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For: Resende-Lara PT, Perahia D, Scott AL, Braz ASK. Unveiling functional motions based on point mutations in biased signaling systems: A normal mode study on nerve growth factor bound to TrkA. PLoS One 2020;15:e0231542. [PMID: 32497034 DOI: 10.1371/journal.pone.0231542] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 03/26/2020] [Indexed: 11/19/2022]  Open
Number Cited by Other Article(s)
1
Gasparini P, Philot EA, Pantaleão SQ, Torres-Bonfim NESM, Kliousoff A, Quiroz RCN, Perahia D, Simões RP, Magro AJ, Scott AL. Unveiling mutation effects on the structural dynamics of the main protease from SARS-CoV-2 with hybrid simulation methods. J Mol Graph Model 2023;121:108443. [PMID: 36870228 PMCID: PMC9945984 DOI: 10.1016/j.jmgm.2023.108443] [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: 10/10/2022] [Revised: 02/15/2023] [Accepted: 02/21/2023] [Indexed: 02/25/2023]
2
Quiroz RCN, Philot EA, General IJ, Perahia D, Scott AL. Effect of phosphorylation on the structural dynamics, thermal stability of human dopamine transporter: A simulation study using normal modes, molecular dynamics and Markov State Model. J Mol Graph Model 2023;118:108359. [PMID: 36279761 DOI: 10.1016/j.jmgm.2022.108359] [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: 07/26/2022] [Revised: 10/04/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022]
3
Kaynak BT, Krieger JM, Dudas B, Dahmani ZL, Costa MGS, Balog E, Scott AL, Doruker P, Perahia D, Bahar I. Sampling of Protein Conformational Space Using Hybrid Simulations: A Critical Assessment of Recent Methods. Front Mol Biosci 2022;9:832847. [PMID: 35187088 PMCID: PMC8855042 DOI: 10.3389/fmolb.2022.832847] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/12/2022] [Indexed: 12/17/2022]  Open
4
HARP: a database of structural impacts of systematic missense mutations in drug targets of Mycobacterium leprae. Comput Struct Biotechnol J 2020;18:3692-3704. [PMID: 33304465 PMCID: PMC7711215 DOI: 10.1016/j.csbj.2020.11.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 11/08/2020] [Indexed: 12/20/2022]  Open
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