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For: Kumar S, Clarke D, Gerstein M. Localized structural frustration for evaluating the impact of sequence variants. Nucleic Acids Res 2016;44:10062-10073. [PMID: 27915290 PMCID: PMC5137452 DOI: 10.1093/nar/gkw927] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 09/30/2016] [Accepted: 10/14/2016] [Indexed: 12/13/2022]  Open
Number Cited by Other Article(s)
1
Vankova P, Pacheco-Garcia JL, Loginov DS, Gómez-Mulas A, Kádek A, Martín-Garcia JM, Salido E, Man P, Pey AL. Insights into the pathogenesis of primary hyperoxaluria type I from the structural dynamics of alanine:glyoxylate aminotransferase variants. FEBS Lett 2024;598:485-499. [PMID: 38243391 DOI: 10.1002/1873-3468.14800] [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: 10/13/2023] [Revised: 12/06/2023] [Accepted: 12/20/2023] [Indexed: 01/21/2024]
2
Freiberger MI, Ruiz-Serra V, Pontes C, Romero-Durana M, Galaz-Davison P, Ramírez-Sarmiento CA, Schuster CD, Marti MA, Wolynes PG, Ferreiro DU, Parra RG, Valencia A. Local energetic frustration conservation in protein families and superfamilies. Nat Commun 2023;14:8379. [PMID: 38104123 PMCID: PMC10725452 DOI: 10.1038/s41467-023-43801-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 11/20/2023] [Indexed: 12/19/2023]  Open
3
Pacini L, Lesieur C. A computational methodology to diagnose sequence-variant dynamic perturbations by comparing atomic protein structures. Bioinformatics 2021;38:703-709. [PMID: 34694373 PMCID: PMC8574318 DOI: 10.1093/bioinformatics/btab736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 09/29/2021] [Accepted: 10/21/2021] [Indexed: 02/03/2023]  Open
4
Tripathi S, Dsouza NR, Urrutia R, Zimmermann MT. Structural bioinformatics enhances mechanistic interpretation of genomic variation, demonstrated through the analyses of 935 distinct RAS family mutations. Bioinformatics 2021;37:1367-1375. [PMID: 33226070 PMCID: PMC8208742 DOI: 10.1093/bioinformatics/btaa972] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/04/2020] [Accepted: 11/11/2020] [Indexed: 12/26/2022]  Open
5
Kumar S, Harmanci A, Vytheeswaran J, Gerstein MB. SVFX: a machine learning framework to quantify the pathogenicity of structural variants. Genome Biol 2020;21:274. [PMID: 33168059 PMCID: PMC7650198 DOI: 10.1186/s13059-020-02178-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 10/12/2020] [Indexed: 02/07/2023]  Open
6
Leveraging protein dynamics to identify cancer mutational hotspots using 3D structures. Proc Natl Acad Sci U S A 2019;116:18962-18970. [PMID: 31462496 PMCID: PMC6754584 DOI: 10.1073/pnas.1901156116] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]  Open
7
Posey JE, O'Donnell-Luria AH, Chong JX, Harel T, Jhangiani SN, Coban Akdemir ZH, Buyske S, Pehlivan D, Carvalho CMB, Baxter S, Sobreira N, Liu P, Wu N, Rosenfeld JA, Kumar S, Avramopoulos D, White JJ, Doheny KF, Witmer PD, Boehm C, Sutton VR, Muzny DM, Boerwinkle E, Günel M, Nickerson DA, Mane S, MacArthur DG, Gibbs RA, Hamosh A, Lifton RP, Matise TC, Rehm HL, Gerstein M, Bamshad MJ, Valle D, Lupski JR. Insights into genetics, human biology and disease gleaned from family based genomic studies. Genet Med 2019;21:798-812. [PMID: 30655598 PMCID: PMC6691975 DOI: 10.1038/s41436-018-0408-7] [Citation(s) in RCA: 122] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 12/05/2018] [Indexed: 12/16/2022]  Open
8
Karami Y, Bitard-Feildel T, Laine E, Carbone A. "Infostery" analysis of short molecular dynamics simulations identifies highly sensitive residues and predicts deleterious mutations. Sci Rep 2018;8:16126. [PMID: 30382169 PMCID: PMC6208415 DOI: 10.1038/s41598-018-34508-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 10/17/2018] [Indexed: 11/09/2022]  Open
9
Ferreiro DU, Komives EA, Wolynes PG. Frustration, function and folding. Curr Opin Struct Biol 2017;48:68-73. [PMID: 29101782 DOI: 10.1016/j.sbi.2017.09.006] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 09/25/2017] [Accepted: 09/27/2017] [Indexed: 01/08/2023]
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