• Reference Citation Analysis
  • v
  • v
  • Find an Article
Find an Article PDF (4615184)   Today's Articles (5740)   Subscriber (49392)
For: Hu J, Chen T, Wang M, Chan HS, Zhang Z. A critical comparison of coarse-grained structure-based approaches and atomic models of protein folding. Phys Chem Chem Phys 2018;19:13629-13639. [PMID: 28530269 DOI: 10.1039/c7cp01532a] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Number Cited by Other Article(s)
1
Oliveira RJD. Coordinate-Dependent Drift-Diffusion Reveals the Kinetic Intermediate Traps of Top7-Based Proteins. J Phys Chem B 2022;126:10854-10869. [PMID: 36519977 DOI: 10.1021/acs.jpcb.2c07031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
2
Sarkar A, Gasic AG, Cheung MS, Morrison G. Effects of Protein Crowders and Charge on the Folding of Superoxide Dismutase 1 Variants: A Computational Study. J Phys Chem B 2022;126:4458-4471. [PMID: 35686856 DOI: 10.1021/acs.jpcb.2c00819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
3
Freitas FC, Maldonado M, Oliveira Junior AB, Onuchic JN, Oliveira RJD. Biotin-painted proteins have thermodynamic stability switched by kinetic folding routes. J Chem Phys 2022;156:195101. [PMID: 35597640 DOI: 10.1063/5.0083875] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]  Open
4
Beltrán HI, Alas-Guardado SJ, González-Pérez PP. Improving coarse-grained models of protein folding through weighting of polar-polar/hydrophobic-hydrophobic interactions into crowded spaces. J Mol Model 2022;28:87. [PMID: 35262807 DOI: 10.1007/s00894-022-05071-5] [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: 05/26/2021] [Accepted: 02/26/2022] [Indexed: 10/18/2022]
5
The folding and misfolding mechanisms of multidomain proteins. MEDICINE IN DRUG DISCOVERY 2022. [DOI: 10.1016/j.medidd.2022.100126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
6
Structural and thermodynamical insights into the binding and inhibition of FIH-1 by the N-terminal disordered region of Mint3. J Biol Chem 2021;297:101304. [PMID: 34655613 PMCID: PMC8571082 DOI: 10.1016/j.jbc.2021.101304] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 10/09/2021] [Accepted: 10/12/2021] [Indexed: 11/29/2022]  Open
7
Nie QM, Sun LZ, Li HB, Chu X, Wang J. Effects of electrostatic interactions on global folding and local conformational dynamics of a multidomain Y-family DNA polymerase. Phys Chem Chem Phys 2021;23:20841-20847. [PMID: 34533560 DOI: 10.1039/d1cp02832d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
8
Giulini M, Rigoli M, Mattiotti G, Menichetti R, Tarenzi T, Fiorentini R, Potestio R. From System Modeling to System Analysis: The Impact of Resolution Level and Resolution Distribution in the Computer-Aided Investigation of Biomolecules. Front Mol Biosci 2021;8:676976. [PMID: 34164432 PMCID: PMC8215203 DOI: 10.3389/fmolb.2021.676976] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 05/06/2021] [Indexed: 12/18/2022]  Open
9
Zhong Q, Li G. Adaptively Iterative Multiscale Switching Simulation Strategy and Applications to Protein Folding and Structure Prediction. J Phys Chem Lett 2021;12:3151-3162. [PMID: 33755493 DOI: 10.1021/acs.jpclett.1c00618] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
10
Alas-Guardado SJ, González-Pérez PP, Beltrán HI. Contributions of topological polar-polar contacts to achieve better folding stability of 2D/3D HP lattice proteins: An in silico approach. AIMS BIOPHYSICS 2021. [DOI: 10.3934/biophy.2021023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]  Open
11
Chu X, Suo Z, Wang J. Investigating the trade-off between folding and function in a multidomain Y-family DNA polymerase. eLife 2020;9:60434. [PMID: 33079059 PMCID: PMC7641590 DOI: 10.7554/elife.60434] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/16/2020] [Indexed: 01/01/2023]  Open
12
Aumpuchin P, Hamaue S, Kikuchi T. Prediction of the initial folding sites and the entire folding processes for Ig-like beta-sandwich proteins. Proteins 2019;88:740-758. [PMID: 31833097 DOI: 10.1002/prot.25862] [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: 04/05/2019] [Revised: 11/13/2019] [Accepted: 12/06/2019] [Indexed: 11/12/2022]
13
Gasic AG, Boob MM, Prigozhin MB, Homouz D, Wirth AJ, Daugherty CM, Gruebele M, Cheung MS. Critical phenomena in the temperature-pressure-crowding phase diagram of a protein. PHYSICAL REVIEW. X 2019;9:041035. [PMID: 32642303 PMCID: PMC7343146 DOI: 10.1103/physrevx.9.041035] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
14
Observation of Continuous Contraction and a Metastable Misfolded State during the Collapse and Folding of a Small Protein. J Mol Biol 2019;431:3814-3826. [DOI: 10.1016/j.jmb.2019.07.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 07/12/2019] [Accepted: 07/12/2019] [Indexed: 01/22/2023]
15
Alas SDJ, González-Pérez PP, Beltrán HI. In silico minimalist approach to study 2D HP protein folding into an inhomogeneous space mimicking osmolyte effect: First trial in the search of foldameric backbones. Biosystems 2019;181:31-43. [PMID: 31029589 DOI: 10.1016/j.biosystems.2019.04.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 04/01/2019] [Accepted: 04/08/2019] [Indexed: 12/22/2022]
16
Aumpuchin P, Kikuchi T. Prediction of folding mechanisms for Ig-like beta sandwich proteins based on inter-residue average distance statistics methods. Proteins 2018;87:120-135. [PMID: 30520530 DOI: 10.1002/prot.25637] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 10/05/2018] [Accepted: 11/29/2018] [Indexed: 11/11/2022]
17
Wang Y, Tian P, Boomsma W, Lindorff-Larsen K. Monte Carlo Sampling of Protein Folding by Combining an All-Atom Physics-Based Model with a Native State Bias. J Phys Chem B 2018;122:11174-11185. [DOI: 10.1021/acs.jpcb.8b06335] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
18
Cheng C, Wu J, Liu G, Shi S, Chen T. Effects of Non-native Interactions on Frustrated Proteins Folding under Confinement. J Phys Chem B 2018;122:7654-7667. [DOI: 10.1021/acs.jpcb.8b04147] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
19
Wu J, Cheng C, Liu G, Zhang P, Chen T. The folding pathways and thermodynamics of semiflexible polymers. J Chem Phys 2018;148:184901. [PMID: 29764123 DOI: 10.1063/1.5018114] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]  Open
20
Gopi S, Paul S, Ranu S, Naganathan AN. Extracting the Hidden Distributions Underlying the Mean Transition State Structures in Protein Folding. J Phys Chem Lett 2018;9:1771-1777. [PMID: 29565127 DOI: 10.1021/acs.jpclett.8b00538] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
21
Ouyang Y, Zhao L, Zhang Z. Characterization of the structural ensembles of p53 TAD2 by molecular dynamics simulations with different force fields. Phys Chem Chem Phys 2018. [DOI: 10.1039/c8cp00067k] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
22
Song J, Gomes GN, Shi T, Gradinaru CC, Chan HS. Conformational Heterogeneity and FRET Data Interpretation for Dimensions of Unfolded Proteins. Biophys J 2017;113:1012-1024. [PMID: 28877485 DOI: 10.1016/j.bpj.2017.07.023] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 07/26/2017] [Accepted: 07/31/2017] [Indexed: 12/28/2022]  Open
23
Wu J, Chen G, Zhang Z, Zhang P, Chen T. The low populated folding intermediate of a mutant of the Fyn SH3 domain identified by a simple model. Phys Chem Chem Phys 2017;19:22321-22328. [DOI: 10.1039/c7cp04139j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
PrevPage 1 of 1 1Next
© 2004-2024 Baishideng Publishing Group Inc. All rights reserved. 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA