3285 related articles for article (PubMed ID: 16526746)
1. 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]
2. Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent.
Mobley DL; Dumont E; Chodera JD; Dill KA
J Phys Chem B; 2007 Mar; 111(9):2242-54. PubMed ID: 17291029
[TBL] [Abstract][Full Text] [Related]
3. 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]
4. 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]
5. Derivation of class II force fields. VIII. Derivation of a general quantum mechanical force field for organic compounds.
Ewig CS; Berry R; Dinur U; Hill JR; Hwang MJ; Li H; Liang C; Maple J; Peng Z; Stockfisch TP; Thacher TS; Yan L; Ni X; Hagler AT
J Comput Chem; 2001 Nov; 22(15):1782-1800. PubMed ID: 12116411
[TBL] [Abstract][Full Text] [Related]
6. Molecular mechanics (MM3) calculations on lithium amide compounds.
Yoshida T; Sakakibara K; Asami M; Chen KH; Lii JH; Allinger NL
J Comput Chem; 2003 Feb; 24(3):319-27. PubMed ID: 12548723
[TBL] [Abstract][Full Text] [Related]
7. A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations.
Duan Y; Wu C; Chowdhury S; Lee MC; Xiong G; Zhang W; Yang R; Cieplak P; Luo R; Lee T; Caldwell J; Wang J; Kollman P
J Comput Chem; 2003 Dec; 24(16):1999-2012. PubMed ID: 14531054
[TBL] [Abstract][Full Text] [Related]
8. General methodology to optimize damping functions to account for charge penetration effects in electrostatic calculations using multicentered multipolar expansions.
Werneck AS; Filho TM; Dardenne LE
J Phys Chem A; 2008 Jan; 112(2):268-80. PubMed ID: 18095663
[TBL] [Abstract][Full Text] [Related]
9. 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]
10. Ab initio study of hydrogen-bond formation between aliphatic and phenolic hydroxy groups and selected amino acid side chains.
Nagy PI; Erhardt PW
J Phys Chem A; 2008 May; 112(18):4342-54. PubMed ID: 18373368
[TBL] [Abstract][Full Text] [Related]
11. An improved OPLS-AA force field for carbohydrates.
Kony D; Damm W; Stoll S; Van Gunsteren WF
J Comput Chem; 2002 Nov; 23(15):1416-29. PubMed ID: 12370944
[TBL] [Abstract][Full Text] [Related]
12. 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]
13. Accuracy of free energies of hydration using CM1 and CM3 atomic charges.
Udier-Blagović M; Morales De Tirado P; Pearlman SA; Jorgensen WL
J Comput Chem; 2004 Aug; 25(11):1322-32. PubMed ID: 15185325
[TBL] [Abstract][Full Text] [Related]
14. Structures and energies of D-galactose and galabiose conformers as calculated by ab initio and semiempirical methods.
Rahal-Sekkal M; Sekkal N; Kleb DC; Bleckmann P
J Comput Chem; 2003 May; 24(7):806-18. PubMed ID: 12692790
[TBL] [Abstract][Full Text] [Related]
15. Protein imperfections: separating intrinsic from extrinsic variation of torsion angles.
Butterfoss GL; Richardson JS; Hermans J
Acta Crystallogr D Biol Crystallogr; 2005 Jan; 61(Pt 1):88-98. PubMed ID: 15608380
[TBL] [Abstract][Full Text] [Related]
16. 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]
17. Spectroscopically determined force field for water dimer: physically enhanced treatment of hydrogen bonding in molecular mechanics energy functions.
Mannfors B; Palmo K; Krimm S
J Phys Chem A; 2008 Dec; 112(49):12667-78. PubMed ID: 19012387
[TBL] [Abstract][Full Text] [Related]
18. Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation.
Jakalian A; Jack DB; Bayly CI
J Comput Chem; 2002 Dec; 23(16):1623-41. PubMed ID: 12395429
[TBL] [Abstract][Full Text] [Related]
19. The structure and binding energies of the van der Waals complexes of Ar and N2 with phenol and its cation, studied by high level ab initio and density functional theory calculations.
Vincent MA; Hillier IH; Morgado CA; Burton NA; Shan X
J Chem Phys; 2008 Jan; 128(4):044313. PubMed ID: 18247955
[TBL] [Abstract][Full Text] [Related]
20. The limitations of Slater's element-dependent exchange functional from analytic density-functional theory.
Zope RR; Dunlap BI
J Chem Phys; 2006 Jan; 124(4):044107. PubMed ID: 16460149
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
