10.1021/Ci700291X |
0.359 |
|
2008 |
Liu J, Nussinov R. Allosteric effects in the marginally stable von Hippel-Lindau tumor suppressor protein and allostery-based rescue mutant design. Proceedings of the National Academy of Sciences of the United States of America. 105: 901-6. PMID 18195360 DOI: 10.1073/Pnas.0707401105 |
0.369 |
|
2008 |
Jang H, Zheng J, Lal R, Nussinov R. New structures help the modeling of toxic amyloidbeta ion channels. Trends in Biochemical Sciences. 33: 91-100. PMID 18182298 DOI: 10.1016/J.Tibs.2007.10.007 |
0.323 |
|
2008 |
Shatsky M, Nussinov R, Wolfson HJ. Algorithms for multiple protein structure alignment and structure-derived multiple sequence alignment. Methods in Molecular Biology (Clifton, N.J.). 413: 125-46. PMID 18075164 DOI: 10.1007/978-1-59745-574-9_5 |
0.4 |
|
2008 |
Schneidman-Duhovny D, Nussinov R, Wolfson HJ. Automatic prediction of protein interactions with large scale motion. Proteins. 69: 764-73. PMID 17886339 DOI: 10.1002/Prot.21759 |
0.331 |
|
2008 |
Emekli U, Schneidman-Duhovny D, Wolfson HJ, Nussinov R, Haliloglu T. HingeProt: automated prediction of hinges in protein structures. Proteins. 70: 1219-27. PMID 17847101 DOI: 10.1002/Prot.21613 |
0.392 |
|
2008 |
Haspel N, Zanuy D, Tsai HH, Ma B, Wolfson H, Nussinov R. Computational Approaches and Tools for Establishing Structural Models for Short Amyloid-forming Peptides Amyloid Proteins: the Beta Sheet Conformation and Disease. 1: 301-315. DOI: 10.1002/9783527619344.ch13 |
0.61 |
|
2007 |
Curcó D, Nussinov R, Alemán C. Coarse-graining the self-assembly of beta-helical protein building blocks. The Journal of Physical Chemistry. B. 111: 14006-11. PMID 18027921 DOI: 10.1021/Jp075386F |
0.337 |
|
2007 |
Fishelovitch D, Hazan C, Hirao H, Wolfson HJ, Nussinov R, Shaik S. QM/MM study of the active species of the human cytochrome P450 3A4, and the influence thereof of the multiple substrate binding. The Journal of Physical Chemistry. B. 111: 13822-32. PMID 18020326 DOI: 10.1021/Jp076401J |
0.3 |
|
2007 |
Shulman-Peleg A, Shatsky M, Nussinov R, Wolfson HJ. Spatial chemical conservation of hot spot interactions in protein-protein complexes. Bmc Biology. 5: 43. PMID 17925020 DOI: 10.1186/1741-7007-5-43 |
0.362 |
|
2007 |
Zanuy D, Rodríguez-Ropero F, Nussinov R, Alemán C. Testing beta-helix terminal coils stability by targeted substitutions with non-proteogenic amino acids: a molecular dynamics study. Journal of Structural Biology. 160: 177-89. PMID 17897839 DOI: 10.1016/J.Jsb.2007.07.014 |
0.326 |
|
2007 |
Zanuy D, Rodríguez-Ropero F, Haspel N, Zheng J, Nussinov R, Aleman C. Stability of tubular structures based on beta-helical proteins: self-assembled versus polymerized nanoconstructs and wild-type versus mutated sequences. Biomacromolecules. 8: 3135-46. PMID 17854222 DOI: 10.1021/Bm700561T |
0.678 |
|
2007 |
Curcó D, Nussinov R, Aleman C. Coarse-grained representation of beta-helical protein building blocks. The Journal of Physical Chemistry. B. 111: 10538-49. PMID 17691836 DOI: 10.1021/Jp072832Q |
0.363 |
|
2007 |
Zheng J, Jang H, Ma B, Tsai CJ, Nussinov R. Modeling the Alzheimer Abeta17-42 fibril architecture: tight intermolecular sheet-sheet association and intramolecular hydrated cavities. Biophysical Journal. 93: 3046-57. PMID 17675353 DOI: 10.1529/Biophysj.107.110700 |
0.347 |
|
2007 |
Andrusier N, Nussinov R, Wolfson HJ. FireDock: fast interaction refinement in molecular docking. Proteins. 69: 139-59. PMID 17598144 DOI: 10.1002/Prot.21495 |
0.338 |
|
2007 |
Hu Z, Bowen D, Southerland WM, Del Sol A, Pan Y, Nussinov R, Ma B. Ligand binding and circular permutation modify residue interaction network in DHFR Plos Computational Biology. 3: 1097-1107. PMID 17571919 DOI: 10.1371/Journal.Pcbi.0030117 |
0.316 |
|
2007 |
Cohen-Gihon I, Nussinov R, Sharan R. Comprehensive analysis of co-occurring domain sets in yeast proteins. Bmc Genomics. 8: 161. PMID 17562021 DOI: 10.1186/1471-2164-8-161 |
0.345 |
|
2007 |
Del Sol A, Araúzo-Bravo MJ, Amoros D, Nussinov R. Modular architecture of protein structures and allosteric communications: potential implications for signaling proteins and regulatory linkages. Genome Biology. 8: R92. PMID 17531094 DOI: 10.1186/Gb-2007-8-5-R92 |
0.314 |
|
2007 |
Ma B, Nussinov R. Trp/Met/Phe hot spots in protein-protein interactions: potential targets in drug design. Current Topics in Medicinal Chemistry. 7: 999-1005. PMID 17508933 DOI: 10.2174/156802607780906717 |
0.415 |
|
2007 |
Haspel N, Zanuy D, Zheng J, Aleman C, Wolfson H, Nussinov R. Changing the charge distribution of beta-helical-based nanostructures can provide the conditions for charge transfer. Biophysical Journal. 93: 245-53. PMID 17416628 DOI: 10.1529/Biophysj.106.100644 |
0.664 |
|
2007 |
Jang H, Ma B, Nussinov R. Conformational study of the protegrin-1 (PG-1) dimer interaction with lipid bilayers and its effect. Bmc Structural Biology. 7: 21. PMID 17407565 DOI: 10.1186/1472-6807-7-21 |
0.324 |
|
2007 |
Tsai CJ, Zheng J, Zanuy D, Haspel N, Wolfson H, Alemán C, Nussinov R. Principles of nanostructure design with protein building blocks. Proteins. 68: 1-12. PMID 17407160 DOI: 10.1002/Prot.21413 |
0.665 |
|
2007 |
Zanuy D, Jiménez AI, Cativiela C, Nussinov R, Alemán C. Use of constrained synthetic amino acids in beta-helix proteins for conformational control. The Journal of Physical Chemistry. B. 111: 3236-42. PMID 17388467 DOI: 10.1021/Jp065025K |
0.362 |
|
2007 |
Keskin O, Nussinov R. Similar binding sites and different partners: implications to shared proteins in cellular pathways. Structure (London, England : 1993). 15: 341-54. PMID 17355869 DOI: 10.1016/J.Str.2007.01.007 |
0.386 |
|
2007 |
Fishelovitch D, Hazan C, Shaik S, Wolfson HJ, Nussinov R. Structural dynamics of the cooperative binding of organic molecules in the human cytochrome P450 3A4 Journal of the American Chemical Society. 129: 1602-1611. PMID 17284003 DOI: 10.1021/Ja066007J |
0.309 |
|
2007 |
Lasker K, Dror O, Shatsky M, Nussinov R, Wolfson HJ. EMatch: discovery of high resolution structural homologues of protein domains in intermediate resolution cryo-EM maps. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 4: 28-39. PMID 17277411 DOI: 10.1109/Tcbb.2007.1003 |
0.327 |
|
2007 |
Zheng J, Zanuy D, Haspel N, Tsai CJ, Alemán C, Nussinov R. Nanostructure design using protein building blocks enhanced by conformationally constrained synthetic residues. Biochemistry. 46: 1205-18. PMID 17260950 DOI: 10.1021/Bi061674A |
0.703 |
|
2007 |
Dror O, Lasker K, Nussinov R, Wolfson H. EMatch: an efficient method for aligning atomic resolution subunits into intermediate-resolution cryo-EM maps of large macromolecular assemblies. Acta Crystallographica. Section D, Biological Crystallography. 63: 42-9. PMID 17164525 DOI: 10.1107/S0907444906041059 |
0.321 |
|
2007 |
Liu J, Pan Y, Ma B, Nussinov R. "Similarity trap" in protein-protein interactions could be carcinogenic: simulations of p53 core domain complexed with 53BP1 and BRCA1 BRCT domains. Structure (London, England : 1993). 14: 1811-21. PMID 17161371 DOI: 10.1016/J.Str.2006.10.009 |
0.368 |
|
2007 |
Aleman C, Zanuy D, Casanovas J, Cativiela C, Nussinov R. Backbone conformational preferences and pseudorotational ring puckering of 1-aminocyclopentane-1-carboxylic acid. The Journal of Physical Chemistry. B. 110: 21264-71. PMID 17048955 DOI: 10.1021/Jp062804S |
0.316 |
|
2007 |
Haspel N, Wainreb G, Inbar Y, Tsai HH, Tsai CJ, Wolfson HJ, Nussinov R. A hierarchical protein folding scheme based on the building block folding model. Methods in Molecular Biology (Clifton, N.J.). 350: 189-204. PMID 16957324 DOI: 10.1385/1-59745-189-4:189 |
0.672 |
|
2007 |
Keskin O, Ma B, Rogale K, Gunasekaran K, Nussinov R. Protein-protein interactions: organization, cooperativity and mapping in a bottom-up Systems Biology approach. Physical Biology. 2: S24-35. PMID 16204846 DOI: 10.1088/1478-3975/2/2/S03 |
0.374 |
|
2007 |
Dror O, Nussinov R, Wolfson H. ARTS: alignment of RNA tertiary structures. Bioinformatics (Oxford, England). ii47-53. PMID 16204124 DOI: 10.1093/Bioinformatics/Bti1108 |
0.303 |
|
2007 |
Ahmad S, Keskin O, Nussinov R, Sarai A. 1P257 Clusters of conserved residue in DNA-binding proteins : Analogy with hot spots and implications to prediction(Bioinformatics-structural, functional, and comparative genomics,Oral Presentations) Seibutsu Butsuri. 47: S87. DOI: 10.2142/Biophys.47.S87_4 |
0.338 |
|
2006 |
Gunasekaran K, Nussinov R. How different are structurally flexible and rigid binding sites? Sequence and structural features discriminating proteins that do and do not undergo conformational change upon ligand binding. Journal of Molecular Biology. 365: 257-73. PMID 17059826 DOI: 10.1016/J.Jmb.2006.09.062 |
0.401 |
|
2006 |
Zheng J, Ma B, Nussinov R. Consensus features in amyloid fibrils: sheet-sheet recognition via a (polar or nonpolar) zipper structure. Physical Biology. 3: P1-4. PMID 17021379 DOI: 10.1088/1478-3975/3/3/P01 |
0.34 |
|
2006 |
Ertekin A, Nussinov R, Haliloglu T. Association of putative concave protein-binding sites with the fluctuation behavior of residues. Protein Science : a Publication of the Protein Society. 15: 2265-77. PMID 17008715 DOI: 10.1110/Ps.051815006 |
0.344 |
|
2006 |
Ma B, Nussinov R. Simulations as analytical tools to understand protein aggregation and predict amyloid conformation. Current Opinion in Chemical Biology. 10: 445-52. PMID 16935548 DOI: 10.1016/J.Cbpa.2006.08.018 |
0.374 |
|
2006 |
Tsai CJ, Zheng J, Alemán C, Nussinov R. Structure by design: from single proteins and their building blocks to nanostructures. Trends in Biotechnology. 24: 449-54. PMID 16935374 DOI: 10.1016/J.Tibtech.2006.08.004 |
0.364 |
|
2006 |
del Sol A, Fujihashi H, Amoros D, Nussinov R. Residue centrality, functionally important residues, and active site shape: analysis of enzyme and non-enzyme families. Protein Science : a Publication of the Protein Society. 15: 2120-8. PMID 16882992 DOI: 10.1110/Ps.062249106 |
0.356 |
|
2006 |
Dror O, Nussinov R, Wolfson HJ. The ARTS web server for aligning RNA tertiary structures. Nucleic Acids Research. 34: W412-5. PMID 16845038 DOI: 10.1093/Nar/Gkl312 |
0.309 |
|
2006 |
Haspel N, Zanuy D, Alemán C, Wolfson H, Nussinov R. De novo tubular nanostructure design based on self-assembly of beta-helical protein motifs. Structure (London, England : 1993). 14: 1137-48. PMID 16843895 DOI: 10.1016/J.Str.2006.05.016 |
0.686 |
|
2006 |
Tsai HH, Gunasekaran K, Nussinov R. Sequence and structure analysis of parallel beta helices: implication for constructing amyloid structural models. Structure (London, England : 1993). 14: 1059-72. PMID 16765899 DOI: 10.1016/J.Str.2006.03.015 |
0.363 |
|
2006 |
del Sol A, Fujihashi H, Amoros D, Nussinov R. Residues crucial for maintaining short paths in network communication mediate signaling in proteins. Molecular Systems Biology. 2: 2006.0019. PMID 16738564 DOI: 10.1038/Msb4100063 |
0.397 |
|
2006 |
Tsai CJ, Zheng J, Nussinov R. Designing a nanotube using naturally occurring protein building blocks. Plos Computational Biology. 2: e42. PMID 16683021 DOI: 10.1371/Journal.Pcbi.0020042 |
0.381 |
|
2006 |
Zheng J, Ma B, Tsai CJ, Nussinov R. Structural stability and dynamics of an amyloid-forming peptide GNNQQNY from the yeast prion sup-35. Biophysical Journal. 91: 824-33. PMID 16679374 DOI: 10.1529/Biophysj.106.083246 |
0.361 |
|
2006 |
Shatsky M, Shulman-Peleg A, Nussinov R, Wolfson HJ. The multiple common point set problem and its application to molecule binding pattern detection. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 13: 407-28. PMID 16597249 DOI: 10.1089/Cmb.2006.13.407 |
0.342 |
|
2006 |
Zanuy D, Nussinov R, Alemán C. From peptide-based material science to protein fibrils: discipline convergence in nanobiology. Physical Biology. 3: S80-90. PMID 16582467 DOI: 10.1088/1478-3975/3/1/S08 |
0.31 |
|
2006 |
Alemán C, Zanuy D, Jiménez AI, Cativiela C, Haspel N, Zheng J, Casanovas J, Wolfson H, Nussinov R. Concepts and schemes for the re-engineering of physical protein modules: generating nanodevices via targeted replacements with constrained amino acids. Physical Biology. 3: S54-62. PMID 16582465 DOI: 10.1088/1478-3975/3/1/S06 |
0.653 |
|
2006 |
Pan Y, Ma B, Levine AJ, Nussinov R. Comparison of the human and worm p53 structures suggests a way for enhancing stability. Biochemistry. 45: 3925-33. PMID 16548519 DOI: 10.1021/Bi052242N |
0.367 |
|
2006 |
Wainreb G, Haspel N, Wolfson HJ, Nussinov R. A permissive secondary structure-guided superposition tool for clustering of protein fragments toward protein structure prediction via fragment assembly. Bioinformatics (Oxford, England). 22: 1343-52. PMID 16543273 DOI: 10.1093/Bioinformatics/Btl098 |
0.671 |
|
2006 |
Zanuy D, Gunasekaran K, Lesk AM, Nussinov R. Computational study of the fibril organization of polyglutamine repeats reveals a common motif identified in beta-helices. Journal of Molecular Biology. 358: 330-45. PMID 16503338 DOI: 10.1016/J.Jmb.2006.01.070 |
0.34 |
|
2006 |
Ma B, Nussinov R. The stability of monomeric intermediates controls amyloid formation: Abeta25-35 and its N27Q mutant. Biophysical Journal. 90: 3365-74. PMID 16500972 DOI: 10.1529/Biophysj.105.075309 |
0.325 |
|
2006 |
Gnanakaran S, Nussinov R, GarcÃa AE. Atomic-level description of amyloid beta-dimer formation. Journal of the American Chemical Society. 128: 2158-9. PMID 16478138 DOI: 10.1021/Ja0548337 |
0.366 |
|
2006 |
Shatsky M, Nussinov R, Wolfson HJ. Optimization of multiple-sequence alignment based on multiple-structure alignment. Proteins. 62: 209-17. PMID 16294339 DOI: 10.1002/Prot.20665 |
0.339 |
|
2006 |
Nussinov R, Alemán C. Nanobiology: from physics and engineering to biology Physical Biology. 3. DOI: 10.1088/1478-3975/3/1/E01 |
0.34 |
|
2005 |
Inbar Y, Benyamini H, Nussinov R, Wolfson HJ. Combinatorial docking approach for structure prediction of large proteins and multi-molecular assemblies. Physical Biology. 2: S156-65. PMID 16280621 DOI: 10.1088/1478-3975/2/4/S10 |
0.391 |
|
2005 |
Ma B, Pan Y, Gunasekaran K, Keskin O, Venkataraghavan RB, Levine AJ, Nussinov R. The contribution of the Trp/Met/Phe residues to physical interactions of p53 with cellular proteins. Physical Biology. 2: S56-66. PMID 16204849 DOI: 10.1088/1478-3975/2/2/S06 |
0.396 |
|
2005 |
Mintz S, Shulman-Peleg A, Wolfson HJ, Nussinov R. Generation and analysis of a protein-protein interface data set with similar chemical and spatial patterns of interactions. Proteins. 61: 6-20. PMID 16184518 DOI: 10.1002/Prot.20580 |
0.379 |
|
2005 |
Benyamini H, Gunasekaran K, Wolfson H, Nussinov R. Fibril modelling by sequence and structure conservation analysis combined with protein docking techniques: beta(2)-microglobulin amyloidosis. Biochimica Et Biophysica Acta. 1753: 121-30. PMID 16107326 DOI: 10.1016/J.Bbapap.2005.07.012 |
0.366 |
|
2005 |
Tsai CJ, Nussinov R. The implications of higher (or lower) success in secondary structure prediction of chain fragments. Protein Science : a Publication of the Protein Society. 14: 1943-4. PMID 16046621 DOI: 10.1110/Ps.051581805 |
0.342 |
|
2005 |
Ogmen U, Keskin O, Aytuna AS, Nussinov R, Gursoy A. PRISM: protein interactions by structural matching. Nucleic Acids Research. 33: W331-6. PMID 15991339 DOI: 10.1093/Nar/Gki585 |
0.371 |
|
2005 |
Inbar Y, Schneidman-Duhovny D, Halperin I, Oron A, Nussinov R, Wolfson HJ. Approaching the CAPRI challenge with an efficient geometry-based docking. Proteins. 60: 217-23. PMID 15981251 DOI: 10.1002/Prot.20561 |
0.304 |
|
2005 |
Schneidman-Duhovny D, Inbar Y, Nussinov R, Wolfson HJ. PatchDock and SymmDock: servers for rigid and symmetric docking. Nucleic Acids Research. 33: W363-7. PMID 15980490 DOI: 10.1093/Nar/Gki481 |
0.371 |
|
2005 |
Shulman-Peleg A, Nussinov R, Wolfson HJ. SiteEngines: recognition and comparison of binding sites and protein-protein interfaces. Nucleic Acids Research. 33: W337-41. PMID 15980484 DOI: 10.1093/Nar/Gki482 |
0.4 |
|
2005 |
Pan Y, Ma B, Nussinov R. CD4 binding partially locks the bridging sheet in gp120 but leaves the beta2/3 strands flexible. Journal of Molecular Biology. 350: 514-27. PMID 15946678 DOI: 10.1016/J.Jmb.2005.05.009 |
0.369 |
|
2005 |
Tsai HH, Reches M, Tsai CJ, Gunasekaran K, Gazit E, Nussinov R. Energy landscape of amyloidogenic peptide oligomerization by parallel-tempering molecular dynamics simulation: Significant role of Asn ladder Proceedings of the National Academy of Sciences of the United States of America. 102: 8174-8179. PMID 15923262 DOI: 10.1073/Pnas.0408653102 |
0.377 |
|
2005 |
Inbar Y, Benyamini H, Nussinov R, Wolfson HJ. Prediction of multimolecular assemblies by multiple docking. Journal of Molecular Biology. 349: 435-47. PMID 15890207 DOI: 10.1016/J.Jmb.2005.03.039 |
0.346 |
|
2005 |
Wolfson HJ, Shatsky M, Schneidman-Duhovny D, Dror O, Shulman-Peleg A, Ma B, Nussinov R. From structure to function: methods and applications. Current Protein & Peptide Science. 6: 171-83. PMID 15853653 DOI: 10.2174/1389203053545435 |
0.344 |
|
2005 |
Keskin O, Nussinov R. Favorable scaffolds: proteins with different sequence, structure and function may associate in similar ways. Protein Engineering, Design & Selection : Peds. 18: 11-24. PMID 15790576 DOI: 10.1093/Protein/Gzh095 |
0.392 |
|
2005 |
Ma B, Pan Y, Gunasekaran K, Venkataraghavan RB, Levine AJ, Nussinov R. Comparison of the protein-protein interfaces in the p53-DNA crystal structures: towards elucidation of the biological interface. Proceedings of the National Academy of Sciences of the United States of America. 102: 3988-93. PMID 15738397 DOI: 10.1073/Pnas.0500215102 |
0.332 |
|
2005 |
Pan Y, Ma B, Venkataraghavan RB, Levine AJ, Nussinov R. In the quest for stable rescuing mutants of p53: computational mutagenesis of flexible loop L1. Biochemistry. 44: 1423-32. PMID 15683227 DOI: 10.1021/Bi047845Y |
0.339 |
|
2005 |
Haspel N, Zanuy D, Ma B, Wolfson H, Nussinov R. A comparative study of amyloid fibril formation by residues 15-19 of the human calcitonin hormone: a single beta-sheet model with a small hydrophobic core. Journal of Molecular Biology. 345: 1213-27. PMID 15644216 DOI: 10.1016/J.Jmb.2004.11.002 |
0.672 |
|
2005 |
Li X, Keskin O, Ma B, Nussinov R, Liang J. Protein-protein interactions: hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states: implications for docking. Journal of Molecular Biology. 344: 781-95. PMID 15533445 DOI: 10.1016/J.Jmb.2004.09.051 |
0.426 |
|
2005 |
Kumar S, Nussinov R. Experiment-guided thermodynamic simulations on reversible two-state proteins: implications for protein thermostability. Biophysical Chemistry. 111: 235-46. PMID 15501567 DOI: 10.1016/J.Bpc.2004.06.005 |
0.337 |
|
2005 |
Gunasekaran K, Ma B, Nussinov R. Is allostery an intrinsic property of all dynamic proteins? Proteins. 57: 433-43. PMID 15382234 DOI: 10.1002/Prot.20232 |
0.397 |
|
2005 |
Inbar Y, Wolfson HJ, Nussinov R. Multiple Docking for Protein Structure Prediction The International Journal of Robotics Research. 24: 131-150. DOI: 10.1177/0278364905050358 |
0.362 |
|
2005 |
Nussinov R, Tsai C. Protein–protein interactions: principles and predictions Physical Biology. 2. DOI: 10.1088/1478-3975/2/2/E01 |
0.41 |
|
2005 |
Shulman-Peleg A, Shatsky M, Nussinov R, Wolfson HJ. MAPPIS: multiple 3D alignment of protein-protein interfaces Lecture Notes in Computer Science. 91-103. DOI: 10.1007/11560500_9 |
0.39 |
|
2004 |
Zanuy D, Haspel N, Tsai HH, Ma B, Gunasekaran K, Wolfson HJ, Nussinov R. Side chain interactions determine the amyloid organization: a single layer beta-sheet molecular structure of the calcitonin peptide segment 15-19. Physical Biology. 1: 89-99. PMID 16204826 DOI: 10.1088/1478-3967/1/2/005 |
0.676 |
|
2004 |
Keskin O, Ma B, Nussinov R. Hot regions in protein--protein interactions: the organization and contribution of structurally conserved hot spot residues. Journal of Molecular Biology. 345: 1281-94. PMID 15644221 DOI: 10.1016/J.Jmb.2004.10.077 |
0.41 |
|
2004 |
Haliloglu T, Keskin O, Ma B, Nussinov R. How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues. Biophysical Journal. 88: 1552-9. PMID 15596504 DOI: 10.1529/Biophysj.104.051342 |
0.388 |
|
2004 |
Zanuy D, Gunasekaran K, Ma B, Tsai HH, Tsai CJ, Nussinov R. Insights into amyloid structural formation and assembly through computational approaches. Amyloid : the International Journal of Experimental and Clinical Investigation : the Official Journal of the International Society of Amyloidosis. 11: 143-61. PMID 15523917 DOI: 10.1080/13506120400000798 |
0.367 |
|
2004 |
Ma B, Nussinov R. Release factors eRF1 and RF2: a universal mechanism controls the large conformational changes. The Journal of Biological Chemistry. 279: 53875-85. PMID 15475364 DOI: 10.1074/Jbc.M407412200 |
0.385 |
|
2004 |
Tsai HH, Tsai CJ, Ma B, Nussinov R. In silico protein design by combinatorial assembly of protein building blocks. Protein Science : a Publication of the Protein Society. 13: 2753-65. PMID 15388863 DOI: 10.1110/Ps.04774004 |
0.4 |
|
2004 |
Gunasekaran K, Tsai CJ, Nussinov R. Analysis of ordered and disordered protein complexes reveals structural features discriminating between stable and unstable monomers. Journal of Molecular Biology. 341: 1327-41. PMID 15321724 DOI: 10.1016/J.Jmb.2004.07.002 |
0.388 |
|
2004 |
Barzilai A, Kumar S, Wolfson H, Nussinov R. Potential folding-function interrelationship in proteins. Proteins. 56: 635-49. PMID 15281117 DOI: 10.1002/Prot.20132 |
0.388 |
|
2004 |
Halperin I, Wolfson H, Nussinov R. Protein-protein interactions: Coupling of structurally conserved residues and of hot spots across interfaces. Implications for docking Structure. 12: 1027-1038. PMID 15274922 DOI: 10.1016/J.Str.2004.04.009 |
0.386 |
|
2004 |
Tsai HH, Zanuy D, Haspel N, Gunasekaran K, Ma B, Tsai CJ, Nussinov R. The stability and dynamics of the human calcitonin amyloid peptide DFNKF. Biophysical Journal. 87: 146-58. PMID 15240453 DOI: 10.1529/Biophysj.104.040352 |
0.657 |
|
2004 |
Shatsky M, Dror O, Schneidman-Duhovny D, Nussinov R, Wolfson HJ. BioInfo3D: a suite of tools for structural bioinformatics. Nucleic Acids Research. 32: W503-7. PMID 15215437 DOI: 10.1093/Nar/Gkh413 |
0.37 |
|
2004 |
Shatsky M, Nussinov R, Wolfson HJ. A method for simultaneous alignment of multiple protein structures. Proteins. 56: 143-56. PMID 15162494 DOI: 10.1002/Prot.10628 |
0.413 |
|
2004 |
Shulman-Peleg A, Nussinov R, Wolfson HJ. Recognition of functional sites in protein structures. Journal of Molecular Biology. 339: 607-33. PMID 15147845 DOI: 10.1016/J.Jmb.2004.04.012 |
0.374 |
|
2004 |
Pan Y, Ma B, Keskin O, Nussinov R. Characterization of the conformational state and flexibility of HIV-1 glycoprotein gp120 core domain. The Journal of Biological Chemistry. 279: 30523-30. PMID 15131118 DOI: 10.1074/Jbc.M404364200 |
0.347 |
|
2004 |
Shatsky M, Nussinov R, Wolfson HJ. FlexProt: alignment of flexible protein structures without a predefinition of hinge regions. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 11: 83-106. PMID 15072690 DOI: 10.1089/106652704773416902 |
0.39 |
|
2004 |
Keskin O, Tsai CJ, Wolfson H, Nussinov R. A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications. Protein Science : a Publication of the Protein Society. 13: 1043-55. PMID 15044734 DOI: 10.1110/Ps.03484604 |
0.356 |
|
2004 |
Zanuy D, Porat Y, Gazit E, Nussinov R. Peptide sequence and amyloid formation: Molecular simulations and experimental study of a human islet amyloid polypeptide fragment and its analogs Structure. 12: 439-455. PMID 15016360 DOI: 10.1016/J.Str.2004.02.002 |
0.368 |
|
2004 |
Kumar S, Nussinov R. Different roles of electrostatics in heat and in cold: adaptation by citrate synthase. Chembiochem : a European Journal of Chemical Biology. 5: 280-90. PMID 14997520 DOI: 10.1002/Cbic.200300627 |
0.349 |
|
2004 |
Gunasekaran K, Nussinov R. Modulating functional loop movements: the role of highly conserved residues in the correlated loop motions. Chembiochem : a European Journal of Chemical Biology. 5: 224-30. PMID 14760744 DOI: 10.1002/Cbic.200300732 |
0.347 |
|
2004 |
Schneidman-Duhovny D, Nussinov R, Wolfson HJ. Predicting molecular interactions in silico: II. Protein-protein and protein-drug docking. Current Medicinal Chemistry. 11: 91-107. PMID 14754428 DOI: 10.2174/0929867043456223 |
0.343 |
|
2004 |
Dror O, Shulman-Peleg A, Nussinov R, Wolfson HJ. Predicting molecular interactions in silico: I. A guide to pharmacophore identification and its applications to drug design. Current Medicinal Chemistry. 11: 71-90. PMID 14754427 DOI: 10.2174/0929867043456287 |
0.338 |
|
2004 |
Dror O, Benyamini H, Nussinov R, Wolfson HJ. Multiple structural alignment by secondary structures: algorithm and applications. Protein Science : a Publication of the Protein Society. 12: 2492-507. PMID 14573862 DOI: 10.1110/Ps.03200603 |
0.355 |
|
2004 |
Ma B, Nussinov R. Energy landscape and dynamics of the beta-hairpin G peptide and its isomers: Topology and sequences. Protein Science : a Publication of the Protein Society. 12: 1882-93. PMID 12930988 DOI: 10.1110/Ps.0306103 |
0.33 |
|
2004 |
Dror O, Benyamini H, Nussinov R, Wolfson H. MASS: multiple structural alignment by secondary structures. Bioinformatics (Oxford, England). i95-104. PMID 12855444 DOI: 10.1093/Bioinformatics/Btg1012 |
0.343 |
|
2003 |
Gunasekaran K, Ma B, Nussinov R. Triggering loops and enzyme function: identification of loops that trigger and modulate movements. Journal of Molecular Biology. 332: 143-59. PMID 12946353 DOI: 10.1016/S0022-2836(03)00893-3 |
0.36 |
|
2003 |
Inbar Y, Benyamini H, Nussinov R, Wolfson HJ. Protein structure prediction via combinatorial assembly of sub-structural units. Bioinformatics (Oxford, England). 19: i158-68. PMID 12855452 DOI: 10.1093/Bioinformatics/Btg1020 |
0.396 |
|
2003 |
Halperin I, Wolfson H, Nussinov R. SiteLight: Binding-site prediction using phage display libraries Protein Science. 12: 1344-1359. PMID 12824481 DOI: 10.1110/Ps.0237103 |
0.337 |
|
2003 |
Benyamini H, Gunasekaran K, Wolfson H, Nussinov R. Beta2-microglobulin amyloidosis: insights from conservation analysis and fibril modelling by protein docking techniques. Journal of Molecular Biology. 330: 159-74. PMID 12818210 DOI: 10.1016/S0022-2836(03)00557-6 |
0.374 |
|
2003 |
Schneidman-Duhovny D, Inbar Y, Polak V, Shatsky M, Halperin I, Benyamini H, Barzilai A, Dror O, Haspel N, Nussinov R, Wolfson HJ. Taking geometry to its edge: fast unbound rigid (and hinge-bent) docking. Proteins. 52: 107-12. PMID 12784375 DOI: 10.1002/Prot.10397 |
0.632 |
|
2003 |
Zanuy D, Nussinov R. The sequence dependence of fiber organization. A comparative molecular dynamics study of the islet amyloid polypeptide segments 22-27 and 22-29. Journal of Molecular Biology. 329: 565-84. PMID 12767835 DOI: 10.1016/S0022-2836(03)00491-1 |
0.361 |
|
2003 |
Haspel N, Tsai CJ, Wolfson H, Nussinov R. Reducing the computational complexity of protein folding via fragment folding and assembly. Protein Science : a Publication of the Protein Society. 12: 1177-87. PMID 12761388 DOI: 10.1110/Ps.0232903 |
0.689 |
|
2003 |
Ma B, Elkayam T, Wolfson H, Nussinov R. Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces. Proceedings of the National Academy of Sciences of the United States of America. 100: 5772-7. PMID 12730379 DOI: 10.1073/Pnas.1030237100 |
0.39 |
|
2003 |
Kumar S, Tsai CJ, Nussinov R. Temperature range of thermodynamic stability for the native state of reversible two-state proteins. Biochemistry. 42: 4864-73. PMID 12718527 DOI: 10.1021/Bi027184+ |
0.337 |
|
2003 |
Gunasekaran K, Ma B, Ramakrishnan B, Qasba PK, Nussinov R. Interdependence of backbone flexibility, residue conservation, and enzyme function: A case study on β1,4-Galactosyltransferase-I Biochemistry. 42: 3674-3687. PMID 12667057 DOI: 10.1021/Bi034046R |
0.375 |
|
2003 |
Benyamini H, Gunasekaran K, Wolfson H, Nussinov R. Conservation and amyloid formation: a study of the gelsolin-like family. Proteins. 51: 266-82. PMID 12660995 DOI: 10.1002/Prot.10359 |
0.37 |
|
2003 |
Haspel N, Tsai CJ, Wolfson H, Nussinov R. Hierarchical protein folding pathways: a computational study of protein fragments. Proteins. 51: 203-15. PMID 12660989 DOI: 10.1002/Prot.10294 |
0.684 |
|
2003 |
Zanuy D, Ma B, Nussinov R. Short peptide amyloid organization: stabilities and conformations of the islet amyloid peptide NFGAIL. Biophysical Journal. 84: 1884-94. PMID 12609890 DOI: 10.1016/S0006-3495(03)74996-0 |
0.343 |
|
2003 |
Gunasekaran K, Tsai CJ, Kumar S, Zanuy D, Nussinov R. Extended disordered proteins: targeting function with less scaffold. Trends in Biochemical Sciences. 28: 81-5. PMID 12575995 DOI: 10.1016/S0968-0004(03)00003-3 |
0.349 |
|
2003 |
Kumar S, Nussinov R. Close-range electrostatic interactions in proteins. Chembiochem : a European Journal of Chemical Biology. 3: 604-17. PMID 12324994 DOI: 10.1002/1439-7633(20020703)3:7<604::Aid-Cbic604>3.0.Co;2-X |
0.432 |
|
2003 |
Ma B, Nussinov R. Molecular dynamics simulations of alanine rich beta-sheet oligomers: Insight into amyloid formation. Protein Science : a Publication of the Protein Society. 11: 2335-50. PMID 12237456 DOI: 10.1110/Ps.4270102 |
0.36 |
|
2002 |
Shatsky M, Nussinov R, Wolfson HJ. Flexible protein alignment and hinge detection. Proteins. 48: 242-56. PMID 12112693 DOI: 10.1002/Prot.10100 |
0.382 |
|
2002 |
Tsai CJ, Polverino de Laureto P, Fontana A, Nussinov R. Comparison of protein fragments identified by limited proteolysis and by computational cutting of proteins. Protein Science : a Publication of the Protein Society. 11: 1753-70. PMID 12070328 DOI: 10.1110/Ps.4100102 |
0.383 |
|
2002 |
Tsai CJ, Maizel JV, Nussinov R. The hydrophobic effect: a new insight from cold denaturation and a two-state water structure. Critical Reviews in Biochemistry and Molecular Biology. 37: 55-69. PMID 12027264 DOI: 10.1080/10409230290771456 |
0.351 |
|
2002 |
Halperin I, Ma B, Wolfson H, Nussinov R. Principles of docking: An overview of search algorithms and a guide to scoring functions. Proteins. 47: 409-43. PMID 12001221 DOI: 10.1002/Prot.10115 |
0.403 |
|
2002 |
Kumar S, Tsai CJ, Nussinov R. Maximal stabilities of reversible two-state proteins. Biochemistry. 41: 5359-74. PMID 11969396 DOI: 10.1021/Bi012154C |
0.351 |
|
2002 |
Tsai CJ, Nussinov R. Transient, highly populated, building blocks folding model. Cell Biochemistry and Biophysics. 34: 209-35. PMID 11898865 DOI: 10.1385/Cbb:34:2:209 |
0.414 |
|
2002 |
Sham YY, Ma B, Tsai CJ, Nussinov R. Thermal unfolding molecular dynamics simulation of Escherichia coli dihydrofolate reductase: Thermal stability of protein domains and unfolding pathway Proteins: Structure, Function and Genetics. 46: 308-320. PMID 11835506 DOI: 10.1002/Prot.10040 |
0.663 |
|
2002 |
Ma B, Shatsky M, Wolfson HJ, Nussinov R. Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations. Protein Science : a Publication of the Protein Society. 11: 184-97. PMID 11790828 DOI: 10.1110/Ps.21302 |
0.352 |
|
2002 |
Sinha N, Tsa CJ, Nussinov R. Building blocks, hinge-bending motions and protein topology. Journal of Biomolecular Structure & Dynamics. 19: 369-80. PMID 11790137 DOI: 10.1080/07391102.2001.10506747 |
0.379 |
|
2002 |
Tsai CJ, Nussinov R. The building block folding model and the kinetics of protein folding. Protein Engineering. 14: 723-33. PMID 11739890 DOI: 10.1093/Protein/14.10.723 |
0.39 |
|
2002 |
Sinha N, Kumar S, Nussinov R. Interdomain interactions in hinge-bending transitions. Structure (London, England : 1993). 9: 1165-81. PMID 11738043 DOI: 10.1016/S0969-2126(01)00687-6 |
0.317 |
|
2002 |
Tsai CD, Ma B, Kumar S, Wolfson H, Nussinov R. Protein folding: binding of conformationally fluctuating building blocks via population selection. Critical Reviews in Biochemistry and Molecular Biology. 36: 399-433. PMID 11724155 DOI: 10.1080/20014091074228 |
0.406 |
|
2002 |
Kumar S, Tsai CJ, Nussinov R. Thermodynamic differences among homologous thermophilic and mesophilic proteins. Biochemistry. 40: 14152-65. PMID 11714268 DOI: 10.1021/Bi0106383 |
0.331 |
|
2001 |
Kumar S, Nussinov R. How do thermophilic proteins deal with heat? Cellular and Molecular Life Sciences : Cmls. 58: 1216-33. PMID 11577980 DOI: 10.1007/Pl00000935 |
0.406 |
|
2001 |
Tsai CJ, Buyong M, Sham YY, Kumar S, Nussinov R. Structured disorder and conformational selection Proteins: Structure, Function and Genetics. 44: 418-427. PMID 11484219 DOI: 10.1002/Prot.1107 |
0.651 |
|
2001 |
Leibowitz N, Nussinov R, Wolfson HJ. MUSTA--a general, efficient, automated method for multiple structure alignment and detection of common motifs: application to proteins. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 8: 93-121. PMID 11454300 DOI: 10.1089/106652701300312896 |
0.381 |
|
2001 |
Ma B, Wolfson HJ, Nussinov R. Protein functional epitopes: hot spots, dynamics and combinatorial libraries. Current Opinion in Structural Biology. 11: 364-9. PMID 11406388 DOI: 10.1016/S0959-440X(00)00216-5 |
0.392 |
|
2001 |
Kumar S, Nussinov R. Fluctuations in ion pairs and their stabilities in proteins. Proteins. 43: 433-54. PMID 11340660 DOI: 10.1002/Prot.1056 |
0.369 |
|
2001 |
Kumar S, Sham YY, Tsai CJ, Nussinov R. Protein folding and function: The N-terminal fragment in adenylate kinase Biophysical Journal. 80: 2439-2454. PMID 11325743 DOI: 10.1016/S0006-3495(01)76213-3 |
0.7 |
|
2001 |
Sinha N, Tsai CJ, Nussinov R. A proposed structural model for amyloid fibril elongation: domain swapping forms an interdigitating beta-structure polymer. Protein Engineering. 14: 93-103. PMID 11297667 DOI: 10.1093/Protein/14.2.93 |
0.368 |
|
2001 |
Leibowitz N, Fligelman ZY, Nussinov R, Wolfson HJ. Automated multiple structure alignment and detection of a common substructural motif. Proteins. 43: 235-45. PMID 11288173 DOI: 10.1002/Prot.1034 |
0.402 |
|
2001 |
Sham YY, Ma B, Tsai CJ, Nussinov R. Molecular dynamics simulation of Escherichia coli dihydrofolate reductase and its protein fragments: relative stabilities in experiment and simulations. Protein Science : a Publication of the Protein Society. 10: 135-48. PMID 11266602 DOI: 10.1110/Ps.33301 |
0.672 |
|
2001 |
Sinha N, Nussinov R. Point mutations and sequence variability in proteins: redistributions of preexisting populations. Proceedings of the National Academy of Sciences of the United States of America. 98: 3139-44. PMID 11248045 DOI: 10.1073/Pnas.051399098 |
0.398 |
|
2001 |
Xiong J, Lubkowski J, Nussinov R. Homology modeling and molecular dynamics simulations of lymphotactin. Protein Science : a Publication of the Protein Society. 9: 2192-9. PMID 11152129 DOI: 10.1110/Ps.9.11.2192 |
0.386 |
|
2001 |
Kumar S, Nussinov R. Fluctuations between stabilizing and destabilizing electrostatic contributions of ion pairs in conformers of the c-Myc-Max leucine zipper. Proteins. 41: 485-97. PMID 11056036 DOI: 10.1002/1097-0134(20001201)41:4<485::Aid-Prot60>3.0.Co;2-E |
0.343 |
|
2001 |
Ma B, Tsai CJ, Nussinov R. A systematic study of the vibrational free energies of polypeptides in folded and random states. Biophysical Journal. 79: 2739-53. PMID 11053147 DOI: 10.1016/S0006-3495(00)76513-1 |
0.377 |
|
2001 |
Tsai CJ, Ma B, Sham YY, Kumar S, Wolfson HJ, Nussinov R. A hierarchical, building-block-based computational scheme for protein structure prediction Ibm Journal of Research and Development. 45: 513-523. DOI: 10.1147/Rd.453.0513 |
0.675 |
|
2001 |
Kumar S, Wolfson HJ, Nussinov R. Protein flexibility and electrostatic interactions Ibm Journal of Research and Development. 45: 499-512. DOI: 10.1147/Rd.453.0499 |
0.413 |
|
2000 |
Ma B, Tsai CJ, Nussinov R. Binding and folding: in search of intramolecular chaperone-like building block fragments. Protein Engineering. 13: 617-27. PMID 11054456 DOI: 10.1093/Protein/13.9.617 |
0.398 |
|
2000 |
Tsai CJ, Maizel JV, Nussinov R. Anatomy of protein structures: visualizing how a one-dimensional protein chain folds into a three-dimensional shape. Proceedings of the National Academy of Sciences of the United States of America. 97: 12038-43. PMID 11050234 DOI: 10.1073/Pnas.97.22.12038 |
0.389 |
|
2000 |
Hu Z, Ma B, Wolfson H, Nussinov R. Conservation of polar residues as hot spots at protein interfaces. Proteins. 39: 331-42. PMID 10813815 DOI: 10.1002/(Sici)1097-0134(20000601)39:4<331::Aid-Prot60>3.0.Co;2-A |
0.39 |
|
2000 |
Kumar S, Tsai CJ, Nussinov R. Factors enhancing protein thermostability. Protein Engineering. 13: 179-91. PMID 10775659 DOI: 10.1093/Protein/13.3.179 |
0.386 |
|
2000 |
Kumar S, Ma B, Tsai CJ, Sinha N, Nussinov R. Folding and binding cascades: dynamic landscapes and population shifts. Protein Science : a Publication of the Protein Society. 9: 10-9. PMID 10739242 DOI: 10.1110/Ps.9.1.10 |
0.371 |
|
2000 |
Ma B, Kumar S, Tsai CJ, Hu Z, Nussinov R. Transition-state ensemble in enzyme catalysis: possibility, reality, or necessity? Journal of Theoretical Biology. 203: 383-97. PMID 10736215 DOI: 10.1006/Jtbi.2000.1097 |
0.307 |
|
2000 |
Kumar S, Ma B, Tsai CJ, Nussinov R. Electrostatic strengths of salt bridges in thermophilic and mesophilic glutamate dehydrogenase monomers. Proteins. 38: 368-83. PMID 10707024 DOI: 10.1002/(Sici)1097-0134(20000301)38:4<368::Aid-Prot3>3.0.Co;2-R |
0.359 |
|
2000 |
Ma B, Nussinov R. Molecular dynamics simulations of a beta-hairpin fragment of protein G: balance between side-chain and backbone forces. Journal of Molecular Biology. 296: 1091-104. PMID 10686106 DOI: 10.1006/Jmbi.2000.3518 |
0.36 |
|
2000 |
Kumar S, Nussinov R. Salt bridge stability in monomeric proteins. Journal of Molecular Biology. 293: 1241-55. PMID 10547298 DOI: 10.1006/Jmbi.1999.3218 |
0.362 |
|
2000 |
Ma B, Kumar S, Tsai CJ, Nussinov R. Folding funnels and binding mechanisms. Protein Engineering. 12: 713-20. PMID 10506280 DOI: 10.1093/Protein/12.9.713 |
0.377 |
|
1999 |
Kumar S, Ma B, Tsai CJ, Wolfson H, Nussinov R. Folding funnels and conformational transitions via hinge-bending motions. Cell Biochemistry and Biophysics. 31: 141-64. PMID 10593256 DOI: 10.1007/Bf02738169 |
0.33 |
|
1999 |
Tsai CJ, Maizel JV, Nussinov R. Distinguishing between sequential and nonsequentially folded proteins: implications for folding and misfolding. Protein Science : a Publication of the Protein Society. 8: 1591-604. PMID 10452603 DOI: 10.1110/Ps.8.8.1591 |
0.406 |
|
1999 |
Ma B, Nussinov R. Explicit and implicit water simulations of a beta-hairpin peptide. Proteins. 37: 73-87. PMID 10451552 DOI: 10.1002/(Sici)1097-0134(19991001)37:1<73::Aid-Prot8>3.0.Co;2-Z |
0.348 |
|
1999 |
Norel R, Petrey D, Wolfson HJ, Nussinov R. Examination of shape complementarity in docking of unbound proteins. Proteins. 36: 307-17. PMID 10409824 DOI: 10.1002/(Sici)1097-0134(19990815)36:3<307::Aid-Prot5>3.0.Co;2-R |
0.395 |
|
1999 |
Tsai CJ, Kumar S, Ma B, Nussinov R. Folding funnels, binding funnels, and protein function. Protein Science : a Publication of the Protein Society. 8: 1181-90. PMID 10386868 DOI: 10.1110/Ps.8.6.1181 |
0.399 |
|
1999 |
Sandak B, Nussinov R, Wolfson HJ. A method for biomolecular structural recognition and docking allowing conformational flexibility. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 5: 631-54. PMID 10072081 DOI: 10.1089/Cmb.1998.5.631 |
0.381 |
|
1999 |
Verbitsky G, Nussinov R, Wolfson H. Flexible structural comparison allowing hinge-bending, swiveling motions. Proteins. 34: 232-54. PMID 10022359 DOI: 10.1002/(Sici)1097-0134(19990201)34:2<232::Aid-Prot9>3.0.Co;2-9 |
0.376 |
|
1998 |
Sandak B, Wolfson HJ, Nussinov R. Flexible docking allowing induced fit in proteins: insights from an open to closed conformational isomers. Proteins. 32: 159-74. PMID 9714156 DOI: 10.1002/(Sici)1097-0134(19980801)32:2<159::Aid-Prot3>3.0.Co;2-G |
0.344 |
|
1998 |
Tsai CJ, Xu D, Nussinov R. Protein folding via binding and vice versa. Folding & Design. 3: R71-80. PMID 9710571 DOI: 10.1016/S1359-0278(98)00032-7 |
0.326 |
|
1998 |
Rosen M, Lin SL, Wolfson H, Nussinov R. Molecular shape comparisons in searches for active sites and functional similarity. Protein Engineering. 11: 263-77. PMID 9680188 DOI: 10.1093/Protein/11.4.263 |
0.318 |
|
1998 |
Xu D, Tsai CJ, Nussinov R. Mechanism and evolution of protein dimerization. Protein Science : a Publication of the Protein Society. 7: 533-44. PMID 9541384 DOI: 10.1002/Pro.5560070301 |
0.355 |
|
1998 |
Xu D, Nussinov R. Favorable domain size in proteins. Folding & Design. 3: 11-7. PMID 9502316 DOI: 10.1016/S1359-0278(98)00004-2 |
0.349 |
|
1998 |
Azarya-Sprinzak E, Naor D, Wolfson HJ, Nussinov R. Interchanges of spatially neighbouring residues in structurally conserved environments. Protein Engineering. 10: 1109-22. PMID 9488136 DOI: 10.1093/Protein/10.10.1109 |
0.343 |
|
1998 |
Xu D, Tsai CJ, Nussinov R. Hydrogen bonds and salt bridges across protein-protein interfaces. Protein Engineering. 10: 999-1012. PMID 9464564 DOI: 10.1093/Protein/10.9.999 |
0.362 |
|
1998 |
Tsai CJ, Xu D, Nussinov R. Structural motifs at protein-protein interfaces: protein cores versus two-state and three-state model complexes. Protein Science : a Publication of the Protein Society. 6: 1793-805. PMID 9300480 DOI: 10.1002/Pro.5560060901 |
0.414 |
|
1998 |
Wolfson HJ, Nussinov R. Chapter 14 – From computer vision to protein structure and association New Comprehensive Biochemistry. 32: 313-334. DOI: 10.1016/S0167-7306(08)60471-8 |
0.371 |
|
1997 |
Lin SL, Xu D, Li A, Rosen M, Wolfson HJ, Nussinov R. Investigation of the enzymatic mechanism of the yeast chorismate mutase by docking a transition state analog. Journal of Molecular Biology. 271: 838-45. PMID 9299331 DOI: 10.1006/Jmbi.1997.1168 |
0.313 |
|
1997 |
Tsai CJ, Nussinov R. Hydrophobic folding units at protein-protein interfaces: implications to protein folding and to protein-protein association. Protein Science : a Publication of the Protein Society. 6: 1426-37. PMID 9232644 DOI: 10.1002/Pro.5560060707 |
0.391 |
|
1997 |
Alesker V, Nussinov R, Wolfson HJ. Detection of non-topological motifs in protein structures. Protein Engineering. 9: 1103-19. PMID 9010924 DOI: 10.1093/Protein/9.12.1103 |
0.399 |
|
1997 |
Tsai CJ, Lin SL, Wolfson HJ, Nussinov R. Studies of protein-protein interfaces: a statistical analysis of the hydrophobic effect. Protein Science : a Publication of the Protein Society. 6: 53-64. PMID 9007976 DOI: 10.1002/Pro.5560060106 |
0.398 |
|
1997 |
Xu D, Lin SL, Nussinov R. Protein binding versus protein folding: The role of hydrophilic bridges in protein associations Journal of Molecular Biology. 265: 68-84. PMID 8995525 DOI: 10.1006/Jmbi.1996.0712 |
0.412 |
|
1996 |
Lin SL, Nussinov R. Molecular recognition via face center representation of a molecular surface Journal of Molecular Graphics. 14: 78-90. PMID 8835775 DOI: 10.1016/0263-7855(96)00030-6 |
0.337 |
|
1996 |
Fischer D, Tsai CJ, Nussinov R, Wolfson H. A 3D sequence-independent representation of the protein data bank. Protein Engineering. 8: 981-97. PMID 8771179 DOI: 10.1093/Protein/8.10.981 |
0.383 |
|
1996 |
Tsai CJ, Lin SL, Wolfson HJ, Nussinov R. A dataset of protein-protein interfaces generated with a sequence-order-independent comparison technique. Journal of Molecular Biology. 260: 604-20. PMID 8759323 DOI: 10.1006/Jmbi.1996.0424 |
0.382 |
|
1996 |
Tsai CJ, Lin SL, Wolfson HJ, Nussinov R. Protein-protein interfaces: architectures and interactions in protein-protein interfaces and in protein cores. Their similarities and differences. Critical Reviews in Biochemistry and Molecular Biology. 31: 127-52. PMID 8740525 DOI: 10.3109/10409239609106582 |
0.422 |
|
1996 |
Naor D, Fischer D, Jernigan RL, Wolfson HJ, Nussinov R. Amino acid pair interchanges at spatially conserved locations. Journal of Molecular Biology. 256: 924-38. PMID 8601843 DOI: 10.1006/Jmbi.1996.0138 |
0.357 |
|
1996 |
Tsai C, Lin SL, Wolfson HJ, Nussinov R. Techniques for searching for structural similarities between protein cores, protein surfaces and between protein-protein interfaces Techniques in Protein Chemistry. 7: 419-429. DOI: 10.1016/S1080-8914(96)80046-9 |
0.377 |
|
1995 |
Sandak B, Nussinov R, Wolfson HJ. An automated computer vision and robotics-based technique for 3-D flexible biomolecular docking and matching. Computer Applications in the Biosciences : Cabios. 11: 87-99. PMID 7796279 DOI: 10.1093/Bioinformatics/11.1.87 |
0.342 |
|
1995 |
Fischer D, Lin SL, Wolfson HL, Nussinov R. A geometry-based suite of molecular docking processes. Journal of Molecular Biology. 248: 459-77. PMID 7739053 DOI: 10.1016/S0022-2836(95)80063-8 |
0.328 |
|
1995 |
Lin SL, Tsai CJ, Nussinov R. A study of four-helix bundles: Investigating protein folding via similar architectural motifs in protein cores and in subunit interfaces Journal of Molecular Biology. 248: 151-161. PMID 7731040 DOI: 10.1006/Jmbi.1995.0208 |
0.411 |
|
1995 |
Norel R, Lin SL, Wolfson HJ, Nussinov R. Molecular surface complementarity at protein-protein interfaces: the critical role played by surface normals at well placed, sparse, points in docking. Journal of Molecular Biology. 252: 263-73. PMID 7674306 DOI: 10.1006/Jmbi.1995.0493 |
0.334 |
|
1995 |
Lin SL, Nussinov R. A disulphide-reinforced structural scaffold shared by small proteins with diverse functions Nature Structural Biology. 2: 835-837. PMID 7552703 DOI: 10.1038/Nsb1095-835 |
0.34 |
|
1994 |
Fischer D, Wolfson H, Nussinov R. Spatial, sequence-order-independent structural comparison of alpha/beta proteins: evolutionary implications. Journal of Biomolecular Structure & Dynamics. 11: 367-80. PMID 8286062 DOI: 10.1080/07391102.1993.10508732 |
0.355 |
|
1994 |
Fischer D, Wolfson H, Lin SL, Nussinov R. Three-dimensional, sequence order-independent structural comparison of a serine protease against the crystallographic database reveals active site similarities: potential implications to evolution and to protein folding. Protein Science : a Publication of the Protein Society. 3: 769-78. PMID 8061606 DOI: 10.1002/Pro.5560030506 |
0.394 |
|
1994 |
Norel R, Lin SL, Wolfson HJ, Nussinov R. Shape complementarity at protein-protein interfaces. Biopolymers. 34: 933-40. PMID 8054472 DOI: 10.1002/Bip.360340711 |
0.334 |
|
1993 |
Bachar O, Fischer D, Nussinov R, Wolfson H. A computer vision based technique for 3-D sequence-independent structural comparison of proteins. Protein Engineering. 6: 279-88. PMID 8506262 DOI: 10.1093/Protein/6.3.279 |
0.344 |
|
1993 |
Fischer D, Norel R, Wolfson H, Nussinov R. Surface motifs by a computer vision technique: searches, detection, and implications for protein-ligand recognition. Proteins. 16: 278-92. PMID 8394000 DOI: 10.1002/Prot.340160306 |
0.343 |
|
1993 |
Nussinov R. The eukaryotic CCAAT and TATA boxes, DNA spacer flexibility and looping. Journal of Theoretical Biology. 155: 243-70. PMID 1453699 DOI: 10.1016/S0022-5193(05)80597-1 |
0.337 |
|
1992 |
Nussinov R, Wolfson HJ. Efficient detection of three-dimensional structural motifs in biological macromolecules by computer vision techniques. Proceedings of the National Academy of Sciences of the United States of America. 88: 10495-9. PMID 1961713 DOI: 10.1073/Pnas.88.23.10495 |
0.352 |
|
1992 |
Nussinov R. DNA sequences at and between the GC and TATA boxes: potential DNA looping and spatial juxtapositioning of the protein factors. Journal of Biomolecular Structure & Dynamics. 9: 1213-37. PMID 1637510 DOI: 10.1080/07391102.1992.10507988 |
0.335 |
|
1992 |
Fischer D, Bachar O, Nussinov R, Wolfson H. An efficient automated computer vision based technique for detection of three dimensional structural motifs in proteins. Journal of Biomolecular Structure & Dynamics. 9: 769-89. PMID 1616630 DOI: 10.1080/07391102.1992.10507955 |
0.394 |
|
1991 |
Nussinov R. Signals in DNA sequences and their potential properties. Computer Applications in the Biosciences : Cabios. 7: 295-9. PMID 1913209 DOI: 10.1093/Bioinformatics/7.3.295 |
0.339 |
|
1990 |
Nussinov R. The predicted presence of large helical structural variation in yeast HIS4 upstream region is correlated with general amino acid control on the CYC1 gene. Journal of Biomolecular Structure & Dynamics. 3: 349-61. PMID 3917026 DOI: 10.1080/07391102.1985.10508422 |
0.319 |
|
1990 |
Jernigan RL, Sarai A, Shapiro B, Nussinov R. Relationship between curved DNA conformations and slow gel migration. Journal of Biomolecular Structure & Dynamics. 4: 561-7. PMID 3271455 DOI: 10.1080/07391102.1987.10507660 |
0.337 |
|
1990 |
Nussinov R. Conserved putative signals in 3' intron junctions in rodents. Journal of Biomolecular Structure & Dynamics. 4: 1051-64. PMID 3270535 DOI: 10.1080/07391102.1987.10507697 |
0.309 |
|
1990 |
Sarai A, Mazur J, Nussinov R, Jernigan RL. Sequence dependence of DNA conformational flexibility. Biochemistry. 28: 7842-9. PMID 2611216 DOI: 10.1021/Bi00445A046 |
0.325 |
|
1990 |
Landau GM, Vishkin U, Nussinov R. Fast alignment of DNA and protein sequences. Methods in Enzymology. 183: 487-502. PMID 2314289 DOI: 10.1016/0076-6879(90)83033-6 |
0.332 |
|
1990 |
Nussinov R. Sequence signals in eukaryotic upstream regions. Critical Reviews in Biochemistry and Molecular Biology. 25: 185-224. PMID 2196161 DOI: 10.3109/10409239009090609 |
0.315 |
|
1989 |
Sarai A, Mazur J, Nussinov R, Jernigan RL. Origin of DNA helical structure and its sequence dependence. Biochemistry. 27: 8498-502. PMID 3242599 DOI: 10.1021/Bi00422A030 |
0.322 |
|
1989 |
Nussinov R. The ordering of the nucleotides in DNA: computational problems in molecular biology. Computers in Biology and Medicine. 19: 269-81. PMID 2478335 DOI: 10.1016/0010-4825(89)90014-0 |
0.322 |
|
1988 |
Nussinov R. Putative elements in the vicinity of viral transcription initiation sites. The International Journal of Biochemistry. 20: 721-30. PMID 3141227 DOI: 10.1016/0020-711X(88)90168-1 |
0.321 |
|
1988 |
Le SY, Chen JH, Nussinov R, Maizel JV. An improved secondary structure computation method and its application to intervening sequence in the human alpha-like globin mRNA precursors. Computer Applications in the Biosciences : Cabios. 4: 337-44. PMID 3046713 DOI: 10.1093/Bioinformatics/4.3.337 |
0.34 |
|
1986 |
Nussinov R, Owens J, Maizel JV. Sequence signals in eukaryotic upstream regions. Biochimica Et Biophysica Acta. 866: 109-19. PMID 3955051 DOI: 10.1016/0167-4781(86)90107-7 |
0.306 |
|
1986 |
Nussinov R. Structural wrinkles and the genomic regulatory sites of eukaryotes. Journal of Molecular Evolution. 22: 150-9. PMID 3934394 DOI: 10.1007/Bf02101693 |
0.333 |
|
1986 |
Jernigan RL, Sarai A, Ting KL, Nussinov R. Hydrophobic interactions in the major groove can influence DNA local structure. Journal of Biomolecular Structure & Dynamics. 4: 41-8. PMID 3271434 DOI: 10.1080/07391102.1986.10507645 |
0.319 |
|
1986 |
Nussinov R, Weisberg RA. Bacteriophage lambda int protein may recognize structural features of the attachment sites. Journal of Biomolecular Structure & Dynamics. 3: 1133-44. PMID 2978733 DOI: 10.1080/07391102.1986.10508490 |
0.377 |
|
1985 |
Nussinov R, Shapiro B, Lipkin LE, Maizel JV. Enhancer elements share local homologous twist-angle variations with a helical periodicity. Biochimica Et Biophysica Acta. 783: 246-57. PMID 6095913 DOI: 10.1016/0167-4781(84)90035-6 |
0.306 |
|
1985 |
Nussinov R. Large helical conformational deviations from ideal B-DNA and prokaryotic regulatory sites. Journal of Theoretical Biology. 115: 179-89. PMID 2412072 DOI: 10.1016/S0022-5193(85)80094-1 |
0.341 |
|
1984 |
Nussinov R, Pieczenik G. Folding of two large nucleotide chains. Journal of Theoretical Biology. 106: 261-73. PMID 6232430 DOI: 10.1016/0022-5193(84)90030-4 |
0.703 |
|
1984 |
Nussinov R, Pieczenik G. Structural and combinatorial constraints on base pairing in large nucleotide sequences. Journal of Theoretical Biology. 106: 245-59. PMID 6201680 DOI: 10.1016/0022-5193(84)90029-8 |
0.724 |
|
1984 |
Nussinov R, Shapiro B, Lipkin LE, Maizel JV. DNAase I hypersensitive sites may be correlated with genomic regions of large structural variation. Journal of Molecular Biology. 177: 591-607. PMID 6090673 DOI: 10.1016/0022-2836(84)90039-1 |
0.303 |
|
1980 |
Nussinov R, Jacobson AB. Fast algorithm for predicting the secondary structure of single-stranded RNA Proceedings of the National Academy of Sciences of the United States of America. 77: 6903-6913. PMID 6161375 DOI: 10.1073/Pnas.77.11.6309 |
0.316 |
|
1978 |
Nussinov R, Pieczenik G, Griggs JR, Kleitman DJ. Algorithms for Loop Matchings Siam Journal On Applied Mathematics. 35: 68-82. DOI: 10.1137/0135006 |
0.713 |
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