209 related articles for article (PubMed ID: 24044772)
1. Specific and non-specific protein association in solution: computation of solvent effects and prediction of first-encounter modes for efficient configurational bias Monte Carlo simulations.
Cardone A; Pant H; Hassan SA
J Phys Chem B; 2013 Oct; 117(41):12360-74. PubMed ID: 24044772
[TBL] [Abstract][Full Text] [Related]
2. Detection and characterization of nonspecific, sparsely populated binding modes in the early stages of complexation.
Cardone A; Bornstein A; Pant HC; Brady M; Sriram R; Hassan SA
J Comput Chem; 2015 May; 36(13):983-95. PubMed ID: 25782918
[TBL] [Abstract][Full Text] [Related]
3. Self-adaptive multiscaling algorithm for efficient simulations of many-protein systems in crowded conditions.
Hassan SA
Phys Chem Chem Phys; 2018 Nov; 20(45):28544-28557. PubMed ID: 30421760
[TBL] [Abstract][Full Text] [Related]
4. DICE: A Monte Carlo Code for Molecular Simulation Including the Configurational Bias Monte Carlo Method.
Cezar HM; Canuto S; Coutinho K
J Chem Inf Model; 2020 Jul; 60(7):3472-3488. PubMed ID: 32470296
[TBL] [Abstract][Full Text] [Related]
5. Implicit treatment of solvent dispersion forces in protein simulations.
Hassan SA
J Comput Chem; 2014 Aug; 35(22):1621-9. PubMed ID: 24919463
[TBL] [Abstract][Full Text] [Related]
6. Water-exclusion and liquid-structure forces in implicit solvation.
Hassan SA; Steinbach PJ
J Phys Chem B; 2011 Dec; 115(49):14668-82. PubMed ID: 22007697
[TBL] [Abstract][Full Text] [Related]
7. Solvent-amino acid interaction energies in three-dimensional-lattice Monte Carlo simulations of a model 27-mer protein: Folding thermodynamics and kinetics.
Leonhard K; Prausnitz JM; Radke CJ
Protein Sci; 2004 Feb; 13(2):358-69. PubMed ID: 14739322
[TBL] [Abstract][Full Text] [Related]
8. Enhanced conformational sampling in Monte Carlo simulations of proteins: application to a constrained peptide.
Kidera A
Proc Natl Acad Sci U S A; 1995 Oct; 92(21):9886-9. PubMed ID: 7568238
[TBL] [Abstract][Full Text] [Related]
9. Coupling Monte Carlo, Variational Implicit Solvation, and Binary Level-Set for Simulations of Biomolecular Binding.
Zhang Z; Ricci CG; Fan C; Cheng LT; Li B; McCammon JA
J Chem Theory Comput; 2021 Apr; 17(4):2465-2478. PubMed ID: 33650860
[TBL] [Abstract][Full Text] [Related]
10. ES/IS: estimation of conformational free energy by combining dynamics simulations with explicit solvent with an implicit solvent continuum model.
Vorobjev YN; Hermans J
Biophys Chem; 1999 Apr; 78(1-2):195-205. PubMed ID: 10343388
[TBL] [Abstract][Full Text] [Related]
11. Predicting the acid/base behavior of proteins: a constant-pH Monte Carlo approach with generalized born solvent.
Aleksandrov A; Polydorides S; Archontis G; Simonson T
J Phys Chem B; 2010 Aug; 114(32):10634-48. PubMed ID: 20701391
[TBL] [Abstract][Full Text] [Related]
12. Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10-14 June 2012).
Foffi G; Pastore A; Piazza F; Temussi PA
Phys Biol; 2013 Aug; 10(4):040301. PubMed ID: 23912807
[TBL] [Abstract][Full Text] [Related]
13. MC-PHS: a Monte Carlo implementation of the primary hydration shell for protein folding and design.
Kentsis A; Mezei M; Osman R
Biophys J; 2003 Feb; 84(2 Pt 1):805-15. PubMed ID: 12547765
[TBL] [Abstract][Full Text] [Related]
14. Identifying native-like protein structures with scoring functions based on all-atom ECEPP force fields, implicit solvent models and structure relaxation.
Arnautova YA; Vorobjev YN; Vila JA; Scheraga HA
Proteins; 2009 Oct; 77(1):38-51. PubMed ID: 19384995
[TBL] [Abstract][Full Text] [Related]
15. Replica exchange simulations of transient encounter complexes in protein-protein association.
Kim YC; Tang C; Clore GM; Hummer G
Proc Natl Acad Sci U S A; 2008 Sep; 105(35):12855-60. PubMed ID: 18728193
[TBL] [Abstract][Full Text] [Related]
16. Enhancing water sampling of buried binding sites using nonequilibrium candidate Monte Carlo.
Bergazin TD; Ben-Shalom IY; Lim NM; Gill SC; Gilson MK; Mobley DL
J Comput Aided Mol Des; 2021 Feb; 35(2):167-177. PubMed ID: 32968887
[TBL] [Abstract][Full Text] [Related]
17. Enzyme-inhibitor association thermodynamics: explicit and continuum solvent studies.
Resat H; Marrone TJ; McCammon JA
Biophys J; 1997 Feb; 72(2 Pt 1):522-32. PubMed ID: 9017183
[TBL] [Abstract][Full Text] [Related]
18. A free-energy perturbation method based on Monte Carlo simulations using quantum mechanical calculations (QM/MC/FEP method): application to highly solvent-dependent reactions.
Hori K; Yamaguchi T; Uezu K; Sumimoto M
J Comput Chem; 2011 Apr; 32(5):778-86. PubMed ID: 21341291
[TBL] [Abstract][Full Text] [Related]
19. Biopolymer structure simulation and optimization via fragment regrowth Monte Carlo.
Zhang J; Kou SC; Liu JS
J Chem Phys; 2007 Jun; 126(22):225101. PubMed ID: 17581081
[TBL] [Abstract][Full Text] [Related]
20. The SAAP force field. A simple approach to a new all-atom protein force field by using single amino acid potential (SAAP) functions in various solvents.
Iwaoka M; Tomoda S
J Comput Chem; 2003 Jul; 24(10):1192-200. PubMed ID: 12820126
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
