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For: Coucke A, Uguzzoni G, Oteri F, Cocco S, Monasson R, Weigt M. Direct coevolutionary couplings reflect biophysical residue interactions in proteins. J Chem Phys 2016;145:174102. [DOI: 10.1063/1.4966156] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]  Open
Number Cited by Other Article(s)
1
Rocha REO, Mariano DCB, Almeida TS, CorrêaCosta LS, Fischer PHC, Santos LH, Caffarena ER, da Silveira CH, Lamp LM, Fernandez-Quintero ML, Liedl KR, de Melo-Minardi RC, de Lima LHF. Thermostabilizing mechanisms of canonical single amino acid substitutions at a GH1 β-glucosidase probed by multiple MD and computational approaches. Proteins 2023;91:218-236. [PMID: 36114781 DOI: 10.1002/prot.26424] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 09/01/2022] [Accepted: 09/06/2022] [Indexed: 01/07/2023]
2
Sun J, Kulandaisamy A, Liu J, Hu K, Gromiha MM, Zhang Y. Machine learning in computational modelling of membrane protein sequences and structures: From methodologies to applications. Comput Struct Biotechnol J 2023;21:1205-1226. [PMID: 36817959 PMCID: PMC9932300 DOI: 10.1016/j.csbj.2023.01.036] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/16/2023] [Accepted: 01/25/2023] [Indexed: 01/29/2023]  Open
3
Tresnak DT, Hackel BJ. Deep Antimicrobial Activity and Stability Analysis Inform Lysin Sequence-Function Mapping. ACS Synth Biol 2023;12:249-264. [PMID: 36599162 PMCID: PMC10822705 DOI: 10.1021/acssynbio.2c00509] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
4
Torielli L, Serapian SA, Mussolin L, Moroni E, Colombo G. Integrating Protein Interaction Surface Prediction with a Fragment-Based Drug Design: Automatic Design of New Leads with Fragments on Energy Surfaces. J Chem Inf Model 2023;63:343-353. [PMID: 36574607 PMCID: PMC9832486 DOI: 10.1021/acs.jcim.2c01408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
5
Do HN, Haldane A, Levy RM, Miao Y. Unique features of different classes of G-protein-coupled receptors revealed from sequence coevolutionary and structural analysis. Proteins 2022;90:601-614. [PMID: 34599827 PMCID: PMC8738117 DOI: 10.1002/prot.26256] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/21/2021] [Accepted: 09/27/2021] [Indexed: 02/03/2023]
6
Schmidt M, Hamacher K. Identification of biophysical interaction patterns in direct coupling analysis. Phys Rev E 2021;103:042418. [PMID: 34005861 DOI: 10.1103/physreve.103.042418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 03/27/2021] [Indexed: 11/07/2022]
7
Liu CY, Cecylia Severin L, Lyu CJ, Zhu WL, Wang HP, Jiang CJ, Mei LH, Liu HG, Huang J. Improving thermostability of (R)-selective amine transaminase from Aspergillus terreus by evolutionary coupling saturation mutagenesis. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.107926] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
8
Serapian SA, Triveri A, Marchetti F, Castelli M, Colombo G. Exploiting Folding and Degradation Machineries To Target Undruggable Proteins: What Can a Computational Approach Tell Us? ChemMedChem 2021;16:1593-1599. [PMID: 33443306 DOI: 10.1002/cmdc.202000960] [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] [Received: 12/11/2020] [Indexed: 01/03/2023]
9
Mariano D, Pantuza N, Santos LH, Rocha REO, de Lima LHF, Bleicher L, de Melo-Minardi RC. Glutantβase: a database for improving the rational design of glucose-tolerant β-glucosidases. BMC Mol Cell Biol 2020;21:50. [PMID: 32611314 PMCID: PMC7329481 DOI: 10.1186/s12860-020-00293-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 06/22/2020] [Indexed: 11/22/2022]  Open
10
Interaction specificity of clustered protocadherins inferred from sequence covariation and structural analysis. Proc Natl Acad Sci U S A 2019;116:17825-17830. [PMID: 31431536 DOI: 10.1073/pnas.1821063116] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]  Open
11
Astl L, Verkhivker GM. Data-driven computational analysis of allosteric proteins by exploring protein dynamics, residue coevolution and residue interaction networks. Biochim Biophys Acta Gen Subj 2019:S0304-4165(19)30179-5. [PMID: 31330173 DOI: 10.1016/j.bbagen.2019.07.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 07/15/2019] [Accepted: 07/17/2019] [Indexed: 02/07/2023]
12
Haldane A, Flynn WF, He P, Levy RM. Coevolutionary Landscape of Kinase Family Proteins: Sequence Probabilities and Functional Motifs. Biophys J 2019;114:21-31. [PMID: 29320688 DOI: 10.1016/j.bpj.2017.10.028] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 09/11/2017] [Accepted: 10/17/2017] [Indexed: 01/25/2023]  Open
13
Marchetti F, Capelli R, Rizzato F, Laio A, Colombo G. The Subtle Trade-Off between Evolutionary and Energetic Constraints in Protein-Protein Interactions. J Phys Chem Lett 2019;10:1489-1497. [PMID: 30855965 DOI: 10.1021/acs.jpclett.9b00191] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
14
Haldane A, Levy RM. Influence of multiple-sequence-alignment depth on Potts statistical models of protein covariation. Phys Rev E 2019;99:032405. [PMID: 30999494 PMCID: PMC6508952 DOI: 10.1103/physreve.99.032405] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Indexed: 02/02/2023]
15
dos Santos RN, Khan S, Morcos F. Characterization of C-ring component assembly in flagellar motors from amino acid coevolution. ROYAL SOCIETY OPEN SCIENCE 2018;5:171854. [PMID: 29892378 PMCID: PMC5990795 DOI: 10.1098/rsos.171854] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Accepted: 04/05/2018] [Indexed: 06/08/2023]
16
Nicoludis JM, Gaudet R. Applications of sequence coevolution in membrane protein biochemistry. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2018;1860:895-908. [PMID: 28993150 PMCID: PMC5807202 DOI: 10.1016/j.bbamem.2017.10.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 09/28/2017] [Accepted: 10/02/2017] [Indexed: 12/22/2022]
17
Cocco S, Feinauer C, Figliuzzi M, Monasson R, Weigt M. Inverse statistical physics of protein sequences: a key issues review. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2018;81:032601. [PMID: 29120346 DOI: 10.1088/1361-6633/aa9965] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
18
Schmidt M, Hamacher K. Three-body interactions improve contact prediction within direct-coupling analysis. Phys Rev E 2017;96:052405. [PMID: 29347718 DOI: 10.1103/physreve.96.052405] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Indexed: 11/07/2022]
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