362 related articles for article (PubMed ID: 16426059)
1. Grand canonical Monte Carlo simulation of ligand-protein binding.
Clark M; Guarnieri F; Shkurko I; Wiseman J
J Chem Inf Model; 2006; 46(1):231-42. PubMed ID: 16426059
[TBL] [Abstract][Full Text] [Related]
2. Grand canonical free-energy calculations of protein-ligand binding.
Clark M; Meshkat S; Wiseman JS
J Chem Inf Model; 2009 Apr; 49(4):934-43. PubMed ID: 19309088
[TBL] [Abstract][Full Text] [Related]
3. Fragment-based computation of binding free energies by systematic sampling.
Clark M; Meshkat S; Talbot GT; Carnevali P; Wiseman JS
J Chem Inf Model; 2009 Aug; 49(8):1901-13. PubMed ID: 19610599
[TBL] [Abstract][Full Text] [Related]
4. Ligand mapping on protein surfaces by the 3D-RISM theory: toward computational fragment-based drug design.
Imai T; Oda K; Kovalenko A; Hirata F; Kidera A
J Am Chem Soc; 2009 Sep; 131(34):12430-40. PubMed ID: 19655800
[TBL] [Abstract][Full Text] [Related]
5. Modeling protein-small molecule interactions: structure and thermodynamics of noble gases binding in a cavity in mutant phage T4 lysozyme L99A.
Mann G; Hermans J
J Mol Biol; 2000 Sep; 302(4):979-89. PubMed ID: 10993736
[TBL] [Abstract][Full Text] [Related]
6. Algorithms for computational solvent mapping of proteins.
Kortvelyesi T; Dennis S; Silberstein M; Brown L; Vajda S
Proteins; 2003 May; 51(3):340-51. PubMed ID: 12696046
[TBL] [Abstract][Full Text] [Related]
7. Protein-ligand binding free energies from exhaustive docking.
Purisima EO; Hogues H
J Phys Chem B; 2012 Jun; 116(23):6872-9. PubMed ID: 22432509
[TBL] [Abstract][Full Text] [Related]
8. Monte Carlo simulation of protein folding in the presence of residue-specific binding sites.
Rossinsky E; Srebnik S
Biopolymers; 2005 Dec; 79(5):259-68. PubMed ID: 16134169
[TBL] [Abstract][Full Text] [Related]
9. Molecular insight into pseudolysin inhibition using the MM-PBSA and LIE methods.
Adekoya OA; Willassen NP; Sylte I
J Struct Biol; 2006 Feb; 153(2):129-44. PubMed ID: 16376106
[TBL] [Abstract][Full Text] [Related]
10. Towards understanding the mechanisms of molecular recognition by computer simulations of ligand-protein interactions.
Verkhivker GM; Rejto PA; Bouzida D; Arthurs S; Colson AB; Freer ST; Gehlhaar DK; Larson V; Luty BA; Marrone T; Rose PW
J Mol Recognit; 1999; 12(6):371-89. PubMed ID: 10611647
[TBL] [Abstract][Full Text] [Related]
11. Method for computing protein binding affinity.
Karney CF; Ferrara JE; Brunner S
J Comput Chem; 2005 Feb; 26(3):243-51. PubMed ID: 15614799
[TBL] [Abstract][Full Text] [Related]
12. Role of proximal His93 in nitric oxide binding to metmyoglobin. Application of continuum solvation in Monte Carlo protein simulations.
Keserü GM; Menyhárd DK
Biochemistry; 1999 May; 38(20):6614-22. PubMed ID: 10350480
[TBL] [Abstract][Full Text] [Related]
13. Calculation of the standard binding free energy of sparsomycin to the ribosomal peptidyl-transferase P-site using molecular dynamics simulations with restraining potentials.
Ge X; Roux B
J Mol Recognit; 2010; 23(2):128-41. PubMed ID: 20151411
[TBL] [Abstract][Full Text] [Related]
14. Computational approach to de novo discovery of fragment binding for novel protein states.
Konteatis ZD; Klon AE; Zou J; Meshkat S
Methods Enzymol; 2011; 493():357-80. PubMed ID: 21371598
[TBL] [Abstract][Full Text] [Related]
15. Computation of binding free energy with molecular dynamics and grand canonical Monte Carlo simulations.
Deng Y; Roux B
J Chem Phys; 2008 Mar; 128(11):115103. PubMed ID: 18361618
[TBL] [Abstract][Full Text] [Related]
16. A multistep approach to structure-based drug design: studying ligand binding at the human neutrophil elastase.
Steinbrecher T; Case DA; Labahn A
J Med Chem; 2006 Mar; 49(6):1837-44. PubMed ID: 16539369
[TBL] [Abstract][Full Text] [Related]
17. Characterization of protein-ligand interaction sites using experimental and computational methods.
Vajda S; Guarnieri F
Curr Opin Drug Discov Devel; 2006 May; 9(3):354-62. PubMed ID: 16729732
[TBL] [Abstract][Full Text] [Related]
18. Molecular mechanics methods for predicting protein-ligand binding.
Huang N; Kalyanaraman C; Bernacki K; Jacobson MP
Phys Chem Chem Phys; 2006 Nov; 8(44):5166-77. PubMed ID: 17203140
[TBL] [Abstract][Full Text] [Related]
19. Fitting an inhibitor into the active site of thermolysin: a molecular dynamics case study.
Wasserman ZR; Hodge CN
Proteins; 1996 Feb; 24(2):227-37. PubMed ID: 8820489
[TBL] [Abstract][Full Text] [Related]
20. Molecular anchors with large stability gaps ensure linear binding free energy relationships for hydrophobic substituents.
Rejto PA; Verkhivker GM
Pac Symp Biocomput; 1998; ():362-73. PubMed ID: 9697196
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]