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For: Cukuroglu E, Gursoy A, Keskin O. HotRegion: a database of predicted hot spot clusters. Nucleic Acids Res 2011;40:D829-33. [PMID: 22080558 PMCID: PMC3245113 DOI: 10.1093/nar/gkr929] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]  Open
Number Cited by Other Article(s)
1
Abali Z, Aydin Z, Khokhar M, Can Ates Y, Gursoy A, Keskin O. PPInterface: A Comprehensive Dataset of 3D Protein-Protein Interface Structures. J Mol Biol 2024:168686. [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 05/25/2024] [Accepted: 06/20/2024] [Indexed: 06/29/2024]
2
Tang J, Hu R, Liu Y, Liu J, Wang G, Lv J, Cheng L, He T, Liu Y, Shao PL, Zhang B. Deciphering ACE2-RBD binding affinity through peptide scanning: A molecular dynamics simulation approach. Comput Biol Med 2024;173:108325. [PMID: 38513389 DOI: 10.1016/j.compbiomed.2024.108325] [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: 08/28/2023] [Revised: 03/15/2024] [Accepted: 03/15/2024] [Indexed: 03/23/2024]
3
Pandey M, Shah SK, Gromiha MM. Computational approaches for identifying disease-causing mutations in proteins. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023;139:141-171. [PMID: 38448134 DOI: 10.1016/bs.apcsb.2023.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
4
Konc J, Janežič D. Protein binding sites for drug design. Biophys Rev 2022;14:1413-1421. [PMID: 36532870 PMCID: PMC9734416 DOI: 10.1007/s12551-022-01028-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 12/01/2022] [Indexed: 12/13/2022]  Open
5
Ozdemir ES, Gomes MM, Fischer JM. Computational Modeling of TP63-TP53 Interaction and Rational Design of Inhibitors: Implications for Therapeutics. Mol Cancer Ther 2022;21:1846-1856. [PMID: 36190964 DOI: 10.1158/1535-7163.mct-22-0008] [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: 01/10/2022] [Revised: 08/16/2022] [Accepted: 09/23/2022] [Indexed: 01/12/2023]
6
Sarma H, Jamir E, Sastry GN. Protein-protein interaction of RdRp with its co-factor NSP8 and NSP7 to decipher the interface hotspot residues for drug targeting: A comparison between SARS-CoV-2 and SARS-CoV. J Mol Struct 2022;1257:132602. [PMID: 35153334 PMCID: PMC8824464 DOI: 10.1016/j.molstruc.2022.132602] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 02/03/2022] [Accepted: 02/07/2022] [Indexed: 02/09/2023]
7
Ghobadi Z, Mahnam K, Shakhsi-Niaei M. In-silico design of peptides for inhibition of HLA-A*03-KLIETYFSK complex as a new drug design for treatment of multiples sclerosis disease. J Mol Graph Model 2021;111:108079. [PMID: 34837787 DOI: 10.1016/j.jmgm.2021.108079] [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: 09/01/2021] [Revised: 11/03/2021] [Accepted: 11/14/2021] [Indexed: 10/19/2022]
8
Gamma Carbonic Anhydrases from Hydrothermal Vent Bacteria: Cases of Alternating Active Site Due to a Long Loop with Proton Shuttle Residue. Catalysts 2021. [DOI: 10.3390/catal11101177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]  Open
9
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, Dinler Doganay G. Interactome analysis of Bag-1 isoforms reveals novel interaction partners in endoplasmic reticulum-associated degradation. PLoS One 2021;16:e0256640. [PMID: 34428256 PMCID: PMC8384158 DOI: 10.1371/journal.pone.0256640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/11/2021] [Indexed: 11/24/2022]  Open
10
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]
11
Khan MIK, Charles RCM, Ramachandran R, Gupta S, Govindaraju G, Mishra R, Rajavelu A, Coumar MS, Chavali S, Dhayalan A. The ribosomal protein eL21 interacts with the protein lysine methyltransferase SMYD2 and regulates its steady state levels. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021;1868:119079. [PMID: 34147559 DOI: 10.1016/j.bbamcr.2021.119079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/24/2021] [Accepted: 06/13/2021] [Indexed: 01/23/2023]
12
Eren M, Tuncbag N, Jang H, Nussinov R, Gursoy A, Keskin O. Normal Mode Analysis of KRas4B Reveals Partner Specific Dynamics. J Phys Chem B 2021;125:5210-5221. [PMID: 33978412 PMCID: PMC9969846 DOI: 10.1021/acs.jpcb.1c00891] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
13
Direct Keap1-kelch inhibitors as potential drug candidates for oxidative stress-orchestrated diseases: A review on In silico perspective. Pharmacol Res 2021;167:105577. [PMID: 33774182 DOI: 10.1016/j.phrs.2021.105577] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/23/2021] [Accepted: 03/21/2021] [Indexed: 12/11/2022]
14
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. Front Hum Neurosci 2021;15:656313. [PMID: 33833673 PMCID: PMC8021734 DOI: 10.3389/fnhum.2021.656313] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 02/23/2021] [Indexed: 12/16/2022]  Open
15
In Silico Investigation of Potential Applications of Gamma Carbonic Anhydrases as Catalysts of CO2 Biomineralization Processes: A Visit to the Thermophilic Bacteria Persephonella hydrogeniphila, Persephonella marina, Thermosulfidibacter takaii, and Thermus thermophilus. Int J Mol Sci 2021;22:ijms22062861. [PMID: 33799806 PMCID: PMC8000050 DOI: 10.3390/ijms22062861] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 11/29/2022]  Open
16
In-silico Design of Multi-epitope Vaccine against Nipah Virus using Immunoinformatics Approach. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2021. [DOI: 10.22207/jpam.15.1.16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
17
Albuquerque ADO, da Silva Junior HC, Sartori GR, Martins da Silva JH. Computationally-obtained structural insights into the molecular interactions between Pidilizumab and binding partners DLL1 and PD-1. J Biomol Struct Dyn 2021;40:6450-6462. [PMID: 33559526 DOI: 10.1080/07391102.2021.1885492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
18
Ghosh G, Sharma PV, Kumar A, Jain S, Sen R. Design of novel peptide inhibitors against the conserved bacterial transcription terminator, Rho. J Biol Chem 2021;296:100653. [PMID: 33845047 PMCID: PMC8141534 DOI: 10.1016/j.jbc.2021.100653] [Citation(s) in RCA: 1] [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: 12/15/2020] [Revised: 03/28/2021] [Accepted: 04/08/2021] [Indexed: 11/15/2022]  Open
19
Mafakher L, Rismani E, Rahimi H, Enayatkhani M, Azadmanesh K, Teimoori-Toolabi L. Computational design of antagonist peptides based on the structure of secreted frizzled-related protein-1 (SFRP1) aiming to inhibit Wnt signaling pathway. J Biomol Struct Dyn 2020;40:2169-2188. [DOI: 10.1080/07391102.2020.1835718] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
20
Syahbanu F, Giriwono PE, Tjandrawinata RR, Suhartono MT. Molecular analysis of a fibrin-degrading enzyme from Bacillus subtilis K2 isolated from the Indonesian soybean-based fermented food moromi. Mol Biol Rep 2020;47:8553-8563. [PMID: 33111172 DOI: 10.1007/s11033-020-05898-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 10/03/2020] [Indexed: 10/23/2022]
21
Manyumwa CV, Emameh RZ, Tastan Bishop Ö. Alpha-Carbonic Anhydrases from Hydrothermal Vent Sources as Potential Carbon Dioxide Sequestration Agents: In Silico Sequence, Structure and Dynamics Analyses. Int J Mol Sci 2020;21:E8066. [PMID: 33138066 PMCID: PMC7662607 DOI: 10.3390/ijms21218066] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/22/2020] [Accepted: 10/27/2020] [Indexed: 12/27/2022]  Open
22
Chemometric Models of Differential Amino Acids at the Navα and Navβ Interface of Mammalian Sodium Channel Isoforms. Molecules 2020;25:molecules25153551. [PMID: 32756517 PMCID: PMC7435598 DOI: 10.3390/molecules25153551] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 12/19/2022]  Open
23
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. J Mol Biol 2020;432:3395-3403. [PMID: 32061934 PMCID: PMC7261632 DOI: 10.1016/j.jmb.2020.01.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 11/28/2019] [Accepted: 01/14/2020] [Indexed: 02/07/2023]
24
da Silva FCV, Pessoa Costa E, Moreira Gomes V, de Oliveira Carvalho A. Inhibition mechanism of human salivary α-amylase by lipid transfer protein from Vigna unguiculata. Comput Biol Chem 2020;85:107193. [DOI: 10.1016/j.compbiolchem.2019.107193] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 12/06/2019] [Accepted: 12/11/2019] [Indexed: 01/09/2023]
25
Upfold N, Ross C, Tastan Bishop Ö, Knox C. The In Silico Prediction of Hotspot Residues that Contribute to the Structural Stability of Subunit Interfaces of a Picornavirus Capsid. Viruses 2020;12:v12040387. [PMID: 32244486 PMCID: PMC7232237 DOI: 10.3390/v12040387] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 03/26/2020] [Accepted: 03/28/2020] [Indexed: 11/16/2022]  Open
26
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 Mitogen-activated Protein Kinase Signaling. J Mol Biol 2020;432:1199-1215. [PMID: 31931009 PMCID: PMC8533050 DOI: 10.1016/j.jmb.2020.01.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 12/31/2019] [Accepted: 01/07/2020] [Indexed: 02/07/2023]
27
Pooley JR, Rivers CA, Kilcooley MT, Paul SN, Cavga AD, Kershaw YM, Muratcioglu S, Gursoy A, Keskin O, Lightman SL. Beyond the heterodimer model for mineralocorticoid and glucocorticoid receptor interactions in nuclei and at DNA. PLoS One 2020;15:e0227520. [PMID: 31923266 PMCID: PMC6953809 DOI: 10.1371/journal.pone.0227520] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 12/19/2019] [Indexed: 12/20/2022]  Open
28
Tobias-Santos V, Guerra-Almeida D, Mury F, Ribeiro L, Berni M, Araujo H, Logullo C, Feitosa NM, de Souza-Menezes J, Pessoa Costa E, Nunes-da-Fonseca R. Multiple Roles of the Polycistronic Gene Tarsal-less/Mille-Pattes/Polished-Rice During Embryogenesis of the Kissing Bug Rhodnius prolixus. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00379] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
29
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: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
30
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: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
31
Ngounou Wetie AG, Sokolowska I, Channaveerappa D, Dupree EJ, Jayathirtha M, Woods AG, Darie CC. Proteomics and Non-proteomics Approaches to Study Stable and Transient Protein-Protein Interactions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019;1140:121-142. [DOI: 10.1007/978-3-030-15950-4_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
32
Huang D, Wen W, Liu X, Li Y, Zhang JZH. Computational analysis of hot spots and binding mechanism in the PD-1/PD-L1 interaction. RSC Adv 2019;9:14944-14956. [PMID: 35516311 PMCID: PMC9064197 DOI: 10.1039/c9ra01369e] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 05/05/2019] [Indexed: 12/14/2022]  Open
33
In silico structure-based design of enhanced peptide inhibitors targeting RNA polymerase PAN-PB1C interaction. Comput Biol Chem 2019;78:273-281. [PMID: 30597438 DOI: 10.1016/j.compbiolchem.2018.12.009] [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: 10/15/2018] [Revised: 12/05/2018] [Accepted: 12/21/2018] [Indexed: 12/17/2022]
34
Lin X, Zhang X. Prediction of Hot Regions in PPIs Based on Improved Local Community Structure Detecting. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018;15:1470-1479. [PMID: 29994749 DOI: 10.1109/tcbb.2018.2793858] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
35
PPInS: a repository of protein-protein interaction sitesbase. Sci Rep 2018;8:12453. [PMID: 30127348 PMCID: PMC6102274 DOI: 10.1038/s41598-018-30999-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 08/03/2018] [Indexed: 01/14/2023]  Open
36
Ozdemir ES, Jang H, Gursoy A, Keskin O, Nussinov R. Arl2-Mediated Allosteric Release of Farnesylated KRas4B from Shuttling Factor PDEδ. J Phys Chem B 2018;122:7503-7513. [PMID: 29961325 PMCID: PMC8087113 DOI: 10.1021/acs.jpcb.8b04347] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
37
Mishra V, Pathak C. Structural insights into pharmacophore-assisted in silico identification of protein-protein interaction inhibitors for inhibition of human toll-like receptor 4 - myeloid differentiation factor-2 (hTLR4-MD-2) complex. J Biomol Struct Dyn 2018;37:1968-1991. [PMID: 29842849 DOI: 10.1080/07391102.2018.1474804] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
38
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. J Biol Chem 2018;293:3685-3699. [PMID: 29358323 PMCID: PMC5846150 DOI: 10.1074/jbc.ra117.001596] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 01/12/2018] [Indexed: 12/22/2022]  Open
39
Shin WH, Christoffer CW, Kihara D. In silico structure-based approaches to discover protein-protein interaction-targeting drugs. Methods 2017;131:22-32. [PMID: 28802714 PMCID: PMC5683929 DOI: 10.1016/j.ymeth.2017.08.006] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/08/2017] [Accepted: 08/08/2017] [Indexed: 02/07/2023]  Open
40
Understanding Insulin Endocrinology in Decapod Crustacea: Molecular Modelling Characterization of an Insulin-Binding Protein and Insulin-Like Peptides in the Eastern Spiny Lobster, Sagmariasus verreauxi. Int J Mol Sci 2017;18:ijms18091832. [PMID: 28832524 PMCID: PMC5618481 DOI: 10.3390/ijms18091832] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 08/18/2017] [Accepted: 08/19/2017] [Indexed: 12/13/2022]  Open
41
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: 12] [Impact Index Per Article: 1.7] [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
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PRMT7 Interacts with ASS1 and Citrullinemia Mutations Disrupt the Interaction. J Mol Biol 2017;429:2278-2289. [DOI: 10.1016/j.jmb.2017.05.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Revised: 05/25/2017] [Accepted: 05/31/2017] [Indexed: 11/23/2022]
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Murakami Y, Tripathi LP, Prathipati P, Mizuguchi K. Network analysis and in silico prediction of protein-protein interactions with applications in drug discovery. Curr Opin Struct Biol 2017;44:134-142. [PMID: 28364585 DOI: 10.1016/j.sbi.2017.02.005] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Revised: 02/05/2017] [Accepted: 02/23/2017] [Indexed: 11/29/2022]
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Liu D, Xu D, Liu M, Knabe WE, Yuan C, Zhou D, Huang M, Meroueh SO. Small Molecules Engage Hot Spots through Cooperative Binding To Inhibit a Tight Protein-Protein Interaction. Biochemistry 2017;56:1768-1784. [PMID: 28186725 DOI: 10.1021/acs.biochem.6b01039] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Bearne SL. The interdigitating loop of the enolase superfamily as a specificity binding determinant or 'flying buttress'. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017;1865:619-630. [PMID: 28179138 DOI: 10.1016/j.bbapap.2017.02.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 11/21/2016] [Accepted: 02/03/2017] [Indexed: 12/25/2022]
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Sarvagalla S, Coumar MS. Protein-Protein Interactions (PPIs) as an Alternative to Targeting the ATP Binding Site of Kinase. PHARMACEUTICAL SCIENCES 2017. [DOI: 10.4018/978-1-5225-1762-7.ch043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]  Open
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Exploring Protein-Protein Interactions as Drug Targets for Anti-cancer Therapy with In Silico Workflows. Methods Mol Biol 2017;1647:221-236. [PMID: 28809006 DOI: 10.1007/978-1-4939-7201-2_15] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Simões ICM, Costa IPD, Coimbra JTS, Ramos MJ, Fernandes PA. New Parameters for Higher Accuracy in the Computation of Binding Free Energy Differences upon Alanine Scanning Mutagenesis on Protein–Protein Interfaces. J Chem Inf Model 2016;57:60-72. [DOI: 10.1021/acs.jcim.6b00378] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Improving hot region prediction by parameter optimization of density clustering in PPI. Methods 2016;110:35-43. [PMID: 27474164 DOI: 10.1016/j.ymeth.2016.07.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 06/08/2016] [Accepted: 07/26/2016] [Indexed: 11/21/2022]  Open
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Hu J, Li J, Chen N, Zhang X. Conservation of hot regions in protein–protein interaction in evolution. Methods 2016;110:73-80. [DOI: 10.1016/j.ymeth.2016.06.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Revised: 06/08/2016] [Accepted: 06/21/2016] [Indexed: 11/28/2022]  Open
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