| Year |
Citation |
Score |
| 2024 |
Sayin AZ, Abali Z, Senyuz S, Cankara F, Gursoy A, Keskin O. Conformational diversity and protein-protein interfaces in drug repurposing in Ras signaling pathway. Scientific Reports. 14: 1239. PMID 38216592 DOI: 10.1038/s41598-023-50913-8 |
0.41 |
|
| 2024 |
Kosoglu K, Aydin Z, Tuncbag N, Gursoy A, Keskin O. Structural coverage of the human interactome. Briefings in Bioinformatics. 25. PMID 38180828 DOI: 10.1093/bib/bbad496 |
0.356 |
|
| 2022 |
Lim H, Tsai CJ, Keskin O, Nussinov R, Gursoy A. HMI-PRED 2.0: a biologist-oriented web application for prediction of host-microbe protein-protein interaction by interface mimicry. Bioinformatics (Oxford, England). PMID 36124958 DOI: 10.1093/bioinformatics/btac633 |
0.363 |
|
| 2021 |
Ovek D, Abali Z, Zeylan ME, Keskin O, Gursoy A, Tuncbag N. Artificial intelligence based methods for hot spot prediction. Current Opinion in Structural Biology. 72: 209-218. PMID 34954608 DOI: 10.1016/j.sbi.2021.11.003 |
0.358 |
|
| 2021 |
Ovek D, Taweel A, Abali Z, Tezsezen E, Koroglu YE, Tsai CJ, Nussinov R, Keskin O, Gursoy A. Web interface for 3D visualization and analysis of SARS-CoV-2-human mimicry and interactions. Bioinformatics (Oxford, England). PMID 34864889 DOI: 10.1093/bioinformatics/btab799 |
0.375 |
|
| 2021 |
Can ND, Basturk E, Kizilboga T, Akcay IM, Dingiloglu B, Tatli O, Acar S, Ozfiliz Kilbas P, Elbeyli E, Muratcioglu S, Jannuzzi AT, Gursoy A, Keskin O, Doganay HL, Karademir Yilmaz B, et al. Interactome analysis of Bag-1 isoforms reveals novel interaction partners in endoplasmic reticulum-associated degradation. Plos One. 16: e0256640. PMID 34428256 DOI: 10.1371/journal.pone.0256640 |
0.383 |
|
| 2021 |
Eren M, Tuncbag N, Jang H, Nussinov R, Gursoy A, Keskin O. Normal Mode Analysis of KRas4B Reveals Partner Specific Dynamics. The Journal of Physical Chemistry. B. PMID 33978412 DOI: 10.1021/acs.jpcb.1c00891 |
0.349 |
|
| 2021 |
Yapici-Eser H, Koroglu YE, Oztop-Cakmak O, Keskin O, Gursoy A, Gursoy-Ozdemir Y. Neuropsychiatric Symptoms of COVID-19 Explained by SARS-CoV-2 Proteins' Mimicry of Human Protein Interactions. Frontiers in Human Neuroscience. 15: 656313. PMID 33833673 DOI: 10.3389/fnhum.2021.656313 |
0.366 |
|
| 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 |
0.406 |
|
| 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 |
0.315 |
|
| 2020 |
Halakou F, Gursoy A, Keskin O. Embedding Alternative Conformations of Proteins in Protein-Protein Interaction Networks. Methods in Molecular Biology (Clifton, N.J.). 2074: 113-124. PMID 31583634 DOI: 10.1007/978-1-4939-9873-9_9 |
0.501 |
|
| 2019 |
Ibrahim Uba A, Weako J, Keskin Ö, Gürsoy A, Yelekçi K. Examining the stability of binding modes of the co-crystallized inhibitors of human HDAC8 by molecular dynamics simulation. Journal of Biomolecular Structure & Dynamics. 1-14. PMID 31057077 DOI: 10.1080/07391102.2019.1615989 |
0.33 |
|
| 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 |
0.39 |
|
| 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 |
0.464 |
|
| 2018 |
Ozdemir ES, Gursoy A, Keskin O. Analysis of single amino acid variations in singlet hot spots of protein-protein interfaces. Bioinformatics (Oxford, England). 34: i795-i801. PMID 30423104 DOI: 10.1093/Bioinformatics/Bty569 |
0.421 |
|
| 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 |
0.398 |
|
| 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 |
0.412 |
|
| 2017 |
Halakou F, Kilic ES, Cukuroglu E, Keskin O, Gursoy A. Enriching Traditional Protein-protein Interaction Networks with Alternative Conformations of Proteins. Scientific Reports. 7: 7180. PMID 28775330 DOI: 10.1038/S41598-017-07351-0 |
0.507 |
|
| 2017 |
Ozgur B, Ozdemir ES, Gursoy A, Keskin O. Relation between Protein Intrinsic Normal Mode Weights and Pre-Existing Conformer Populations. The Journal of Physical Chemistry. B. 121: 3686-3700. PMID 28181436 DOI: 10.1021/Acs.Jpcb.6B10401 |
0.385 |
|
| 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 |
0.499 |
|
| 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 |
0.362 |
|
| 2016 |
Keskin O, Tuncbag N, Gursoy A. Predicting Protein-Protein Interactions from the Molecular to the Proteome Level. Chemical Reviews. 116: 4884-909. PMID 27074302 DOI: 10.1021/Acs.Chemrev.5B00683 |
0.486 |
|
| 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 |
0.311 |
|
| 2016 |
Nussinov R, Muratcioglu S, Tsai CJ, Jang H, Gursoy A, Keskin O. K-Ras4B/calmodulin/PI3Kα: A promising new adenocarcinoma-specific drug target? Expert Opinion On Therapeutic Targets. 1-12. PMID 26873344 DOI: 10.1517/14728222.2016.1135131 |
0.3 |
|
| 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 |
0.332 |
|
| 2015 |
Bonvin AM, Keskin O. Editorial overview: Protein-protein interactions. Current Opinion in Structural Biology. PMID 26631291 DOI: 10.1016/J.Sbi.2015.11.004 |
0.468 |
|
| 2015 |
Muratcioglu S, Guven-Maiorov E, Keskin Ö, Gursoy A. Advances in template-based protein docking by utilizing interfaces towards completing structural interactome. Current Opinion in Structural Biology. 35: 87-92. PMID 26539658 DOI: 10.1016/J.Sbi.2015.10.001 |
0.492 |
|
| 2015 |
Keskin O, Dyson HJ, Bahar I. Biomolecular Systems Interactions, Dynamics, and Allostery: Reflections and New Directions. Biophysical Journal. 109: E01-2. PMID 26377787 DOI: 10.1016/J.Bpj.2015.08.005 |
0.485 |
|
| 2015 |
Guven-Maiorov E, Keskin O, Gursoy A, VanWaes C, Chen Z, Tsai CJ, Nussinov R. The Architecture of the TIR Domain Signalosome in the Toll-like Receptor-4 Signaling Pathway. Scientific Reports. 5: 13128. PMID 26293885 DOI: 10.1038/Srep13128 |
0.303 |
|
| 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 |
0.448 |
|
| 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 |
0.408 |
|
| 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 |
0.341 |
|
| 2015 |
Cavga AD, Karahan N, Keskin O, Gursoy A. Taming Oncogenic Signaling at Protein Interfaces: Challenges and Opportunities. Current Topics in Medicinal Chemistry. 15: 2005-18. PMID 25986691 DOI: 10.2174/1568026615666150519101956 |
0.505 |
|
| 2014 |
Cukuroglu E, Engin HB, Gursoy A, Keskin O. Hot spots in protein-protein interfaces: towards drug discovery. Progress in Biophysics and Molecular Biology. 116: 165-73. PMID 24997383 DOI: 10.1016/J.Pbiomolbio.2014.06.003 |
0.469 |
|
| 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 |
0.419 |
|
| 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 |
0.485 |
|
| 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 |
0.439 |
|
| 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 |
0.518 |
|
| 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 |
0.433 |
|
| 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 |
0.347 |
|
| 2013 |
Engin HB, Guney E, Keskin O, Oliva B, Gursoy A. Integrating structure to protein-protein interaction networks that drive metastasis to brain and lung in breast cancer. Plos One. 8: e81035. PMID 24278371 DOI: 10.1371/Journal.Pone.0081035 |
0.452 |
|
| 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 |
0.394 |
|
| 2013 |
An O, Gursoy A, Gurgey A, Keskin O. Structural and functional analysis of perforin mutations in association with clinical data of familial hemophagocytic lymphohistiocytosis type 2 (FHL2) patients. Protein Science : a Publication of the Protein Society. 22: 823-39. PMID 23592409 DOI: 10.1002/Pro.2265 |
0.305 |
|
| 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 |
0.5 |
|
| 2013 |
Kar G, Keskin O, Fraternali F, Gursoy A. Emerging role of the ubiquitin-proteasome system as drug targets. Current Pharmaceutical Design. 19: 3175-89. PMID 23151131 DOI: 10.2174/1381612811319180002 |
0.354 |
|
| 2013 |
Karagulle S, Keskin O, Gursoy A. Critical assessment of the methods and the features used for hot spot residue prediction at protein-protein interfaces F1000research. 4. DOI: 10.7490/F1000Research.1093869.1 |
0.433 |
|
| 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 |
0.422 |
|
| 2012 |
Kar G, Kuzu G, Keskin O, Gursoy A. Protein-protein interfaces integrated into interaction networks: implications on drug design. Current Pharmaceutical Design. 18: 4697-705. PMID 22650259 DOI: 10.2174/138161212802651643 |
0.449 |
|
| 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 |
0.497 |
|
| 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 |
0.453 |
|
| 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 |
0.498 |
|
| 2012 |
Bolia A, Gerek ZN, Keskin O, Banu Ozkan S, Dev KK. The binding affinities of proteins interacting with the PDZ domain of PICK1. Proteins. 80: 1393-408. PMID 22275068 DOI: 10.1002/Prot.24034 |
0.469 |
|
| 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 |
0.478 |
|
| 2012 |
Cukuroglu E, Gursoy A, Keskin O. HotRegion: a database of predicted hot spot clusters. Nucleic Acids Research. 40: D829-33. PMID 22080558 DOI: 10.1093/Nar/Gkr929 |
0.425 |
|
| 2011 |
Sanli D, Keskin O, Gursoy A, Erman B. Structural cooperativity in histone H3 tail modifications. Protein Science : a Publication of the Protein Society. 20: 1982-90. PMID 21956975 DOI: 10.1002/Pro.745 |
0.505 |
|
| 2011 |
Ulucan O, Keskin O, Erman B, Gursoy A. A comparative molecular dynamics study of methylation state specificity of JMJD2A. Plos One. 6: e24664. PMID 21931800 DOI: 10.1371/Journal.Pone.0024664 |
0.562 |
|
| 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 |
0.513 |
|
| 2011 |
Acuner Ozbabacan SE, Engin HB, Gursoy A, Keskin O. Transient protein-protein interactions. Protein Engineering, Design & Selection : Peds. 24: 635-48. PMID 21676899 DOI: 10.1093/Protein/Gzr025 |
0.499 |
|
| 2011 |
Tuncbag N, Gursoy A, Keskin O. Prediction of protein-protein interactions: unifying evolution and structure at protein interfaces. Physical Biology. 8: 035006. PMID 21572173 DOI: 10.1088/1478-3975/8/3/035006 |
0.52 |
|
| 2011 |
Ozboyaci M, Gursoy A, Erman B, Keskin O. Molecular recognition of H3/H4 histone tails by the tudor domains of JMJD2A: a comparative molecular dynamics simulations study. Plos One. 6: e14765. PMID 21464980 DOI: 10.1371/Journal.Pone.0014765 |
0.517 |
|
| 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 |
0.511 |
|
| 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 |
0.349 |
|
| 2010 |
Acuner Ozbabacan SE, 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: 527-37. PMID 20812144 |
0.344 |
|
| 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 |
0.484 |
|
| 2010 |
Kalyoncu S, Keskin O, Gursoy A. Interaction prediction and classification of PDZ domains. Bmc Bioinformatics. 11: 357. PMID 20591147 DOI: 10.1186/1471-2105-11-357 |
0.428 |
|
| 2010 |
Tuncbag N, Salman FS, Keskin O, Gursoy A. Analysis and network representation of hotspots in protein interfaces using minimum cut trees Proteins: Structure, Function and Bioinformatics. 78: 2283-2294. PMID 20544964 DOI: 10.1002/Prot.22741 |
0.388 |
|
| 2010 |
Ahmad S, Keskin O, Mizuguchi K, Sarai A, Nussinov R. CCRXP: exploring clusters of conserved residues in protein structures. Nucleic Acids Research. 38: W398-401. PMID 20457748 DOI: 10.1093/Nar/Gkq360 |
0.47 |
|
| 2010 |
Tuncbag N, Keskin O, Gursoy A. HotPoint: hot spot prediction server for protein interfaces. Nucleic Acids Research. 38: W402-6. PMID 20444871 DOI: 10.1093/Nar/Gkq323 |
0.489 |
|
| 2010 |
Cukuroglu E, Gursoy A, Keskin O. Analysis of hot region organization in hub proteins. Annals of Biomedical Engineering. 38: 2068-78. PMID 20437205 DOI: 10.1007/S10439-010-0048-9 |
0.426 |
|
| 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 |
0.447 |
|
| 2010 |
Atilgan C, Ermez S, Keskin O, Atilgan AR. Functional Pathways in Proteins Are Uncovered By Strong Disorder Biophysical Journal. 98. DOI: 10.1016/J.Bpj.2009.12.161 |
0.465 |
|
| 2009 |
Kar G, Gursoy A, Keskin O. Human cancer protein-protein interaction network: a structural perspective. Plos Computational Biology. 5: e1000601. PMID 20011507 DOI: 10.1371/Journal.Pcbi.1000601 |
0.461 |
|
| 2009 |
Baris I, Tuncel A, Ozber N, Keskin O, Kavakli IH. Investigation of the interaction between the large and small subunits of potato ADP-glucose pyrophosphorylase. Plos Computational Biology. 5: e1000546. PMID 19876371 DOI: 10.1371/Journal.Pcbi.1000546 |
0.386 |
|
| 2009 |
Gerek ZN, Keskin O, Ozkan SB. Identification of specificity and promiscuity of PDZ domain interactions through their dynamic behavior. Proteins. 77: 796-811. PMID 19585657 DOI: 10.1002/Prot.22492 |
0.418 |
|
| 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 |
0.445 |
|
| 2009 |
Tuncbag N, Gursoy A, Keskin O. Identification of computational hot spots in protein interfaces: combining solvent accessibility and inter-residue potentials improves the accuracy. Bioinformatics (Oxford, England). 25: 1513-20. PMID 19357097 DOI: 10.1093/Bioinformatics/Btp240 |
0.478 |
|
| 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 |
0.432 |
|
| 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 |
0.421 |
|
| 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 |
0.47 |
|
| 2009 |
Ozkirimli E, Keskin O. The Role Of Dynamics On Binding Specificity And Promiscuity Biophysical Journal. 96: 443a. DOI: 10.1016/J.Bpj.2008.12.2275 |
0.492 |
|
| 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 |
0.449 |
|
| 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 |
0.453 |
|
| 2008 |
Tuncel A, Kavakli IH, Keskin O. Insights into subunit interactions in the heterotetrameric structure of potato ADP-glucose pyrophosphorylase. Biophysical Journal. 95: 3628-39. PMID 18641076 DOI: 10.1529/Biophysj.107.123042 |
0.359 |
|
| 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 |
0.439 |
|
| 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 |
0.491 |
|
| 2008 |
Keskin O, Tuncbag N, Gursoy A. Characterization and prediction of protein interfaces to infer protein-protein interaction networks. Current Pharmaceutical Biotechnology. 9: 67-76. PMID 18393863 DOI: 10.2174/138920108783955191 |
0.517 |
|
| 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 |
0.47 |
|
| 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 |
0.433 |
|
| 2008 |
Keskin O, Gursoy A, Ma B, Nussinov R. ChemInform Abstract: Principles of Protein-Protein Interactions: What Are the Preferred Ways for Proteins to Interact? Cheminform. 39. DOI: 10.1002/CHIN.200826266 |
0.371 |
|
| 2007 |
Guney E, Tuncbag N, Keskin O, Gursoy A. HotSprint: database of computational hot spots in protein interfaces Nucleic Acids Research. 36: 662-666. PMID 17959648 DOI: 10.1093/Nar/Gkm813 |
0.441 |
|
| 2007 |
Keskin O. Binding induced conformational changes of proteins correlate with their intrinsic fluctuations: a case study of antibodies Bmc Structural Biology. 7: 31-31. PMID 17509130 DOI: 10.1186/1472-6807-7-31 |
0.325 |
|
| 2007 |
Keskin O, Gursoy A, Ma B, Nussinov R. Towards drugs targeting multiple proteins in a systems biology approach. Current Topics in Medicinal Chemistry. 7: 943-51. PMID 17508925 DOI: 10.2174/156802607780906690 |
0.433 |
|
| 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 |
0.468 |
|
| 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 |
0.436 |
|
| 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 |
0.373 |
|
| 2006 |
Gursoy A, Keskin O, Turkay M, Erman B. Relationships between unfolded configurations of proteins and dynamics of folding to the native state Journal of Polymer Science Part B: Polymer Physics. 44: 3667-3678. DOI: 10.1002/Polb.21018 |
0.554 |
|
| 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 |
0.497 |
|
| 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 |
0.475 |
|
| 2005 |
Aytuna AS, Gursoy A, Keskin O. Prediction of protein–protein interactions by combining structure and sequence conservation in protein interfaces Bioinformatics. 21: 2850-2855. PMID 15855251 DOI: 10.1093/Bioinformatics/Bti443 |
0.476 |
|
| 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 |
0.47 |
|
| 2005 |
Demirel MC, Keskin O. Protein interactions and fluctuations in a proteomic network using an elastic network model. Journal of Biomolecular Structure & Dynamics. 22: 381-6. PMID 15588102 DOI: 10.1080/07391102.2005.10507010 |
0.479 |
|
| 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 |
0.509 |
|
| 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 |
0.504 |
|
| 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 |
0.455 |
|
| 2004 |
Keskin O, Yuret D, Gursoy A, Turkay M, Erman B. Relationships between amino acid sequence and backbone torsion angle preferences. Proteins. 55: 992-8. PMID 15146495 DOI: 10.1002/Prot.20100 |
0.555 |
|
| 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 |
0.33 |
|
| 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 |
0.436 |
|
| 2002 |
Keskin O. Comparison of full-atomic and coarse-grained models to examine the molecular fluctuations of c-AMP dependent protein kinase. Journal of Biomolecular Structure & Dynamics. 20: 333-345. PMID 12437372 DOI: 10.1080/07391102.2002.10506852 |
0.375 |
|
| 2002 |
Keskin O, Ji X, Blaszcyk J, Covell DG. Molecular motions and conformational changes of HPPK. Proteins. 49: 191-205. PMID 12211000 DOI: 10.1002/Prot.10205 |
0.376 |
|
| 2002 |
Keskin O, Durell SR, Bahar I, Jernigan RL, Covell DG. Relating molecular flexibility to function: a case study of tubulin. Biophysical Journal. 83: 663-80. PMID 12124255 DOI: 10.1016/S0006-3495(02)75199-0 |
0.547 |
|
| 2002 |
Keskin O, Bahar I, Flatow D, Covell DG, Jernigan RL. Molecular mechanisms of chaperonin GroEL-GroES function. Biochemistry. 41: 491-501. PMID 11781087 DOI: 10.1021/Bi011393X |
0.554 |
|
| 2001 |
Atilgan AR, Durell SR, Jernigan RL, Demirel MC, Keskin O, Bahar I. Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophysical Journal. 80: 505-15. PMID 11159421 DOI: 10.1016/S0006-3495(01)76033-X |
0.617 |
|
| 2000 |
Keskin O, Bahar I, Jernigan RL, Beutler JA, Shoemaker RH, Sausville EA, Covell DG. Characterization of anticancer agents by their growth inhibitory activity and relationships to mechanism of action and structure. Anti-Cancer Drug Design. 15: 79-98. PMID 10901296 DOI: 10.5072/Zenodo.19292 |
0.465 |
|
| 2000 |
Keskin O, Jernigan RL, Bahar I. Proteins with similar architecture exhibit similar large-scale dynamic behavior. Biophysical Journal. 78: 2093-106. PMID 10733987 DOI: 10.1016/S0006-3495(00)76756-7 |
0.581 |
|
| 1999 |
Keskin O, Bahar I. Packing of sidechains in low-resolution models for proteins. Folding & Design. 3: 469-79. PMID 9889162 DOI: 10.1016/S1359-0278(98)00064-9 |
0.542 |
|
| 1999 |
Keskin O, Bahar I, Badretdinov AY, Ptitsyn OB, Jernigan RL. Empirical solvent-mediated potentials hold for both intra-molecular and inter-molecular inter-residue interactions. Protein Science : a Publication of the Protein Society. 7: 2578-86. PMID 9865952 DOI: 10.1002/Pro.5560071211 |
0.583 |
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