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For: Maheshwari S, Brylinski M. Predicting protein interface residues using easily accessible on-line resources. Brief Bioinform 2015;16:1025-34. [PMID: 25797794 DOI: 10.1093/bib/bbv009] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Indexed: 01/20/2023]  Open
Number Cited by Other Article(s)
1
Phung DK, Pilotto S, Matelska D, Blombach F, Pinotsis N, Hovan L, Gervasio FL, Werner F. Archaeal NusA2 is the ancestor of ribosomal protein eS7 in eukaryotes. Structure 2025;33:149-159.e6. [PMID: 39504966 DOI: 10.1016/j.str.2024.10.019] [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: 07/05/2024] [Revised: 09/06/2024] [Accepted: 10/10/2024] [Indexed: 11/08/2024]
2
Zhao B, Basu S, Kurgan L. DescribePROT Database of Residue-Level Protein Structure and Function Annotations. Methods Mol Biol 2025;2867:169-184. [PMID: 39576581 DOI: 10.1007/978-1-0716-4196-5_10] [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: 11/24/2024]
3
Dai Y, Ma S, Guo Y, Zhang X, Liu D, Gao Y, Zhai C, Chen Q, Xiao S, Zhang Z, Yu L. Evolution and Expression of the Meprin and TRAF Homology Domain-Containing Gene Family in Solanaceae. Int J Mol Sci 2023;24:ijms24108782. [PMID: 37240124 DOI: 10.3390/ijms24108782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/01/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023]  Open
4
Shen Y, Parks JM, Smith JC. HLA Class I Supertype Classification Based on Structural Similarity. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023;210:103-114. [PMID: 36453976 DOI: 10.4049/jimmunol.2200685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 10/31/2022] [Indexed: 12/24/2022]
5
Biró B, Zhao B, Kurgan L. Complementarity of the residue-level protein function and structure predictions in human proteins. Comput Struct Biotechnol J 2022;20:2223-2234. [PMID: 35615015 PMCID: PMC9118482 DOI: 10.1016/j.csbj.2022.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/02/2022] [Accepted: 05/02/2022] [Indexed: 11/24/2022]  Open
6
Dynamic, but Not Necessarily Disordered, Human-Virus Interactions Mediated through SLiMs in Viral Proteins. Viruses 2021;13:v13122369. [PMID: 34960638 PMCID: PMC8703344 DOI: 10.3390/v13122369] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/15/2021] [Accepted: 11/16/2021] [Indexed: 12/13/2022]  Open
7
Zhang J, Ghadermarzi S, Katuwawala A, Kurgan L. DNAgenie: accurate prediction of DNA-type-specific binding residues in protein sequences. Brief Bioinform 2021;22:6355416. [PMID: 34415020 DOI: 10.1093/bib/bbab336] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/02/2021] [Accepted: 07/28/2021] [Indexed: 01/02/2023]  Open
8
Zhang J, Ghadermarzi S, Kurgan L. Prediction of protein-binding residues: dichotomy of sequence-based methods developed using structured complexes versus disordered proteins. Bioinformatics 2021;36:4729-4738. [PMID: 32860044 DOI: 10.1093/bioinformatics/btaa573] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 05/22/2020] [Accepted: 06/10/2020] [Indexed: 01/08/2023]  Open
9
Zhao B, Katuwawala A, Oldfield CJ, Dunker AK, Faraggi E, Gsponer J, Kloczkowski A, Malhis N, Mirdita M, Obradovic Z, Söding J, Steinegger M, Zhou Y, Kurgan L. DescribePROT: database of amino acid-level protein structure and function predictions. Nucleic Acids Res 2021;49:D298-D308. [PMID: 33119734 PMCID: PMC7778963 DOI: 10.1093/nar/gkaa931] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/11/2020] [Accepted: 10/05/2020] [Indexed: 12/30/2022]  Open
10
Zhang F, Shi W, Zhang J, Zeng M, Li M, Kurgan L. PROBselect: accurate prediction of protein-binding residues from proteins sequences via dynamic predictor selection. Bioinformatics 2020;36:i735-i744. [DOI: 10.1093/bioinformatics/btaa806] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2020] [Indexed: 12/13/2022]  Open
11
Salmanian S, Pezeshk H, Sadeghi M. Inter-protein residue covariation information unravels physically interacting protein dimers. BMC Bioinformatics 2020;21:584. [PMID: 33334319 PMCID: PMC7745481 DOI: 10.1186/s12859-020-03930-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 12/09/2020] [Indexed: 01/04/2023]  Open
12
Zhang J, Kurgan L. SCRIBER: accurate and partner type-specific prediction of protein-binding residues from proteins sequences. Bioinformatics 2020;35:i343-i353. [PMID: 31510679 PMCID: PMC6612887 DOI: 10.1093/bioinformatics/btz324] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]  Open
13
Andreani J, Quignot C, Guerois R. Structural prediction of protein interactions and docking using conservation and coevolution. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1470] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
14
Reille S, Garnier M, Robert X, Gouet P, Martin J, Launay G. Identification and visualization of protein binding regions with the ArDock server. Nucleic Acids Res 2019;46:W417-W422. [PMID: 29905873 PMCID: PMC6031020 DOI: 10.1093/nar/gky472] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 05/28/2018] [Indexed: 12/21/2022]  Open
15
e Silva KSF, Lima RM, Baeza LC, Lima PDS, Cordeiro TDM, Charneau S, da Silva RA, Soares CMDA, Pereira M. Interactome of Glyceraldehyde-3-Phosphate Dehydrogenase Points to the Existence of Metabolons in Paracoccidioides lutzii. Front Microbiol 2019;10:1537. [PMID: 31338083 PMCID: PMC6629890 DOI: 10.3389/fmicb.2019.01537] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 06/20/2019] [Indexed: 11/13/2022]  Open
16
Wong ETC, Gsponer J. Predicting Protein-Protein Interfaces that Bind Intrinsically Disordered Protein Regions. J Mol Biol 2019;431:3157-3178. [PMID: 31207240 DOI: 10.1016/j.jmb.2019.06.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 06/01/2019] [Accepted: 06/04/2019] [Indexed: 12/18/2022]
17
Zeng B, Hönigschmid P, Frishman D. Residue co-evolution helps predict interaction sites in α-helical membrane proteins. J Struct Biol 2019;206:156-169. [DOI: 10.1016/j.jsb.2019.02.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 01/30/2019] [Accepted: 02/13/2019] [Indexed: 11/29/2022]
18
Sharmeen N, Sulea T, Whiteway M, Wu C. The adaptor protein Ste50 directly modulates yeast MAPK signaling specificity through differential connections of its RA domain. Mol Biol Cell 2019;30:794-807. [PMID: 30650049 PMCID: PMC6589780 DOI: 10.1091/mbc.e18-11-0708] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]  Open
19
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
20
Wong AKC, Sze-To HY, Johanning GL. Pattern to Knowledge: Deep Knowledge-Directed Machine Learning for Residue-Residue Interaction Prediction. Sci Rep 2018;8:14841. [PMID: 30287904 PMCID: PMC6172270 DOI: 10.1038/s41598-018-32834-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 09/17/2018] [Indexed: 11/21/2022]  Open
21
Geometric and amino acid type determinants for protein-protein interaction interfaces. QUANTITATIVE BIOLOGY 2018. [DOI: 10.1007/s40484-018-0138-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
22
Daberdaku S, Ferrari C. Exploring the potential of 3D Zernike descriptors and SVM for protein-protein interface prediction. BMC Bioinformatics 2018;19:35. [PMID: 29409446 PMCID: PMC5802066 DOI: 10.1186/s12859-018-2043-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 01/24/2018] [Indexed: 12/22/2022]  Open
23
Meyer MJ, Beltrán JF, Liang S, Fragoza R, Rumack A, Liang J, Wei X, Yu H. Interactome INSIDER: a structural interactome browser for genomic studies. Nat Methods 2018;15:107-114. [PMID: 29355848 PMCID: PMC6026581 DOI: 10.1038/nmeth.4540] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 10/22/2017] [Indexed: 02/07/2023]
24
Structure-based prediction of ligand-protein interactions on a genome-wide scale. Proc Natl Acad Sci U S A 2017;114:13685-13690. [PMID: 29229851 DOI: 10.1073/pnas.1705381114] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
25
Different protein-protein interface patterns predicted by different machine learning methods. Sci Rep 2017;7:16023. [PMID: 29167570 PMCID: PMC5700192 DOI: 10.1038/s41598-017-16397-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 11/13/2017] [Indexed: 12/02/2022]  Open
26
Yan J, Kurgan L. DRNApred, fast sequence-based method that accurately predicts and discriminates DNA- and RNA-binding residues. Nucleic Acids Res 2017;45:e84. [PMID: 28132027 PMCID: PMC5449545 DOI: 10.1093/nar/gkx059] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 01/24/2017] [Indexed: 01/18/2023]  Open
27
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: 71] [Impact Index Per Article: 8.9] [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]
28
Zhang J, Kurgan L. Review and comparative assessment of sequence-based predictors of protein-binding residues. Brief Bioinform 2017;19:821-837. [DOI: 10.1093/bib/bbx022] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Indexed: 12/31/2022]  Open
29
Integrating computational methods and experimental data for understanding the recognition mechanism and binding affinity of protein-protein complexes. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017;128:33-38. [PMID: 28069340 DOI: 10.1016/j.pbiomolbio.2017.01.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 01/04/2017] [Accepted: 01/05/2017] [Indexed: 01/09/2023]
30
Computational Approaches for Predicting Binding Partners, Interface Residues, and Binding Affinity of Protein-Protein Complexes. Methods Mol Biol 2017;1484:237-253. [PMID: 27787830 DOI: 10.1007/978-1-4939-6406-2_16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
31
Bai F, Morcos F, Cheng RR, Jiang H, Onuchic JN. Elucidating the druggable interface of protein-protein interactions using fragment docking and coevolutionary analysis. Proc Natl Acad Sci U S A 2016;113:E8051-E8058. [PMID: 27911825 PMCID: PMC5167203 DOI: 10.1073/pnas.1615932113] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]  Open
32
Tonddast-Navaei S, Skolnick J. Are protein-protein interfaces special regions on a protein's surface? J Chem Phys 2016;143:243149. [PMID: 26723634 DOI: 10.1063/1.4937428] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]  Open
33
Maheshwari S, Brylinski M. Template-based identification of protein–protein interfaces using eFindSitePPI. Methods 2016;93:64-71. [DOI: 10.1016/j.ymeth.2015.07.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 07/12/2015] [Accepted: 07/29/2015] [Indexed: 11/26/2022]  Open
34
Local Geometry and Evolutionary Conservation of Protein Surfaces Reveal the Multiple Recognition Patches in Protein-Protein Interactions. PLoS Comput Biol 2015;11:e1004580. [PMID: 26690684 PMCID: PMC4686965 DOI: 10.1371/journal.pcbi.1004580] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 10/04/2015] [Indexed: 11/19/2022]  Open
35
Maheshwari S, Brylinski M. Predicted binding site information improves model ranking in protein docking using experimental and computer-generated target structures. BMC STRUCTURAL BIOLOGY 2015;15:23. [PMID: 26597230 PMCID: PMC4657198 DOI: 10.1186/s12900-015-0050-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 10/30/2015] [Indexed: 01/10/2023]
36
Hwang H, Petrey D, Honig B. A hybrid method for protein-protein interface prediction. Protein Sci 2015;25:159-65. [PMID: 26178156 DOI: 10.1002/pro.2744] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 07/02/2015] [Accepted: 07/06/2015] [Indexed: 12/31/2022]
37
Cooper DE, Young PA, Klett EL, Coleman RA. Physiological Consequences of Compartmentalized Acyl-CoA Metabolism. J Biol Chem 2015;290:20023-31. [PMID: 26124277 DOI: 10.1074/jbc.r115.663260] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]  Open
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