647 related articles for article (PubMed ID: 19817469)
41. Molecular dynamics simulations of a beta-hairpin fragment of protein G: balance between side-chain and backbone forces.
Ma B; Nussinov R
J Mol Biol; 2000 Mar; 296(4):1091-104. PubMed ID: 10686106
[TBL] [Abstract][Full Text] [Related]
42. Monte Carlo simulations of protein folding. II. Application to protein A, ROP, and crambin.
Kolinski A; Skolnick J
Proteins; 1994 Apr; 18(4):353-66. PubMed ID: 8208727
[TBL] [Abstract][Full Text] [Related]
43. Dependence of folding dynamics and structural stability on the location of a hydrophobic pair in beta-hairpins.
Imamura H; Chen JZ
Proteins; 2006 May; 63(3):555-70. PubMed ID: 16485280
[TBL] [Abstract][Full Text] [Related]
44. Comparative molecular dynamics and Monte Carlo study of statistical properties for coarse-grained heteropolymers.
Schluttig J; Bachmann M; Janke W
J Comput Chem; 2008 Nov; 29(15):2603-12. PubMed ID: 18478584
[TBL] [Abstract][Full Text] [Related]
45. 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]
46. The coarse-grained OPEP force field for non-amyloid and amyloid proteins.
Chebaro Y; Pasquali S; Derreumaux P
J Phys Chem B; 2012 Aug; 116(30):8741-52. PubMed ID: 22742737
[TBL] [Abstract][Full Text] [Related]
47. The CUMULUS coarse graining method: transferable potentials for water and solutes.
van Hoof B; Markvoort AJ; van Santen RA; Hilbers PA
J Phys Chem B; 2011 Aug; 115(33):10001-12. PubMed ID: 21740053
[TBL] [Abstract][Full Text] [Related]
48. Dynamics of large proteins through hierarchical levels of coarse-grained structures.
Doruker P; Jernigan RL; Bahar I
J Comput Chem; 2002 Jan; 23(1):119-27. PubMed ID: 11913377
[TBL] [Abstract][Full Text] [Related]
49. The folding thermodynamics and kinetics of crambin using an all-atom Monte Carlo simulation.
Shimada J; Kussell EL; Shakhnovich EI
J Mol Biol; 2001 Apr; 308(1):79-95. PubMed ID: 11302709
[TBL] [Abstract][Full Text] [Related]
50. A reduced protein model with accurate native-structure identification ability.
Betancourt MR
Proteins; 2003 Dec; 53(4):889-907. PubMed ID: 14635131
[TBL] [Abstract][Full Text] [Related]
51. Folding 19 proteins to their native state and stability of large proteins from a coarse-grained model.
Kapoor A; Travesset A
Proteins; 2014 Mar; 82(3):505-16. PubMed ID: 24115081
[TBL] [Abstract][Full Text] [Related]
52. Monte Carlo folding of trans-membrane helical peptides in an implicit generalized Born membrane.
Ulmschneider JP; Ulmschneider MB; Di Nola A
Proteins; 2007 Nov; 69(2):297-308. PubMed ID: 17600830
[TBL] [Abstract][Full Text] [Related]
53. Coarse-grained force field for the nucleosome from self-consistent multiscaling.
Voltz K; Trylska J; Tozzini V; Kurkal-Siebert V; Langowski J; Smith J
J Comput Chem; 2008 Jul; 29(9):1429-39. PubMed ID: 18270964
[TBL] [Abstract][Full Text] [Related]
54. 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]
55. HiRE-RNA: a high resolution coarse-grained energy model for RNA.
Pasquali S; Derreumaux P
J Phys Chem B; 2010 Sep; 114(37):11957-66. PubMed ID: 20795690
[TBL] [Abstract][Full Text] [Related]
56. Molecular mechanisms for cooperative folding of proteins.
Hao MH; Scheraga HA
J Mol Biol; 1998 Apr; 277(4):973-83. PubMed ID: 9545385
[TBL] [Abstract][Full Text] [Related]
57. Structural mining: self-consistent design on flexible protein-peptide docking and transferable binding affinity potential.
Liu Z; Dominy BN; Shakhnovich EI
J Am Chem Soc; 2004 Jul; 126(27):8515-28. PubMed ID: 15238009
[TBL] [Abstract][Full Text] [Related]
58. Parametrization of Backbone Flexibility in a Coarse-Grained Force Field for Proteins (COFFDROP) Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of All Possible Two-Residue Peptides.
Frembgen-Kesner T; Andrews CT; Li S; Ngo NA; Shubert SA; Jain A; Olayiwola OJ; Weishaar MR; Elcock AH
J Chem Theory Comput; 2015 May; 11(5):2341-54. PubMed ID: 26574429
[TBL] [Abstract][Full Text] [Related]
59. Transition network based on equilibrium sampling: a new method for extracting kinetic information from Monte Carlo simulations of protein folding.
Klenin KV; Wenzel W
J Chem Phys; 2011 Dec; 135(23):235105. PubMed ID: 22191905
[TBL] [Abstract][Full Text] [Related]
60. Protein flexibility from discrete molecular dynamics simulations using quasi-physical potentials.
Emperador A; Meyer T; Orozco M
Proteins; 2010 Jan; 78(1):83-94. PubMed ID: 19816993
[TBL] [Abstract][Full Text] [Related]
[Previous] [Next] [New Search]
