348 related articles for article (PubMed ID: 23070940)
1. Structure refinement of protein model decoys requires accurate side-chain placement.
Olson MA; Lee MS
Proteins; 2013 Mar; 81(3):469-78. PubMed ID: 23070940
[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. Application of replica exchange umbrella sampling to protein structure refinement of nontemplate models.
Olson MA; Lee MS
J Comput Chem; 2013 Jul; 34(20):1785-93. PubMed ID: 23703032
[TBL] [Abstract][Full Text] [Related]
4. Refinement of NMR structures using implicit solvent and advanced sampling techniques.
Chen J; Im W; Brooks CL
J Am Chem Soc; 2004 Dec; 126(49):16038-47. PubMed ID: 15584737
[TBL] [Abstract][Full Text] [Related]
5. How well can we predict native contacts in proteins based on decoy structures and their energies?
Zhu J; Zhu Q; Shi Y; Liu H
Proteins; 2003 Sep; 52(4):598-608. PubMed ID: 12910459
[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. Folding simulations of Trp-cage mini protein in explicit solvent using biasing potential replica-exchange molecular dynamics simulations.
Kannan S; Zacharias M
Proteins; 2009 Aug; 76(2):448-60. PubMed ID: 19173315
[TBL] [Abstract][Full Text] [Related]
8. Free energy landscape of protein folding in water: explicit vs. implicit solvent.
Zhou R
Proteins; 2003 Nov; 53(2):148-61. PubMed ID: 14517967
[TBL] [Abstract][Full Text] [Related]
9. Rapid refinement of protein interfaces incorporating solvation: application to the docking problem.
Jackson RM; Gabb HA; Sternberg MJ
J Mol Biol; 1998 Feb; 276(1):265-85. PubMed ID: 9514726
[TBL] [Abstract][Full Text] [Related]
10. 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]
11. 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]
12. Distinguish protein decoys by using a scoring function based on a new AMBER force field, short molecular dynamics simulations, and the generalized born solvent model.
Lee MC; Duan Y
Proteins; 2004 May; 55(3):620-34. PubMed ID: 15103626
[TBL] [Abstract][Full Text] [Related]
13. Protein Folding Simulations Combining Self-Guided Langevin Dynamics and Temperature-Based Replica Exchange.
Lee MS; Olson MA
J Chem Theory Comput; 2010 Aug; 6(8):2477-87. PubMed ID: 26613500
[TBL] [Abstract][Full Text] [Related]
14. Sampling of near-native protein conformations during protein structure refinement using a coarse-grained model, normal modes, and molecular dynamics simulations.
Stumpff-Kane AW; Maksimiak K; Lee MS; Feig M
Proteins; 2008 Mar; 70(4):1345-56. PubMed ID: 17876825
[TBL] [Abstract][Full Text] [Related]
15. Progress in protein-protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility.
Schueler-Furman O; Wang C; Baker D
Proteins; 2005 Aug; 60(2):187-94. PubMed ID: 15981249
[TBL] [Abstract][Full Text] [Related]
16. Long dynamics simulations of proteins using atomistic force fields and a continuum representation of solvent effects: calculation of structural and dynamic properties.
Li X; Hassan SA; Mehler EL
Proteins; 2005 Aug; 60(3):464-84. PubMed ID: 15959866
[TBL] [Abstract][Full Text] [Related]
17. A decoy set for the thermostable subdomain from chicken villin headpiece, comparison of different free energy estimators.
Fogolari F; Tosatto SC; Colombo G
BMC Bioinformatics; 2005 Dec; 6():301. PubMed ID: 16354298
[TBL] [Abstract][Full Text] [Related]
18. A new pairwise folding potential based on improved decoy generation and side-chain packing.
Loose C; Klepeis JL; Floudas CA
Proteins; 2004 Feb; 54(2):303-14. PubMed ID: 14696192
[TBL] [Abstract][Full Text] [Related]
19. Molecular dynamics simulations of peptides and proteins with a continuum electrostatic model based on screened Coulomb potentials.
Hassan SA; Mehler EL; Zhang D; Weinstein H
Proteins; 2003 Apr; 51(1):109-25. PubMed ID: 12596268
[TBL] [Abstract][Full Text] [Related]
20. Calculation of protein heat capacity from replica-exchange molecular dynamics simulations with different implicit solvent models.
Yeh IC; Lee MS; Olson MA
J Phys Chem B; 2008 Nov; 112(47):15064-73. PubMed ID: 18959439
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
