163 related articles for article (PubMed ID: 18300245)
21. Using robotics to fold proteins and dock ligands.
Brutlag D; Apaydin S; Guestrin C; Hsu D; Varma C; Singh A; Latombe JC
Bioinformatics; 2002; 18 Suppl 2():S74. PubMed ID: 12385986
[TBL] [Abstract][Full Text] [Related]
22. Monte Carlo replica-exchange based ensemble docking of protein conformations.
Zhang Z; Ehmann U; Zacharias M
Proteins; 2017 May; 85(5):924-937. PubMed ID: 28168752
[TBL] [Abstract][Full Text] [Related]
23. Using the multi-objective optimization replica exchange Monte Carlo enhanced sampling method for protein-small molecule docking.
Wang H; Liu H; Cai L; Wang C; Lv Q
BMC Bioinformatics; 2017 Jul; 18(1):327. PubMed ID: 28693470
[TBL] [Abstract][Full Text] [Related]
24. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations.
Gray JJ; Moughon S; Wang C; Schueler-Furman O; Kuhlman B; Rohl CA; Baker D
J Mol Biol; 2003 Aug; 331(1):281-99. PubMed ID: 12875852
[TBL] [Abstract][Full Text] [Related]
25. Structural basis of hierarchical multiple substates of a protein. IV: Rearrangements in atom packing and local deformations.
Noguti T; Go N
Proteins; 1989; 5(2):125-31. PubMed ID: 2748576
[TBL] [Abstract][Full Text] [Related]
26. Protein docking using spherical polar Fourier correlations.
Ritchie DW; Kemp GJ
Proteins; 2000 May; 39(2):178-94. PubMed ID: 10737939
[TBL] [Abstract][Full Text] [Related]
27. Protein structure prediction with the UNRES force-field using Replica-Exchange Monte Carlo-with-Minimization; Comparison with MCM, CSA, and CFMC.
Nanias M; Chinchio M; Ołdziej S; Czaplewski C; Scheraga HA
J Comput Chem; 2005 Nov; 26(14):1472-86. PubMed ID: 16088925
[TBL] [Abstract][Full Text] [Related]
28. Scoring docked conformations generated by rigid-body protein-protein docking.
Camacho CJ; Gatchell DW; Kimura SR; Vajda S
Proteins; 2000 Aug; 40(3):525-37. PubMed ID: 10861944
[TBL] [Abstract][Full Text] [Related]
29. Native atomic burials, supplemented by physically motivated hydrogen bond constraints, contain sufficient information to determine the tertiary structure of small globular proteins.
Pereira de Araújo AF; Gomes AL; Bursztyn AA; Shakhnovich EI
Proteins; 2008 Feb; 70(3):971-83. PubMed ID: 17847091
[TBL] [Abstract][Full Text] [Related]
30. Monte Carlo minimization with thermalization for global optimization of polypeptide conformations in cartesian coordinate space.
Caflisch A; Niederer P; Anliker M
Proteins; 1992 Sep; 14(1):102-9. PubMed ID: 1409559
[TBL] [Abstract][Full Text] [Related]
31. Protein docking by the underestimation of free energy funnels in the space of encounter complexes.
Shen Y; Paschalidis ICh; Vakili P; Vajda S
PLoS Comput Biol; 2008 Oct; 4(10):e1000191. PubMed ID: 18846200
[TBL] [Abstract][Full Text] [Related]
32. Reaching the global minimum in docking simulations: a Monte Carlo energy minimization approach using Bezier splines.
Trosset JY; Scheraga HA
Proc Natl Acad Sci U S A; 1998 Jul; 95(14):8011-5. PubMed ID: 9653131
[TBL] [Abstract][Full Text] [Related]
33. Protein-inhibitor flexible docking by a multicanonical sampling: native complex structure with the lowest free energy and a free-energy barrier distinguishing the native complex from the others.
Kamiya N; Yonezawa Y; Nakamura H; Higo J
Proteins; 2008 Jan; 70(1):41-53. PubMed ID: 17636570
[TBL] [Abstract][Full Text] [Related]
34. Monte Carlo temperature basin paving with effective fragment potential: an efficient and fast method for finding low-energy structures of water clusters (H2O)20 and (H2O)25.
Shanker S; Bandyopadhyay P
J Phys Chem A; 2011 Oct; 115(42):11866-75. PubMed ID: 21928813
[TBL] [Abstract][Full Text] [Related]
35. Protein-protein docking: is the glass half-full or half-empty?
Vajda S; Camacho CJ
Trends Biotechnol; 2004 Mar; 22(3):110-6. PubMed ID: 15036860
[TBL] [Abstract][Full Text] [Related]
36. Local energy landscape flattening: parallel hyperbolic Monte Carlo sampling of protein folding.
Zhang Y; Kihara D; Skolnick J
Proteins; 2002 Aug; 48(2):192-201. PubMed ID: 12112688
[TBL] [Abstract][Full Text] [Related]
37. 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]
38. 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]
39. 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]
40. Identification of near-native structures by clustering protein docking conformations.
Lorenzen S; Zhang Y
Proteins; 2007 Jul; 68(1):187-94. PubMed ID: 17397057
[TBL] [Abstract][Full Text] [Related]
[Previous] [Next] [New Search]
