133 related articles for article (PubMed ID: 23425457)
1. Amino-acid-dependent main-chain torsion-energy terms for protein systems.
Sakae Y; Okamoto Y
J Chem Phys; 2013 Feb; 138(6):064103. PubMed ID: 23425457
[TBL] [Abstract][Full Text] [Related]
2. The intrinsic conformational features of amino acids from a protein coil library and their applications in force field development.
Jiang F; Han W; Wu YD
Phys Chem Chem Phys; 2013 Mar; 15(10):3413-28. PubMed ID: 23385383
[TBL] [Abstract][Full Text] [Related]
3. Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine "dipeptides" (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution.
Hu H; Elstner M; Hermans J
Proteins; 2003 Feb; 50(3):451-63. PubMed ID: 12557187
[TBL] [Abstract][Full Text] [Related]
4. New-generation amber united-atom force field.
Yang L; Tan CH; Hsieh MJ; Wang J; Duan Y; Cieplak P; Caldwell J; Kollman PA; Luo R
J Phys Chem B; 2006 Jul; 110(26):13166-76. PubMed ID: 16805629
[TBL] [Abstract][Full Text] [Related]
5. Influence of side chain conformations on local conformational features of amino acids and implication for force field development.
Jiang F; Han W; Wu YD
J Phys Chem B; 2010 May; 114(17):5840-50. PubMed ID: 20392111
[TBL] [Abstract][Full Text] [Related]
6. A novel force field parameter optimization method based on LSSVR for ECEPP.
Liu Y; Tao L; Lu J; Xu S; Ma Q; Duan Q
FEBS Lett; 2011 Mar; 585(6):888-92. PubMed ID: 21349275
[TBL] [Abstract][Full Text] [Related]
7. Residue-specific force field based on the protein coil library. RSFF1: modification of OPLS-AA/L.
Jiang F; Zhou CY; Wu YD
J Phys Chem B; 2014 Jun; 118(25):6983-98. PubMed ID: 24815738
[TBL] [Abstract][Full Text] [Related]
8. A comparison of the CHARMM, AMBER and ECEPP potentials for peptides. II. Phi-psi maps for N-acetyl alanine N'-methyl amide: comparisons, contrasts and simple experimental tests.
Roterman IK; Lambert MH; Gibson KD; Scheraga HA
J Biomol Struct Dyn; 1989 Dec; 7(3):421-53. PubMed ID: 2627294
[TBL] [Abstract][Full Text] [Related]
9. Protein simulations with an optimized water model: cooperative helix formation and temperature-induced unfolded state collapse.
Best RB; Mittal J
J Phys Chem B; 2010 Nov; 114(46):14916-23. PubMed ID: 21038907
[TBL] [Abstract][Full Text] [Related]
10. 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]
11. Balance between alpha and beta structures in ab initio protein folding.
Best RB; Mittal J
J Phys Chem B; 2010 Jul; 114(26):8790-8. PubMed ID: 20536262
[TBL] [Abstract][Full Text] [Related]
12. Discrepancies between conformational distributions of a polyalanine peptide in solution obtained from molecular dynamics force fields and amide I' band profiles.
Verbaro D; Ghosh I; Nau WM; Schweitzer-Stenner R
J Phys Chem B; 2010 Dec; 114(51):17201-8. PubMed ID: 21138254
[TBL] [Abstract][Full Text] [Related]
13. A new force field (ECEPP-05) for peptides, proteins, and organic molecules.
Arnautova YA; Jagielska A; Scheraga HA
J Phys Chem B; 2006 Mar; 110(10):5025-44. PubMed ID: 16526746
[TBL] [Abstract][Full Text] [Related]
14. Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations.
Mackerell AD; Feig M; Brooks CL
J Comput Chem; 2004 Aug; 25(11):1400-15. PubMed ID: 15185334
[TBL] [Abstract][Full Text] [Related]
15. The SAAP force field. A simple approach to a new all-atom protein force field by using single amino acid potential (SAAP) functions in various solvents.
Iwaoka M; Tomoda S
J Comput Chem; 2003 Jul; 24(10):1192-200. PubMed ID: 12820126
[TBL] [Abstract][Full Text] [Related]
16. A Maximum-Likelihood Approach to Force-Field Calibration.
Zaborowski B; Jagieła D; Czaplewski C; Hałabis A; Lewandowska A; Żmudzińska W; Ołdziej S; Karczyńska A; Omieczynski C; Wirecki T; Liwo A
J Chem Inf Model; 2015 Sep; 55(9):2050-70. PubMed ID: 26263302
[TBL] [Abstract][Full Text] [Related]
17. Free energy surfaces of beta-hairpin and alpha-helical peptides generated by replica exchange molecular dynamics with the AGBNP implicit solvent model.
Felts AK; Harano Y; Gallicchio E; Levy RM
Proteins; 2004 Aug; 56(2):310-21. PubMed ID: 15211514
[TBL] [Abstract][Full Text] [Related]
18. Improved side-chain torsion potentials for the Amber ff99SB protein force field.
Lindorff-Larsen K; Piana S; Palmo K; Maragakis P; Klepeis JL; Dror RO; Shaw DE
Proteins; 2010 Jun; 78(8):1950-8. PubMed ID: 20408171
[TBL] [Abstract][Full Text] [Related]
19. Amino acid conformational preferences and solvation of polar backbone atoms in peptides and proteins.
Avbelj F
J Mol Biol; 2000 Jul; 300(5):1335-59. PubMed ID: 10903873
[TBL] [Abstract][Full Text] [Related]
20. Combination of the CHARMM27 force field with united-atom lipid force fields.
Sapay N; Tieleman DP
J Comput Chem; 2011 May; 32(7):1400-10. PubMed ID: 21425293
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]