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For: Martins JM, Ramos RM, Pimenta AC, Moreira IS. Solvent-accessible surface area: How well can be applied to hot-spot detection? Proteins 2013;82:479-90. [PMID: 24105801 DOI: 10.1002/prot.24413] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 08/25/2013] [Accepted: 09/02/2013] [Indexed: 11/08/2022]
Number Cited by Other Article(s)
1
Eyush E, Kumar S, Sen K, Sakarwal A, Ram H, Yadav D, Kumar A, Panwar A. Protective efficacy of nafronyl in diabetic retinopathy through targeted inhibition of key enzymes. Biotechnol Appl Biochem 2024. [PMID: 38898746 DOI: 10.1002/bab.2625] [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: 11/28/2023] [Accepted: 05/27/2024] [Indexed: 06/21/2024]
2
Mi T, Gao Z, Mituta Z, Burgess K. Dual-Capped Helical Interface Mimics. J Am Chem Soc 2024;146:10331-10341. [PMID: 38573124 PMCID: PMC11027154 DOI: 10.1021/jacs.3c11717] [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: 10/20/2023] [Revised: 02/25/2024] [Accepted: 03/01/2024] [Indexed: 04/05/2024]
3
Mi T, Siriwibool S, Burgess K. Streamlined Protein-Protein Interface Loop Mimicry. Angew Chem Int Ed Engl 2023;62:e202307092. [PMID: 37849440 DOI: 10.1002/anie.202307092] [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: 06/01/2023] [Revised: 10/12/2023] [Accepted: 10/17/2023] [Indexed: 10/19/2023]
4
Caniceiro AB, Bueschbell B, Barreto CA, Preto AJ, Moreira IS. MUG: A mutation overview of GPCR subfamily A17 receptors. Comput Struct Biotechnol J 2022;21:586-600. [PMID: 36659920 PMCID: PMC9822836 DOI: 10.1016/j.csbj.2022.12.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/15/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]  Open
5
Jaipal N, Ram H, Charan J, Dixit A, Singh G, Singh BP, Kumar A, Panwar A. HMG‐CoA reductase inhibition medicated hypocholesterolemic and antiatherosclerotic potential of phytoconstituents of an aqueous pod extract of Prosopis cineraria  (L.) Druce: In silico, in vitro, and in vivo studies. EFOOD 2022. [DOI: 10.1002/efd2.42] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]  Open
6
Boumezber S, Yelekçi K. Screening of novel and selective inhibitors for neuronal nitric oxide synthase (nNOS) via structure-based drug design techniques. J Biomol Struct Dyn 2022;41:3607-3629. [PMID: 35322764 DOI: 10.1080/07391102.2022.2054471] [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: 10/18/2022]
7
Marques-Pereira C, Pires MN, Gouveia RP, Pereira NN, Caniceiro AB, Rosário-Ferreira N, Moreira IS. SARS-CoV-2 Membrane Protein: From Genomic Data to Structural New Insights. Int J Mol Sci 2022;23:2986. [PMID: 35328409 PMCID: PMC8948900 DOI: 10.3390/ijms23062986] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/07/2022] [Accepted: 03/09/2022] [Indexed: 01/27/2023]  Open
8
Chouhan H, Purohit A, Ram H, Chowdhury S, Kashyap P, Panwar A, Kumar A. The interaction capabilities of phytoconstituents of ethanolic seed extract of cumin ( Cuminum cyminum L.) with HMG‐CoA reductase to subside the hypercholesterolemia: A mechanistic approach. FOOD FRONTIERS 2021. [DOI: 10.1002/fft2.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]  Open
9
Matos-Filipe P, Preto AJ, Koukos PI, Mourão J, Bonvin AMJJ, Moreira IS. MENSAdb: a thorough structural analysis of membrane protein dimers. Database (Oxford) 2021;2021:baab013. [PMID: 33822911 PMCID: PMC8023553 DOI: 10.1093/database/baab013] [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: 05/08/2020] [Revised: 01/19/2021] [Accepted: 03/01/2021] [Indexed: 11/14/2022]
10
Nandakumar R, Dinu V. Developing a machine learning model to identify protein–protein interaction hotspots to facilitate drug discovery. PeerJ 2020;8:e10381. [PMID: 33354416 PMCID: PMC7727375 DOI: 10.7717/peerj.10381] [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: 05/20/2020] [Accepted: 10/27/2020] [Indexed: 02/01/2023]  Open
11
Preto AJ, Moreira IS. SPOTONE: Hot Spots on Protein Complexes with Extremely Randomized Trees via Sequence-Only Features. Int J Mol Sci 2020;21:ijms21197281. [PMID: 33019775 PMCID: PMC7582262 DOI: 10.3390/ijms21197281] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/26/2020] [Accepted: 09/30/2020] [Indexed: 01/02/2023]  Open
12
Yan W, Hu G, Liang Z, Zhou J, Yang Y, Chen J, Shen B. Node-Weighted Amino Acid Network Strategy for Characterization and Identification of Protein Functional Residues. J Chem Inf Model 2018;58:2024-2032. [PMID: 30107728 DOI: 10.1021/acs.jcim.8b00146] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
13
Moreira IS, Koukos PI, Melo R, Almeida JG, Preto AJ, Schaarschmidt J, Trellet M, Gümüş ZH, Costa J, Bonvin AMJJ. SpotOn: High Accuracy Identification of Protein-Protein Interface Hot-Spots. Sci Rep 2017;7:8007. [PMID: 28808256 PMCID: PMC5556074 DOI: 10.1038/s41598-017-08321-2] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 07/07/2017] [Indexed: 12/21/2022]  Open
14
Protein binding hot spots prediction from sequence only by a new ensemble learning method. Amino Acids 2017;49:1773-1785. [DOI: 10.1007/s00726-017-2474-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 07/24/2017] [Indexed: 01/31/2023]
15
Melo R, Fieldhouse R, Melo A, Correia JDG, Cordeiro MNDS, Gümüş ZH, Costa J, Bonvin AMJJ, Moreira IS. A Machine Learning Approach for Hot-Spot Detection at Protein-Protein Interfaces. Int J Mol Sci 2016;17:E1215. [PMID: 27472327 PMCID: PMC5000613 DOI: 10.3390/ijms17081215] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/11/2016] [Accepted: 07/18/2016] [Indexed: 12/17/2022]  Open
16
Ochoa R, Rodriguez CA, Zuluaga AF. Perspectives for the structure-based design of acetylcholinesterase reactivators. J Mol Graph Model 2016;68:176-183. [PMID: 27450771 DOI: 10.1016/j.jmgm.2016.07.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 05/31/2016] [Accepted: 07/17/2016] [Indexed: 02/03/2023]
17
Li B, Mendenhall J, Nguyen ED, Weiner BE, Fischer AW, Meiler J. Accurate Prediction of Contact Numbers for Multi-Spanning Helical Membrane Proteins. J Chem Inf Model 2016;56:423-34. [PMID: 26804342 PMCID: PMC5537626 DOI: 10.1021/acs.jcim.5b00517] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
18
Munteanu CR, Pimenta AC, Fernandez-Lozano C, Melo A, Cordeiro MNDS, Moreira IS. Solvent accessible surface area-based hot-spot detection methods for protein-protein and protein-nucleic acid interfaces. J Chem Inf Model 2015;55:1077-86. [PMID: 25845030 DOI: 10.1021/ci500760m] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
19
Moreira IS, Martins JM, Coimbra JTS, Ramos MJ, Fernandes PA. A new scoring function for protein-protein docking that identifies native structures with unprecedented accuracy. Phys Chem Chem Phys 2014;17:2378-87. [PMID: 25490550 DOI: 10.1039/c4cp04688a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
20
Pimenta AC, Dourado DFAR, Martins JM, Melo A, Dias Soeiro Cordeiro MN, Almeida RD, Morra G, Moreira IS. Dynamic Structure of NGF and proNGF Complexed with p75NTR: Pro-Peptide Effect. J Chem Inf Model 2014;54:2051-67. [DOI: 10.1021/ci500101n] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
21
Liu Q, Hoi SCH, Kwoh CK, Wong L, Li J. Integrating water exclusion theory into β contacts to predict binding free energy changes and binding hot spots. BMC Bioinformatics 2014;15:57. [PMID: 24568581 PMCID: PMC3941611 DOI: 10.1186/1471-2105-15-57] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 02/19/2014] [Indexed: 11/10/2022]  Open
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