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For: Cukuroglu E, Gursoy A, Nussinov R, Keskin O. Non-redundant unique interface structures as templates for modeling protein interactions. PLoS One 2014;9:e86738. [PMID: 24475173 PMCID: PMC3903793 DOI: 10.1371/journal.pone.0086738] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Accepted: 12/18/2013] [Indexed: 01/16/2023]  Open
Number Cited by Other Article(s)
1
Nussinov R. Pioneer in Molecular Biology: Conformational Ensembles in Molecular Recognition, Allostery, and Cell Function. J Mol Biol 2025;437:169044. [PMID: 40015370 PMCID: PMC12021580 DOI: 10.1016/j.jmb.2025.169044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2024] [Revised: 02/20/2025] [Accepted: 02/21/2025] [Indexed: 03/01/2025]
2
Wéber E, Ábrányi-Balogh P, Nagymihály B, Menyhárd DK, Péczka N, Gadanecz M, Schlosser G, Orgován Z, Bogár F, Bajusz D, Kecskeméti G, Szabó Z, Bartus É, Tököli A, Tóth GK, Szalai TV, Takács T, de Araujo E, Buday L, Perczel A, Martinek TA, Keserű GM. Target-Templated Construction of Functional Proteomimetics Using Photo-Foldamer Libraries. Angew Chem Int Ed Engl 2025;64:e202410435. [PMID: 39329252 DOI: 10.1002/anie.202410435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 08/23/2024] [Accepted: 09/26/2024] [Indexed: 09/28/2024]
3
Abali Z, Aydin Z, Khokhar M, Ates YC, Gursoy A, Keskin O. PPInterface: A Comprehensive Dataset of 3D Protein-Protein Interface Structures. J Mol Biol 2024;436:168686. [PMID: 38936693 DOI: 10.1016/j.jmb.2024.168686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 05/25/2024] [Accepted: 06/20/2024] [Indexed: 06/29/2024]
4
Su Z, Dhusia K, Wu Y. Encoding the space of protein-protein binding interfaces by artificial intelligence. Comput Biol Chem 2024;110:108080. [PMID: 38643609 DOI: 10.1016/j.compbiolchem.2024.108080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 04/03/2024] [Accepted: 04/17/2024] [Indexed: 04/23/2024]
5
Nikam R, Jemimah S, Gromiha MM. DeepPPAPredMut: deep ensemble method for predicting the binding affinity change in protein-protein complexes upon mutation. Bioinformatics 2024;40:btae309. [PMID: 38718170 PMCID: PMC11112046 DOI: 10.1093/bioinformatics/btae309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 04/08/2024] [Accepted: 05/08/2024] [Indexed: 05/24/2024]  Open
6
Ovek D, Keskin O, Gursoy A. ProInterVal: Validation of Protein-Protein Interfaces through Learned Interface Representations. J Chem Inf Model 2024;64:2979-2987. [PMID: 38526504 PMCID: PMC11040718 DOI: 10.1021/acs.jcim.3c01788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 03/26/2024]
7
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. Sci Rep 2024;14:1239. [PMID: 38216592 PMCID: PMC10786864 DOI: 10.1038/s41598-023-50913-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 12/27/2023] [Indexed: 01/14/2024]  Open
8
Kuder KJ. Docking Foundations: From Rigid to Flexible Docking. Methods Mol Biol 2024;2780:3-14. [PMID: 38987460 DOI: 10.1007/978-1-0716-3985-6_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
9
Sunny S, Prakash PB, Gopakumar G, Jayaraj PB. DeepBindPPI: Protein-Protein Binding Site Prediction Using Attention Based Graph Convolutional Network. Protein J 2023;42:276-287. [PMID: 37198346 PMCID: PMC10191823 DOI: 10.1007/s10930-023-10121-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2023] [Indexed: 05/19/2023]
10
Ozdemir ES, Nussinov R. Pathogen-driven cancers from a structural perspective: Targeting host-pathogen protein-protein interactions. Front Oncol 2023;13:1061595. [PMID: 36910650 PMCID: PMC9997845 DOI: 10.3389/fonc.2023.1061595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 02/06/2023] [Indexed: 02/25/2023]  Open
11
Lim H, Cankara F, Tsai CJ, Keskin O, Nussinov R, Gursoy A. Artificial intelligence approaches to human-microbiome protein–protein interactions. Curr Opin Struct Biol 2022;73:102328. [PMID: 35152186 DOI: 10.1016/j.sbi.2022.102328] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 12/01/2021] [Accepted: 12/31/2021] [Indexed: 02/08/2023]
12
Protein-Protein Docking: Past, Present, and Future. Protein J 2021;41:1-26. [PMID: 34787783 DOI: 10.1007/s10930-021-10031-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2021] [Indexed: 10/19/2022]
13
Ghadie M, Xia Y. Mutation Edgotype Drives Fitness Effect in Human. FRONTIERS IN BIOINFORMATICS 2021;1:690769. [PMID: 36303776 PMCID: PMC9581054 DOI: 10.3389/fbinf.2021.690769] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 08/18/2021] [Indexed: 11/24/2022]  Open
14
Zhou Y, Chen H, Li S, Chen M. mPPI: a database extension to visualize structural interactome in a one-to-many manner. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021;2021:6307707. [PMID: 34156447 DOI: 10.1093/database/baab036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/10/2021] [Accepted: 05/28/2021] [Indexed: 01/02/2023]
15
Malhotra S, Joseph AP, Thiyagalingam J, Topf M. Assessment of protein-protein interfaces in cryo-EM derived assemblies. Nat Commun 2021;12:3399. [PMID: 34099703 PMCID: PMC8184972 DOI: 10.1038/s41467-021-23692-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 04/14/2021] [Indexed: 02/05/2023]  Open
16
Bianchetti L, Sinar D, Depenveiller C, Dejaegere A. Insights into mineralocorticoid receptor homodimerization from a combined molecular modeling and bioinformatics study. Proteins 2021;89:952-965. [PMID: 33713045 DOI: 10.1002/prot.26073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 02/25/2021] [Accepted: 03/04/2021] [Indexed: 01/01/2023]
17
Ziegler SJ, Mallinson SJ, St. John PC, Bomble YJ. Advances in integrative structural biology: Towards understanding protein complexes in their cellular context. Comput Struct Biotechnol J 2020;19:214-225. [PMID: 33425253 PMCID: PMC7772369 DOI: 10.1016/j.csbj.2020.11.052] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 11/25/2020] [Accepted: 11/28/2020] [Indexed: 01/26/2023]  Open
18
Hadarovich A, Chakravarty D, Tuzikov AV, Ben-Tal N, Kundrotas PJ, Vakser IA. Structural motifs in protein cores and at protein-protein interfaces are different. Protein Sci 2020;30:381-390. [PMID: 33166001 DOI: 10.1002/pro.3996] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 10/30/2020] [Accepted: 10/31/2020] [Indexed: 11/10/2022]
19
Jemimah S, Sekijima M, Gromiha MM. ProAffiMuSeq: sequence-based method to predict the binding free energy change of protein-protein complexes upon mutation using functional classification. Bioinformatics 2020;36:1725-1730. [PMID: 31713585 DOI: 10.1093/bioinformatics/btz829] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/23/2019] [Accepted: 11/11/2019] [Indexed: 12/20/2022]  Open
20
Graves J, Byerly J, Priego E, Makkapati N, Parish SV, Medellin B, Berrondo M. A Review of Deep Learning Methods for Antibodies. Antibodies (Basel) 2020;9:E12. [PMID: 32354020 PMCID: PMC7344881 DOI: 10.3390/antib9020012] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/15/2020] [Accepted: 04/16/2020] [Indexed: 01/09/2023]  Open
21
Kundrotas PJ, Kotthoff I, Choi SW, Copeland MM, Vakser IA. Dockground Tool for Development and Benchmarking of Protein Docking Procedures. Methods Mol Biol 2020;2165:289-300. [PMID: 32621232 DOI: 10.1007/978-1-0716-0708-4_17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
22
Guven-Maiorov E, Tsai CJ, Nussinov R. Oncoviruses Can Drive Cancer by Rewiring Signaling Pathways Through Interface Mimicry. Front Oncol 2019;9:1236. [PMID: 31803618 PMCID: PMC6872517 DOI: 10.3389/fonc.2019.01236] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 10/28/2019] [Indexed: 01/17/2023]  Open
23
Marze NA, Roy Burman SS, Sheffler W, Gray JJ. Efficient flexible backbone protein-protein docking for challenging targets. Bioinformatics 2019;34:3461-3469. [PMID: 29718115 DOI: 10.1093/bioinformatics/bty355] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 04/27/2018] [Indexed: 11/15/2022]  Open
24
Ozdemir ES, Gursoy A, Keskin O. Analysis of single amino acid variations in singlet hot spots of protein-protein interfaces. Bioinformatics 2019;34:i795-i801. [PMID: 30423104 DOI: 10.1093/bioinformatics/bty569] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
25
Developments in integrative modeling with dynamical interfaces. Curr Opin Struct Biol 2019;56:11-17. [DOI: 10.1016/j.sbi.2018.10.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 10/26/2018] [Accepted: 10/27/2018] [Indexed: 11/19/2022]
26
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 Mol Biol 2019;1903:1-21. [PMID: 30547433 PMCID: PMC8185533 DOI: 10.1007/978-1-4939-8955-3_1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
27
Guven-Maiorov E, Tsai CJ, Ma B, Nussinov R. Interface-Based Structural Prediction of Novel Host-Pathogen Interactions. Methods Mol Biol 2019;1851:317-335. [PMID: 30298406 PMCID: PMC8192064 DOI: 10.1007/978-1-4939-8736-8_18] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
28
Nadalin F, Carbone A. Protein-protein interaction specificity is captured by contact preferences and interface composition. Bioinformatics 2018;34:459-468. [PMID: 29028884 PMCID: PMC5860360 DOI: 10.1093/bioinformatics/btx584] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 09/18/2017] [Indexed: 12/24/2022]  Open
29
Budowski-Tal I, Kolodny R, Mandel-Gutfreund Y. A Novel Geometry-Based Approach to Infer Protein Interface Similarity. Sci Rep 2018;8:8192. [PMID: 29844500 PMCID: PMC5974305 DOI: 10.1038/s41598-018-26497-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 05/10/2018] [Indexed: 11/21/2022]  Open
30
Estrin M, Wolfson HJ. SnapDock-template-based docking by Geometric Hashing. Bioinformatics 2018;33:i30-i36. [PMID: 28881968 PMCID: PMC5870628 DOI: 10.1093/bioinformatics/btx233] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]  Open
31
Barradas-Bautista D, Rosell M, Pallara C, Fernández-Recio J. Structural Prediction of Protein–Protein Interactions by Docking: Application to Biomedical Problems. PROTEIN-PROTEIN INTERACTIONS IN HUMAN DISEASE, PART A 2018;110:203-249. [DOI: 10.1016/bs.apcsb.2017.06.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
32
Alihodžić S, Bukvić M, Elenkov IJ, Hutinec A, Koštrun S, Pešić D, Saxty G, Tomašković L, Žiher D. Current Trends in Macrocyclic Drug Discovery and beyond -Ro5. PROGRESS IN MEDICINAL CHEMISTRY 2018;57:113-233. [DOI: 10.1016/bs.pmch.2018.01.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
33
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. J Mol Biol 2017;429:3925-3941. [PMID: 29106933 PMCID: PMC7906438 DOI: 10.1016/j.jmb.2017.10.023] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 10/16/2017] [Accepted: 10/16/2017] [Indexed: 02/07/2023]
34
Kundrotas PJ, Anishchenko I, Dauzhenka T, Kotthoff I, Mnevets D, Copeland MM, Vakser IA. Dockground: A comprehensive data resource for modeling of protein complexes. Protein Sci 2017;27:172-181. [PMID: 28891124 DOI: 10.1002/pro.3295] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 09/06/2017] [Accepted: 09/07/2017] [Indexed: 12/28/2022]
35
Guven-Maiorov E, Tsai CJ, Nussinov R. Structural host-microbiota interaction networks. PLoS Comput Biol 2017;13:e1005579. [PMID: 29023448 PMCID: PMC5638203 DOI: 10.1371/journal.pcbi.1005579] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]  Open
36
Halakou F, Kilic ES, Cukuroglu E, Keskin O, Gursoy A. Enriching Traditional Protein-protein Interaction Networks with Alternative Conformations of Proteins. Sci Rep 2017;7:7180. [PMID: 28775330 PMCID: PMC5543104 DOI: 10.1038/s41598-017-07351-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 06/27/2017] [Indexed: 12/19/2022]  Open
37
Tahir M, Hayat M. Machine learning based identification of protein–protein interactions using derived features of physiochemical properties and evolutionary profiles. Artif Intell Med 2017;78:61-71. [DOI: 10.1016/j.artmed.2017.06.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 06/09/2017] [Accepted: 06/11/2017] [Indexed: 02/09/2023]
38
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 Mol Biol 2017;1558:255-270. [PMID: 28150242 PMCID: PMC7900904 DOI: 10.1007/978-1-4939-6783-4_12] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
39
Xiong P, Zhang C, Zheng W, Zhang Y. BindProfX: Assessing Mutation-Induced Binding Affinity Change by Protein Interface Profiles with Pseudo-Counts. J Mol Biol 2016;429:426-434. [PMID: 27899282 DOI: 10.1016/j.jmb.2016.11.022] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 11/22/2016] [Accepted: 11/23/2016] [Indexed: 11/27/2022]
40
Kuzu G, Keskin O, Nussinov R, Gursoy A. PRISM-EM: template interface-based modelling of multi-protein complexes guided by cryo-electron microscopy density maps. Acta Crystallogr D Struct Biol 2016;72:1137-1148. [PMID: 27710935 PMCID: PMC5053140 DOI: 10.1107/s2059798316013541] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 08/23/2016] [Indexed: 12/29/2022]  Open
41
Keskin O, Tuncbag N, Gursoy A. Predicting Protein–Protein Interactions from the Molecular to the Proteome Level. Chem Rev 2016;116:4884-909. [PMID: 27074302 DOI: 10.1021/acs.chemrev.5b00683] [Citation(s) in RCA: 221] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
42
Paul Y, Hasija Y. Gene Prioritization by Integrated Analysis of Protein Structural and Network Topological Properties for the Protein-Protein Interaction Network of Neurological Disorders. SCIENTIFICA 2016;2016:9589404. [PMID: 27034906 PMCID: PMC4808548 DOI: 10.1155/2016/9589404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 02/11/2016] [Accepted: 02/18/2016] [Indexed: 06/05/2023]
43
Hu G, Xiao F, Li Y, Li Y, Vongsangnak W. Protein-Protein Interface and Disease: Perspective from Biomolecular Networks. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016;160:57-74. [PMID: 27928579 DOI: 10.1007/10_2016_40] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
44
Xue LC, Dobbs D, Bonvin AMJJ, Honavar V. Computational prediction of protein interfaces: A review of data driven methods. FEBS Lett 2015;589:3516-26. [PMID: 26460190 PMCID: PMC4655202 DOI: 10.1016/j.febslet.2015.10.003] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 10/01/2015] [Accepted: 10/02/2015] [Indexed: 01/06/2023]
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Prediction of Protein–Protein Interaction Sites with Machine-Learning-Based Data-Cleaning and Post-Filtering Procedures. J Membr Biol 2015;249:141-53. [DOI: 10.1007/s00232-015-9856-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 11/03/2015] [Indexed: 12/12/2022]
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Muratcioglu S, Guven-Maiorov E, Keskin Ö, Gursoy A. Advances in template-based protein docking by utilizing interfaces towards completing structural interactome. Curr Opin Struct Biol 2015;35:87-92. [PMID: 26539658 DOI: 10.1016/j.sbi.2015.10.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 10/09/2015] [Accepted: 10/13/2015] [Indexed: 11/27/2022]
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Brender JR, Zhang Y. Predicting the Effect of Mutations on Protein-Protein Binding Interactions through Structure-Based Interface Profiles. PLoS Comput Biol 2015;11:e1004494. [PMID: 26506533 PMCID: PMC4624718 DOI: 10.1371/journal.pcbi.1004494] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 08/06/2015] [Indexed: 11/18/2022]  Open
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Musiani F, Ciurli S. Evolution of Macromolecular Docking Techniques: The Case Study of Nickel and Iron Metabolism in Pathogenic Bacteria. Molecules 2015;20:14265-92. [PMID: 26251891 PMCID: PMC6332059 DOI: 10.3390/molecules200814265] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 07/23/2015] [Accepted: 07/28/2015] [Indexed: 11/24/2022]  Open
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Goncearenco A, Shaytan AK, Shoemaker BA, Panchenko AR. Structural Perspectives on the Evolutionary Expansion of Unique Protein-Protein Binding Sites. Biophys J 2015. [PMID: 26213149 DOI: 10.1016/j.bpj.2015.06.056] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]  Open
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Anishchenko I, Kundrotas PJ, Tuzikov AV, Vakser IA. Structural templates for comparative protein docking. Proteins 2015;83:1563-70. [PMID: 25488330 DOI: 10.1002/prot.24736] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 11/15/2014] [Accepted: 11/26/2014] [Indexed: 11/07/2022]
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