286 related articles for article (PubMed ID: 12696057)
1. Solvation parameters for predicting the structure of surface loops in proteins: transferability and entropic effects.
Das B; Meirovitch H
Proteins; 2003 May; 51(3):470-83. PubMed ID: 12696057
[TBL] [Abstract][Full Text] [Related]
2. Optimization of solvation models for predicting the structure of surface loops in proteins.
Das B; Meirovitch H
Proteins; 2001 May; 43(3):303-14. PubMed ID: 11288180
[TBL] [Abstract][Full Text] [Related]
3. Ab initio prediction of the solution structures and populations of a cyclic pentapeptide in DMSO based on an implicit solvation model.
Baysal C; Meirovitch H
Biopolymers; 2000 Apr; 53(5):423-33. PubMed ID: 10738203
[TBL] [Abstract][Full Text] [Related]
4. On the transferability of atomic solvation parameters: Ab initio structural prediction of cyclic heptapeptides in DMSO.
Baysal C; Meirovitch H
Biopolymers; 2000 Nov; 54(6):416-28. PubMed ID: 10951328
[TBL] [Abstract][Full Text] [Related]
5. Optimization of the GB/SA solvation model for predicting the structure of surface loops in proteins.
Szarecka A; Meirovitch H
J Phys Chem B; 2006 Feb; 110(6):2869-80. PubMed ID: 16471897
[TBL] [Abstract][Full Text] [Related]
6. 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]
7. Evaluation of the conformational free energies of loops in proteins.
Smith KC; Honig B
Proteins; 1994 Feb; 18(2):119-32. PubMed ID: 8159662
[TBL] [Abstract][Full Text] [Related]
8. Rational design of ion force fields based on thermodynamic solvation properties.
Horinek D; Mamatkulov SI; Netz RR
J Chem Phys; 2009 Mar; 130(12):124507. PubMed ID: 19334851
[TBL] [Abstract][Full Text] [Related]
9. Conformational analysis of endothelin-1: effects of solvation free energy.
Hempel JC; Fine RM; Hassan M; Ghoul W; Guaragna A; Koerber SC; Li Z; Hagler AT
Biopolymers; 1995 Sep; 36(3):283-301. PubMed ID: 7669916
[TBL] [Abstract][Full Text] [Related]
10. Empirical solvation models in the context of conformational energy searches: application to bovine pancreatic trypsin inhibitor.
Williams RL; Vila J; Perrot G; Scheraga HA
Proteins; 1992 Sep; 14(1):110-9. PubMed ID: 1384032
[TBL] [Abstract][Full Text] [Related]
11. Ab initio computational modeling of loops in G-protein-coupled receptors: lessons from the crystal structure of rhodopsin.
Mehler EL; Hassan SA; Kortagere S; Weinstein H
Proteins; 2006 Aug; 64(3):673-90. PubMed ID: 16729264
[TBL] [Abstract][Full Text] [Related]
12. 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]
13. Estimating protein-ligand binding free energy: atomic solvation parameters for partition coefficient and solvation free energy calculation.
Pei J; Wang Q; Zhou J; Lai L
Proteins; 2004 Dec; 57(4):651-64. PubMed ID: 15390269
[TBL] [Abstract][Full Text] [Related]
14. Distinguishing native conformations of proteins from decoys with an effective free energy estimator based on the OPLS all-atom force field and the Surface Generalized Born solvent model.
Felts AK; Gallicchio E; Wallqvist A; Levy RM
Proteins; 2002 Aug; 48(2):404-22. PubMed ID: 12112706
[TBL] [Abstract][Full Text] [Related]
15. Calculation of the free energy of polarization: quantifying the effect of explicitly treating electronic polarization on the transferability of force-field parameters.
Geerke DP; van Gunsteren WF
J Phys Chem B; 2007 Jun; 111(23):6425-36. PubMed ID: 17508737
[TBL] [Abstract][Full Text] [Related]
16. Universal solvation model based on solute electron density and on a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions.
Marenich AV; Cramer CJ; Truhlar DG
J Phys Chem B; 2009 May; 113(18):6378-96. PubMed ID: 19366259
[TBL] [Abstract][Full Text] [Related]
17. FACTS: Fast analytical continuum treatment of solvation.
Haberthür U; Caflisch A
J Comput Chem; 2008 Apr; 29(5):701-15. PubMed ID: 17918282
[TBL] [Abstract][Full Text] [Related]
18. Ab initio modeling of small, medium, and large loops in proteins.
Galaktionov S; Nikiforovich GV; Marshall GR
Biopolymers; 2001; 60(2):153-68. PubMed ID: 11455548
[TBL] [Abstract][Full Text] [Related]
19. Determination of conformational equilibrium of peptides in solution by NMR spectroscopy and theoretical conformational analysis: application to the calibration of mean-field solvation models.
Groth M; Malicka J; Rodziewicz- Motowidło S; Czaplewski C; Klaudel L; Wiczk W; Liwo A
Biopolymers; 2001; 60(2):79-95. PubMed ID: 11455544
[TBL] [Abstract][Full Text] [Related]
20. An improved protein decoy set for testing energy functions for protein structure prediction.
Tsai J; Bonneau R; Morozov AV; Kuhlman B; Rohl CA; Baker D
Proteins; 2003 Oct; 53(1):76-87. PubMed ID: 12945051
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
