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For: Zimmermann O, Hansmann UH. Understanding protein folding: small proteins in silico. Biochim Biophys Acta 2008;1784:252-8. [PMID: 18036571 PMCID: PMC2244683 DOI: 10.1016/j.bbapap.2007.10.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2007] [Accepted: 10/26/2007] [Indexed: 10/24/2022]
Number Cited by Other Article(s)
1
Cimini M, Hansmann UHE, Gonzalez C, Chesney AD, Truongcao MM, Gao E, Wang T, Roy R, Forte E, Mallaredy V, Thej C, Magadum A, Joladarashi D, Benedict C, Koch WJ, Tükel Ç, Kishore R. Podoplanin Positive Cell-derived Extracellular Vesicles Contribute to Cardiac Amyloidosis After Myocardial Infarction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.28.601297. [PMID: 39005419 PMCID: PMC11244852 DOI: 10.1101/2024.06.28.601297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
2
Miao L, Jia W, Cao X, Jiao L. Computational chemistry for water-splitting electrocatalysis. Chem Soc Rev 2024;53:2771-2807. [PMID: 38344774 DOI: 10.1039/d2cs01068b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
3
Ruiz-Blanco YB, Marrero-Ponce Y, Prieto PJ, Salgado J, García Y, Sotomayor-Torres CM. A Hooke׳s law-based approach to protein folding rate. J Theor Biol 2015;364:407-17. [DOI: 10.1016/j.jtbi.2014.09.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 08/28/2014] [Accepted: 09/02/2014] [Indexed: 10/24/2022]
4
Yaşar F, Sieradzan AK, Hansmann UHE. Folding and self-assembly of a small heterotetramer. J Chem Phys 2014;140:105103. [PMID: 24628212 DOI: 10.1063/1.4868140] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
5
Berhanu WM, Hansmann UHE. Stability of amyloid oligomers. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014;96:113-41. [PMID: 25443956 DOI: 10.1016/bs.apcsb.2014.06.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
6
Sieradzan AK, Liwo A, Hansmann UHE. Folding and self-assembly of a small protein complex. J Chem Theory Comput 2012;8:3416-3422. [PMID: 24039552 DOI: 10.1021/ct300528r] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
7
Jiang P, Hansmann UHE. Modeling Structural Flexibility of Proteins with Go-Models. J Chem Theory Comput 2012;8:2127-2133. [PMID: 24039551 DOI: 10.1021/ct3000469] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
8
Kouza M, Hansmann UHE. Folding simulations of the A and B domains of protein G. J Phys Chem B 2012;116:6645-53. [PMID: 22214186 DOI: 10.1021/jp210497h] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
9
Molecular dynamics. Methods Mol Biol 2012;929:243-85. [PMID: 23007433 DOI: 10.1007/978-1-62703-050-2_11] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
10
Wang J, Zhu W, Li G, Hansmann UHE. Velocity-scaling optimized replica exchange molecular dynamics of proteins in a hybrid explicit/implicit solvent. J Chem Phys 2011;135:084115. [PMID: 21895167 DOI: 10.1063/1.3624401] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]  Open
11
Kouza M, Hansmann UHE. Velocity scaling for optimizing replica exchange molecular dynamics. J Chem Phys 2011;134:044124. [DOI: 10.1063/1.3533236] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
12
Chugunov AO, Efremov RG. [Prediction of the spatial structure of proteins: emphasis on membrane targets]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2010;35:744-60. [PMID: 20208575 DOI: 10.1134/s106816200906003x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
13
Biomolecular Structure and Modeling: Historical Perspective. INTERDISCIPLINARY APPLIED MATHEMATICS 2010. [PMCID: PMC7124002 DOI: 10.1007/978-1-4419-6351-2_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
14
Kar P, Nadler W, Hansmann UHE. Microcanonical replica exchange molecular dynamics simulation of proteins. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2009;80:056703. [PMID: 20365092 DOI: 10.1103/physreve.80.056703] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2009] [Indexed: 05/29/2023]
15
He Y, Xiao Y, Liwo A, Scheraga HA. Exploring the parameter space of the coarse-grained UNRES force field by random search: selecting a transferable medium-resolution force field. J Comput Chem 2009;30:2127-35. [PMID: 19242966 DOI: 10.1002/jcc.21215] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
16
Schlick T. Monte Carlo, harmonic approximation, and coarse-graining approaches for enhanced sampling of biomolecular structure. F1000 BIOLOGY REPORTS 2009;1:48. [PMID: 20948637 PMCID: PMC2924683 DOI: 10.3410/b1-48] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
17
Hall D, Hirota N. Multi-scale modelling of amyloid formation from unfolded proteins using a set of theory derived rate constants. Biophys Chem 2009;140:122-8. [DOI: 10.1016/j.bpc.2008.11.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2008] [Revised: 11/17/2008] [Accepted: 11/17/2008] [Indexed: 01/05/2023]
18
Pandey RB, Heinz H, Feng J, Farmer BL, Slocik JM, Drummy LF, Naik RR. Adsorption of peptides (A3, Flg, Pd2, Pd4) on gold and palladium surfaces by a coarse-grained Monte Carlo simulation. Phys Chem Chem Phys 2009;11:1989-2001. [DOI: 10.1039/b816187a] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
19
Dametto M, Cárdenas AE. Computer simulations of the refolding of sperm whale apomyoglobin from high-temperature denaturated state. J Phys Chem B 2008;112:9501-6. [PMID: 18616314 DOI: 10.1021/jp804300w] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
20
Pandey RB, Farmer BL. Conformation of a coarse-grained protein chain (an aspartic acid protease) model in effective solvent by a bond-fluctuating Monte Carlo simulation. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2008;77:031902. [PMID: 18517417 DOI: 10.1103/physreve.77.031902] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2007] [Indexed: 05/26/2023]
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