194 related articles for article (PubMed ID: 34170125)
1. Accurate Structure Prediction for Protein Loops Based on Molecular Dynamics Simulations with RSFF2C.
Feng JJ; Chen JN; Kang W; Wu YD
J Chem Theory Comput; 2021 Jul; 17(7):4614-4628. PubMed ID: 34170125
[TBL] [Abstract][Full Text] [Related]
2. Comparison between self-guided Langevin dynamics and molecular dynamics simulations for structure refinement of protein loop conformations.
Olson MA; Chaudhury S; Lee MS
J Comput Chem; 2011 Nov; 32(14):3014-22. PubMed ID: 21793008
[TBL] [Abstract][Full Text] [Related]
3. Significant Refinement of Protein Structure Models Using a Residue-Specific Force Field.
Xun S; Jiang F; Wu YD
J Chem Theory Comput; 2015 Apr; 11(4):1949-56. PubMed ID: 26574396
[TBL] [Abstract][Full Text] [Related]
4. Validation of Molecular Dynamics Simulations for Prediction of Three-Dimensional Structures of Small Proteins.
Kato K; Nakayoshi T; Fukuyoshi S; Kurimoto E; Oda A
Molecules; 2017 Oct; 22(10):. PubMed ID: 29023395
[TBL] [Abstract][Full Text] [Related]
5. Assessing the Current State of Amber Force Field Modifications for DNA.
Galindo-Murillo R; Robertson JC; Zgarbová M; Šponer J; Otyepka M; Jurečka P; Cheatham TE
J Chem Theory Comput; 2016 Aug; 12(8):4114-27. PubMed ID: 27300587
[TBL] [Abstract][Full Text] [Related]
6. Application of biasing-potential replica-exchange simulations for loop modeling and refinement of proteins in explicit solvent.
Kannan S; Zacharias M
Proteins; 2010 Oct; 78(13):2809-19. PubMed ID: 20635348
[TBL] [Abstract][Full Text] [Related]
7. Experimental verification of force fields for molecular dynamics simulations using Gly-Pro-Gly-Gly.
Aliev AE; Courtier-Murias D
J Phys Chem B; 2010 Sep; 114(38):12358-75. PubMed ID: 20825228
[TBL] [Abstract][Full Text] [Related]
8. Effects of force fields on the conformational and dynamic properties of amyloid β(1-40) dimer explored by replica exchange molecular dynamics simulations.
Watts CR; Gregory A; Frisbie C; Lovas S
Proteins; 2018 Mar; 86(3):279-300. PubMed ID: 29235155
[TBL] [Abstract][Full Text] [Related]
9. Prediction of protein loop conformations using multiscale modeling methods with physical energy scoring functions.
Olson MA; Feig M; Brooks CL
J Comput Chem; 2008 Apr; 29(5):820-31. PubMed ID: 17876760
[TBL] [Abstract][Full Text] [Related]
10. Assessment of transferable forcefields for protein simulations attests improved description of disordered states and secondary structure propensities, and hints at multi-protein systems as the next challenge for optimization.
Abriata LA; Dal Peraro M
Comput Struct Biotechnol J; 2021; 19():2626-2636. PubMed ID: 34025949
[TBL] [Abstract][Full Text] [Related]
11. Insights into the folding pathway of the Engrailed Homeodomain protein using replica exchange molecular dynamics simulations.
Koulgi S; Sonavane U; Joshi R
J Mol Graph Model; 2010 Nov; 29(3):481-91. PubMed ID: 21035367
[TBL] [Abstract][Full Text] [Related]
12. Evaluating the strengths of salt bridges in the CutA1 protein using molecular dynamic simulations: a comparison of different force fields.
Matsuura Y; Joti Y; Bagautdinov B; Yutani K
FEBS Open Bio; 2019 Nov; 9(11):1939-1956. PubMed ID: 31509647
[TBL] [Abstract][Full Text] [Related]
13. Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields.
Fadrná E; Špačková N; Sarzyñska J; Koča J; Orozco M; Cheatham TE; Kulinski T; Šponer J
J Chem Theory Comput; 2009 Sep; 5(9):2514-30. PubMed ID: 26616629
[TBL] [Abstract][Full Text] [Related]
14. Accurate Prediction for Protein-Peptide Binding Based on High-Temperature Molecular Dynamics Simulations.
Chen JN; Jiang F; Wu YD
J Chem Theory Comput; 2022 Oct; 18(10):6386-6395. PubMed ID: 36149394
[TBL] [Abstract][Full Text] [Related]
15. Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations.
Islam B; Stadlbauer P; Gil-Ley A; Pérez-Hernández G; Haider S; Neidle S; Bussi G; Banas P; Otyepka M; Sponer J
J Chem Theory Comput; 2017 Jun; 13(6):2458-2480. PubMed ID: 28475322
[TBL] [Abstract][Full Text] [Related]
16. A hierarchical approach to all-atom protein loop prediction.
Jacobson MP; Pincus DL; Rapp CS; Day TJ; Honig B; Shaw DE; Friesner RA
Proteins; 2004 May; 55(2):351-67. PubMed ID: 15048827
[TBL] [Abstract][Full Text] [Related]
17. PDB-based protein loop prediction: parameters for selection and methods for optimization.
van Vlijmen HW; Karplus M
J Mol Biol; 1997 Apr; 267(4):975-1001. PubMed ID: 9135125
[TBL] [Abstract][Full Text] [Related]
18. A comparative study of two different force fields on structural and thermodynamics character of H1 peptide via molecular dynamics simulations.
Cao Z; Wang J
J Biomol Struct Dyn; 2010 Apr; 27(5):651-61. PubMed ID: 20085382
[TBL] [Abstract][Full Text] [Related]
19. Convergence of replica exchange molecular dynamics.
Zhang W; Wu C; Duan Y
J Chem Phys; 2005 Oct; 123(15):154105. PubMed ID: 16252940
[TBL] [Abstract][Full Text] [Related]
20. Exploring the energy landscape of protein folding using replica-exchange and conventional molecular dynamics simulations.
Beck DA; White GW; Daggett V
J Struct Biol; 2007 Mar; 157(3):514-23. PubMed ID: 17113307
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
