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For: Chen M, Lin X, Lu W, Onuchic JN, Wolynes PG. Protein Folding and Structure Prediction from the Ground Up II: AAWSEM for α/β Proteins. J Phys Chem B 2016;121:3473-3482. [PMID: 27797194 DOI: 10.1021/acs.jpcb.6b09347] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Number Cited by Other Article(s)
1
Guo L, Yu Q, Wang D, Wu X, Wolynes PG, Chen M. Generating the polymorph landscapes of amyloid fibrils using AI: RibbonFold. Proc Natl Acad Sci U S A 2025;122:e2501321122. [PMID: 40232799 PMCID: PMC12037047 DOI: 10.1073/pnas.2501321122] [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: 01/28/2025] [Accepted: 03/07/2025] [Indexed: 04/16/2025]  Open
2
Wang A, Lin X, Chau KN, Onuchic JN, Levine H, George JT. RACER-m leverages structural features for sparse T cell specificity prediction. SCIENCE ADVANCES 2024;10:eadl0161. [PMID: 38748791 PMCID: PMC11095454 DOI: 10.1126/sciadv.adl0161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 04/10/2024] [Indexed: 05/19/2024]
3
Evans R, Ramisetty S, Kulkarni P, Weninger K. Illuminating Intrinsically Disordered Proteins with Integrative Structural Biology. Biomolecules 2023;13:124. [PMID: 36671509 PMCID: PMC9856150 DOI: 10.3390/biom13010124] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/01/2023] [Accepted: 01/04/2023] [Indexed: 01/11/2023]  Open
4
BAP1 forms a trimer with HMGB1 and HDAC1 that modulates gene × environment interaction with asbestos. Proc Natl Acad Sci U S A 2021;118:2111946118. [PMID: 34815344 DOI: 10.1073/pnas.2111946118] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2021] [Indexed: 12/25/2022]  Open
5
Liwo A, Czaplewski C, Sieradzan AK, Lipska AG, Samsonov SA, Murarka RK. Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems. Biomolecules 2021;11:1347. [PMID: 34572559 PMCID: PMC8465211 DOI: 10.3390/biom11091347] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/03/2021] [Accepted: 09/09/2021] [Indexed: 12/16/2022]  Open
6
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: 5.3] [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
7
Oliveira Junior AB, Lin X, Kulkarni P, Onuchic JN, Roy S, Leite VBP. Exploring Energy Landscapes of Intrinsically Disordered Proteins: Insights into Functional Mechanisms. J Chem Theory Comput 2021;17:3178-3187. [PMID: 33871257 DOI: 10.1021/acs.jctc.1c00027] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
8
Jin S, Miller MD, Chen M, Schafer NP, Lin X, Chen X, Phillips GN, Wolynes PG. Molecular-replacement phasing using predicted protein structures from AWSEM-Suite. IUCRJ 2020;7:1168-1178. [PMID: 33209327 PMCID: PMC7642774 DOI: 10.1107/s2052252520013494] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/07/2020] [Indexed: 06/11/2023]
9
Structural and Dynamical Order of a Disordered Protein: Molecular Insights into Conformational Switching of PAGE4 at the Systems Level. Biomolecules 2019;9:biom9020077. [PMID: 30813315 PMCID: PMC6406393 DOI: 10.3390/biom9020077] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 02/10/2019] [Accepted: 02/10/2019] [Indexed: 01/10/2023]  Open
10
Wu H, Wolynes PG, Papoian GA. AWSEM-IDP: A Coarse-Grained Force Field for Intrinsically Disordered Proteins. J Phys Chem B 2018;122:11115-11125. [PMID: 30091924 PMCID: PMC6713210 DOI: 10.1021/acs.jpcb.8b05791] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
11
Neelamraju S, Gosavi S, Wales DJ. Energy Landscape of the Designed Protein Top7. J Phys Chem B 2018;122:12282-12291. [DOI: 10.1021/acs.jpcb.8b08499] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
12
Chen M, Lin X, Lu W, Schafer NP, Onuchic JN, Wolynes PG. Template-Guided Protein Structure Prediction and Refinement Using Optimized Folding Landscape Force Fields. J Chem Theory Comput 2018;14:6102-6116. [PMID: 30240202 DOI: 10.1021/acs.jctc.8b00683] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
13
Chen M, Schafer NP, Wolynes PG. Surveying the Energy Landscapes of Aβ Fibril Polymorphism. J Phys Chem B 2018;122:11414-11430. [PMID: 30215519 DOI: 10.1021/acs.jpcb.8b07364] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
14
Lin X, Roy S, Jolly MK, Bocci F, Schafer NP, Tsai MY, Chen Y, He Y, Grishaev A, Weninger K, Orban J, Kulkarni P, Rangarajan G, Levine H, Onuchic JN. PAGE4 and Conformational Switching: Insights from Molecular Dynamics Simulations and Implications for Prostate Cancer. J Mol Biol 2018;430:2422-2438. [PMID: 29758263 DOI: 10.1016/j.jmb.2018.05.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 04/13/2018] [Accepted: 05/07/2018] [Indexed: 11/15/2022]
15
Chen M, Schafer NP, Zheng W, Wolynes PG. The Associative Memory, Water Mediated, Structure and Energy Model (AWSEM)-Amylometer: Predicting Amyloid Propensity and Fibril Topology Using an Optimized Folding Landscape Model. ACS Chem Neurosci 2018;9:1027-1039. [PMID: 29241326 DOI: 10.1021/acschemneuro.7b00436] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]  Open
16
Dawid AE, Gront D, Kolinski A. Coarse-Grained Modeling of the Interplay between Secondary Structure Propensities and Protein Fold Assembly. J Chem Theory Comput 2018;14:2277-2287. [PMID: 29486120 DOI: 10.1021/acs.jctc.7b01242] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
17
Sirovetz BJ, Schafer NP, Wolynes PG. Protein structure prediction: making AWSEM AWSEM-ER by adding evolutionary restraints. Proteins 2017;85:2127-2142. [PMID: 28799172 DOI: 10.1002/prot.25367] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 07/29/2017] [Accepted: 08/08/2017] [Indexed: 11/07/2022]
18
Aggregation landscapes of Huntingtin exon 1 protein fragments and the critical repeat length for the onset of Huntington's disease. Proc Natl Acad Sci U S A 2017;114:4406-4411. [PMID: 28400517 DOI: 10.1073/pnas.1702237114] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]  Open
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