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For: Kleinman CL, Rodrigue N, Lartillot N, Philippe H. Statistical potentials for improved structurally constrained evolutionary models. Mol Biol Evol 2010;27:1546-60. [PMID: 20159780 DOI: 10.1093/molbev/msq047] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]  Open
Number Cited by Other Article(s)
1
Bou Dagher L, Madern D, Malbos P, Brochier-Armanet C. Persistent homology reveals strong phylogenetic signal in 3D protein structures. PNAS NEXUS 2024;3:pgae158. [PMID: 38689707 PMCID: PMC11058471 DOI: 10.1093/pnasnexus/pgae158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 04/01/2024] [Indexed: 05/02/2024]
2
Nagar N, Tubiana J, Loewenthal G, Wolfson HJ, Ben Tal N, Pupko T. EvoRator2: Predicting Site-specific Amino Acid Substitutions Based on Protein Structural Information Using Deep Learning. J Mol Biol 2023;435:168155. [PMID: 37356902 DOI: 10.1016/j.jmb.2023.168155] [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: 03/09/2023] [Revised: 05/13/2023] [Accepted: 05/17/2023] [Indexed: 06/27/2023]
3
Sykes J, Holland BR, Charleston MA. A review of visualisations of protein fold networks and their relationship with sequence and function. Biol Rev Camb Philos Soc 2023;98:243-262. [PMID: 36210328 PMCID: PMC10092621 DOI: 10.1111/brv.12905] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 01/12/2023]
4
Susko E. Complex statistical modelling for phylogenetic inference. CAN J STAT 2022. [DOI: 10.1002/cjs.11741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
5
Nagar N, Ben Tal N, Pupko T. EvoRator: Prediction of residue-level evolutionary rates from protein structures using machine learning. J Mol Biol 2022;434:167538. [DOI: 10.1016/j.jmb.2022.167538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/07/2022] [Accepted: 03/07/2022] [Indexed: 10/18/2022]
6
Youssef N, Susko E, Roger AJ, Bielawski JP. Shifts in amino acid preferences as proteins evolve: A synthesis of experimental and theoretical work. Protein Sci 2021;30:2009-2028. [PMID: 34322924 PMCID: PMC8442975 DOI: 10.1002/pro.4161] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/19/2021] [Accepted: 07/26/2021] [Indexed: 11/08/2022]
7
Selberg AGA, Gaucher EA, Liberles DA. Ancestral Sequence Reconstruction: From Chemical Paleogenetics to Maximum Likelihood Algorithms and Beyond. J Mol Evol 2021;89:157-164. [PMID: 33486547 PMCID: PMC7828096 DOI: 10.1007/s00239-021-09993-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 01/04/2021] [Indexed: 12/13/2022]
8
Laurin-Lemay S, Rodrigue N, Lartillot N, Philippe H. Conditional Approximate Bayesian Computation: A New Approach for Across-Site Dependency in High-Dimensional Mutation-Selection Models. Mol Biol Evol 2019;35:2819-2834. [PMID: 30203003 DOI: 10.1093/molbev/msy173] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]  Open
9
Qiu X, Duvvuri VR, Bahl J. Computational Approaches and Challenges to Developing Universal Influenza Vaccines. Vaccines (Basel) 2019;7:E45. [PMID: 31141933 PMCID: PMC6631137 DOI: 10.3390/vaccines7020045] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 05/15/2019] [Accepted: 05/23/2019] [Indexed: 12/25/2022]  Open
10
Ensembles from Ordered and Disordered Proteins Reveal Similar Structural Constraints during Evolution. J Mol Biol 2019;431:1298-1307. [DOI: 10.1016/j.jmb.2019.01.031] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 01/23/2019] [Accepted: 01/24/2019] [Indexed: 01/08/2023]
11
Herman JL. Enhancing Statistical Multiple Sequence Alignment and Tree Inference Using Structural Information. Methods Mol Biol 2019;1851:183-214. [PMID: 30298398 DOI: 10.1007/978-1-4939-8736-8_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
12
Chi PB, Kim D, Lai JK, Bykova N, Weber CC, Kubelka J, Liberles DA. A new parameter-rich structure-aware mechanistic model for amino acid substitution during evolution. Proteins 2017;86:218-228. [PMID: 29178386 DOI: 10.1002/prot.25429] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 11/14/2017] [Accepted: 11/22/2017] [Indexed: 02/06/2023]
13
Parto S, Lartillot N. Detecting consistent patterns of directional adaptation using differential selection codon models. BMC Evol Biol 2017. [PMID: 28645318 PMCID: PMC5481935 DOI: 10.1186/s12862-017-0979-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]  Open
14
Echave J, Wilke CO. Biophysical Models of Protein Evolution: Understanding the Patterns of Evolutionary Sequence Divergence. Annu Rev Biophys 2017;46:85-103. [PMID: 28301766 DOI: 10.1146/annurev-biophys-070816-033819] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
15
Bastolla U, Dehouck Y, Echave J. What evolution tells us about protein physics, and protein physics tells us about evolution. Curr Opin Struct Biol 2017;42:59-66. [DOI: 10.1016/j.sbi.2016.10.020] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 10/19/2016] [Accepted: 10/24/2016] [Indexed: 12/21/2022]
16
Bloom JD. Identification of positive selection in genes is greatly improved by using experimentally informed site-specific models. Biol Direct 2017;12:1. [PMID: 28095902 PMCID: PMC5240389 DOI: 10.1186/s13062-016-0172-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 12/14/2016] [Indexed: 12/23/2022]  Open
17
Chi PB, Liberles DA. Selection on protein structure, interaction, and sequence. Protein Sci 2016;25:1168-78. [PMID: 26808055 PMCID: PMC4918422 DOI: 10.1002/pro.2886] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 01/18/2016] [Accepted: 01/19/2016] [Indexed: 11/10/2022]
18
Echave J, Spielman SJ, Wilke CO. Causes of evolutionary rate variation among protein sites. Nat Rev Genet 2016;17:109-21. [PMID: 26781812 DOI: 10.1038/nrg.2015.18] [Citation(s) in RCA: 206] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
19
Parisi G, Zea DJ, Monzon AM, Marino-Buslje C. Conformational diversity and the emergence of sequence signatures during evolution. Curr Opin Struct Biol 2015;32:58-65. [DOI: 10.1016/j.sbi.2015.02.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 02/02/2015] [Accepted: 02/09/2015] [Indexed: 02/03/2023]
20
Wang K, Yu S, Ji X, Lakner C, Griffing A, Thorne JL. Roles of solvent accessibility and gene expression in modeling protein sequence evolution. Evol Bioinform Online 2015;11:85-96. [PMID: 25987828 PMCID: PMC4415675 DOI: 10.4137/ebo.s22911] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Revised: 02/04/2015] [Accepted: 02/09/2015] [Indexed: 11/05/2022]  Open
21
Sikosek T, Chan HS. Biophysics of protein evolution and evolutionary protein biophysics. J R Soc Interface 2015;11:20140419. [PMID: 25165599 DOI: 10.1098/rsif.2014.0419] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]  Open
22
Goldstein RA, Pollard ST, Shah SD, Pollock DD. Nonadaptive Amino Acid Convergence Rates Decrease over Time. Mol Biol Evol 2015;32:1373-81. [PMID: 25737491 PMCID: PMC4572784 DOI: 10.1093/molbev/msv041] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]  Open
23
Katsonis P, Lichtarge O. A formal perturbation equation between genotype and phenotype determines the Evolutionary Action of protein-coding variations on fitness. Genome Res 2014;24:2050-8. [PMID: 25217195 PMCID: PMC4248321 DOI: 10.1101/gr.176214.114] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
24
Fu M, Huang Z, Mao Y, Tao S. Neighbor preferences of amino acids and context-dependent effects of amino acid substitutions in human, mouse, and dog. Int J Mol Sci 2014;15:15963-80. [PMID: 25210846 PMCID: PMC4200849 DOI: 10.3390/ijms150915963] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Revised: 08/27/2014] [Accepted: 09/02/2014] [Indexed: 12/23/2022]  Open
25
Herman JL, Challis CJ, Novák Á, Hein J, Schmidler SC. Simultaneous Bayesian estimation of alignment and phylogeny under a joint model of protein sequence and structure. Mol Biol Evol 2014;31:2251-66. [PMID: 24899668 PMCID: PMC4137710 DOI: 10.1093/molbev/msu184] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]  Open
26
Bloom JD. An experimentally informed evolutionary model improves phylogenetic fit to divergent lactamase homologs. Mol Biol Evol 2014;31:2753-69. [PMID: 25063439 PMCID: PMC4166927 DOI: 10.1093/molbev/msu220] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]  Open
27
Solis AD. Deriving high-resolution protein backbone structure propensities from all crystal data using the information maximization device. PLoS One 2014;9:e94334. [PMID: 24896099 PMCID: PMC4045576 DOI: 10.1371/journal.pone.0094334] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 03/12/2014] [Indexed: 11/28/2022]  Open
28
Bloom JD. An experimentally determined evolutionary model dramatically improves phylogenetic fit. Mol Biol Evol 2014;31:1956-78. [PMID: 24859245 PMCID: PMC4104320 DOI: 10.1093/molbev/msu173] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]  Open
29
Palopoli N, Lanzarotti E, Parisi G. BeEP Server: Using evolutionary information for quality assessment of protein structure models. Nucleic Acids Res 2013;41:W398-405. [PMID: 23729471 PMCID: PMC3692104 DOI: 10.1093/nar/gkt453] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]  Open
30
Liberles DA, Teichmann SA, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning APJ, Dokholyan NV, Echave J, Elofsson A, Gerloff DL, Goldstein RA, Grahnen JA, Holder MT, Lakner C, Lartillot N, Lovell SC, Naylor G, Perica T, Pollock DD, Pupko T, Regan L, Roger A, Rubinstein N, Shakhnovich E, Sjölander K, Sunyaev S, Teufel AI, Thorne JL, Thornton JW, Weinreich DM, Whelan S. The interface of protein structure, protein biophysics, and molecular evolution. Protein Sci 2012;21:769-85. [PMID: 22528593 PMCID: PMC3403413 DOI: 10.1002/pro.2071] [Citation(s) in RCA: 140] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 03/22/2012] [Accepted: 03/23/2012] [Indexed: 12/20/2022]
31
Juritz E, Palopoli N, Fornasari MS, Fernandez-Alberti S, Parisi G. Protein Conformational Diversity Modulates Sequence Divergence. Mol Biol Evol 2012;30:79-87. [DOI: 10.1093/molbev/mss080] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]  Open
32
Estimating the distribution of selection coefficients from phylogenetic data using sitewise mutation-selection models. Genetics 2011;190:1101-15. [PMID: 22209901 PMCID: PMC3296245 DOI: 10.1534/genetics.111.136432] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]  Open
33
Grahnen JA, Nandakumar P, Kubelka J, Liberles DA. Biophysical and structural considerations for protein sequence evolution. BMC Evol Biol 2011;11:361. [PMID: 22171550 PMCID: PMC3292521 DOI: 10.1186/1471-2148-11-361] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Accepted: 12/16/2011] [Indexed: 12/23/2022]  Open
34
The evolution of protein structures and structural ensembles under functional constraint. Genes (Basel) 2011;2:748-62. [PMID: 24710290 PMCID: PMC3927589 DOI: 10.3390/genes2040748] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2011] [Revised: 10/15/2011] [Accepted: 10/19/2011] [Indexed: 02/06/2023]  Open
35
Grahnen JA, Kubelka J, Liberles DA. Fast Side Chain Replacement in Proteins Using a Coarse-Grained Approach for Evaluating the Effects of Mutation During Evolution. J Mol Evol 2011;73:23-33. [DOI: 10.1007/s00239-011-9454-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Accepted: 07/14/2011] [Indexed: 11/28/2022]
36
Sammet SG, Bastolla U, Porto M. Comparison of translation loads for standard and alternative genetic codes. BMC Evol Biol 2010;10:178. [PMID: 20546599 PMCID: PMC2909233 DOI: 10.1186/1471-2148-10-178] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2009] [Accepted: 06/14/2010] [Indexed: 11/25/2022]  Open
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