These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.
193 related articles for article (PubMed ID: 20435910)
21. Equilibrium distribution from distributed computing (simulations of protein folding). Scalco R; Caflisch A J Phys Chem B; 2011 May; 115(19):6358-65. PubMed ID: 21517045 [TBL] [Abstract][Full Text] [Related]
22. 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]
23. Coarse-grained protein model with residue orientation energies derived from atomic force fields. Betancourt MR J Phys Chem B; 2009 Nov; 113(44):14824-30. PubMed ID: 19817469 [TBL] [Abstract][Full Text] [Related]
24. Hybrid Methods for Modeling Protein Structures Using Molecular Dynamics Simulations and Small-Angle X-Ray Scattering Data. Ekimoto T; Ikeguchi M Adv Exp Med Biol; 2018; 1105():237-258. PubMed ID: 30617833 [TBL] [Abstract][Full Text] [Related]
25. Cherry-picking functionally relevant substates from long md trajectories using a stratified sampling approach. Chandramouli B; Mancini G Theor Biol Forum; 2016 Jan; 109(1-2):49-69. PubMed ID: 29513352 [TBL] [Abstract][Full Text] [Related]
26. Equilibrium thermodynamics and folding kinetics of a short, fast-folding, beta-hairpin. Jimenez-Cruz CA; Garcia AE Phys Chem Chem Phys; 2014 Apr; 16(14):6422-9. PubMed ID: 24472872 [TBL] [Abstract][Full Text] [Related]
27. Simple, yet powerful methodologies for conformational sampling of proteins. Harada R; Takano Y; Baba T; Shigeta Y Phys Chem Chem Phys; 2015 Mar; 17(9):6155-73. PubMed ID: 25659594 [TBL] [Abstract][Full Text] [Related]
28. Improved ligand binding energies derived from molecular dynamics: replicate sampling enhances the search of conformational space. Adler M; Beroza P J Chem Inf Model; 2013 Aug; 53(8):2065-72. PubMed ID: 23845109 [TBL] [Abstract][Full Text] [Related]
29. Explicit Characterization of the Free-Energy Landscape of a Protein in the Space of All Its C Sormani G; Rodriguez A; Laio A J Chem Theory Comput; 2020 Jan; 16(1):80-87. PubMed ID: 31809040 [TBL] [Abstract][Full Text] [Related]
30. Folding of a helix at room temperature is critically aided by electrostatic polarization of intraprotein hydrogen bonds. Duan LL; Mei Y; Zhang D; Zhang QG; Zhang JZ J Am Chem Soc; 2010 Aug; 132(32):11159-64. PubMed ID: 20698682 [TBL] [Abstract][Full Text] [Related]
31. Targeting protein tyrosine phosphatase to unravel possible inhibitors for Streptococcus pneumoniae using molecular docking, molecular dynamics simulations coupled with free energy calculations. Zaman Z; Khan S; Nouroz F; Farooq U; Urooj A Life Sci; 2021 Jan; 264():118621. PubMed ID: 33164832 [TBL] [Abstract][Full Text] [Related]
32. New insights into the folding of a β-sheet miniprotein in a reduced space of collective hydrogen bond variables: application to a hydrodynamic analysis of the folding flow. Kalgin IV; Caflisch A; Chekmarev SF; Karplus M J Phys Chem B; 2013 May; 117(20):6092-105. PubMed ID: 23621790 [TBL] [Abstract][Full Text] [Related]
33. Connecting free energy surfaces in implicit and explicit solvent: an efficient method to compute conformational and solvation free energies. Deng N; Zhang BW; Levy RM J Chem Theory Comput; 2015 Jun; 11(6):2868-78. PubMed ID: 26236174 [TBL] [Abstract][Full Text] [Related]
34. A rapid solvent accessible surface area estimator for coarse grained molecular simulations. Wei S; Brooks CL; Frank AT J Comput Chem; 2017 Jun; 38(15):1270-1274. PubMed ID: 28419507 [TBL] [Abstract][Full Text] [Related]
35. A molecular simulation protocol to avoid sampling redundancy and discover new states. Bacci M; Vitalis A; Caflisch A Biochim Biophys Acta; 2015 May; 1850(5):889-902. PubMed ID: 25193737 [TBL] [Abstract][Full Text] [Related]
36. Free energies for coarse-grained proteins by integrating multibody statistical contact potentials with entropies from elastic network models. Zimmermann MT; Leelananda SP; Gniewek P; Feng Y; Jernigan RL; Kloczkowski A J Struct Funct Genomics; 2011 Jul; 12(2):137-47. PubMed ID: 21674234 [TBL] [Abstract][Full Text] [Related]
37. Accurate free energy calculation along optimized paths. Chen C; Xiao Y J Comput Chem; 2010 May; 31(7):1368-75. PubMed ID: 19859916 [TBL] [Abstract][Full Text] [Related]
38. Pipeline for inferring protein function from dynamics using coarse-grained molecular mechanics forcefield. Bhadra P; Pal D Comput Biol Med; 2017 Apr; 83():134-142. PubMed ID: 28279862 [TBL] [Abstract][Full Text] [Related]
39. Will molecular dynamics simulations of proteins ever reach equilibrium? Genheden S; Ryde U Phys Chem Chem Phys; 2012 Jun; 14(24):8662-77. PubMed ID: 22614001 [TBL] [Abstract][Full Text] [Related]
40. Separation of time scale and coupling in the motion governed by the coarse-grained and fine degrees of freedom in a polypeptide backbone. Murarka RK; Liwo A; Scheraga HA J Chem Phys; 2007 Oct; 127(15):155103. PubMed ID: 17949219 [TBL] [Abstract][Full Text] [Related] [Previous] [Next] [New Search]