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Ruth Nussinov - Publications

Affiliations: 
National Cancer Institute National Institutes of Health, Bethesda, MD 
Website:
https://ccr.cancer.gov/Laboratory-of-Cancer-Immunometabolism/ruth-nussinov
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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, García 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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