473 related articles for article (PubMed ID: 17288418)
21. Modeling water molecules in protein-ligand docking using GOLD.
Verdonk ML; Chessari G; Cole JC; Hartshorn MJ; Murray CW; Nissink JW; Taylor RD; Taylor R
J Med Chem; 2005 Oct; 48(20):6504-15. PubMed ID: 16190776
[TBL] [Abstract][Full Text] [Related]
22. Robust classification of "relevant" water molecules in putative protein binding sites.
Amadasi A; Surface JA; Spyrakis F; Cozzini P; Mozzarelli A; Kellogg GE
J Med Chem; 2008 Feb; 51(4):1063-7. PubMed ID: 18232647
[TBL] [Abstract][Full Text] [Related]
23. Prediction of the binding energy for small molecules, peptides and proteins.
Schapira M; Totrov M; Abagyan R
J Mol Recognit; 1999; 12(3):177-90. PubMed ID: 10398408
[TBL] [Abstract][Full Text] [Related]
24. Absolute free energies of binding of peptide analogs to the HIV-1 protease from molecular dynamics simulations.
Bartels C; Widmer A; Ehrhardt C
J Comput Chem; 2005 Sep; 26(12):1294-305. PubMed ID: 15981257
[TBL] [Abstract][Full Text] [Related]
25. 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]
26. Hydration energy landscape of the active site cavity in cytochrome P450cam.
Helms V; Wade RC
Proteins; 1998 Aug; 32(3):381-96. PubMed ID: 9715913
[TBL] [Abstract][Full Text] [Related]
27. Accurate prediction of protonation state as a prerequisite for reliable MM-PB(GB)SA binding free energy calculations of HIV-1 protease inhibitors.
Wittayanarakul K; Hannongbua S; Feig M
J Comput Chem; 2008 Apr; 29(5):673-85. PubMed ID: 17849388
[TBL] [Abstract][Full Text] [Related]
28. Hydration properties of ligands and drugs in protein binding sites: tightly-bound, bridging water molecules and their effects and consequences on molecular design strategies.
García-Sosa AT
J Chem Inf Model; 2013 Jun; 53(6):1388-405. PubMed ID: 23662606
[TBL] [Abstract][Full Text] [Related]
29. Glycogen phosphorylase inhibitors: a free energy perturbation analysis of glucopyranose spirohydantoin analogues.
Archontis G; Watson KA; Xie Q; Andreou G; Chrysina ED; Zographos SE; Oikonomakos NG; Karplus M
Proteins; 2005 Dec; 61(4):984-98. PubMed ID: 16245298
[TBL] [Abstract][Full Text] [Related]
30. Getting it right: modeling of pH, solvent and "nearly" everything else in virtual screening of biological targets.
Kellogg GE; Fornabaio M; Spyrakis F; Lodola A; Cozzini P; Mozzarelli A; Abraham DJ
J Mol Graph Model; 2004 Jul; 22(6):479-86. PubMed ID: 15182807
[TBL] [Abstract][Full Text] [Related]
31. Characterization of the galectin-1 carbohydrate recognition domain in terms of solvent occupancy.
Di Lella S; Martí MA; Alvarez RM; Estrin DA; Ricci JC
J Phys Chem B; 2007 Jun; 111(25):7360-6. PubMed ID: 17523619
[TBL] [Abstract][Full Text] [Related]
32. Structure-based ligand design by dynamically assembling molecular building blocks at binding site.
Liu H; Duan Z; Luo Q; Shi Y
Proteins; 1999 Sep; 36(4):462-70. PubMed ID: 10450088
[TBL] [Abstract][Full Text] [Related]
33. Role of structural water molecule in HIV protease-inhibitor complexes: a QM/MM study.
Suresh CH; Vargheese AM; Vijayalakshmi KP; Mohan N; Koga N
J Comput Chem; 2008 Aug; 29(11):1840-9. PubMed ID: 18351589
[TBL] [Abstract][Full Text] [Related]
34. Computation of the contribution from the cavity effect to protein-ligand binding free energy.
Grigoriev FV; Gabin SN; Romanov AN; Sulimov VB
J Phys Chem B; 2008 Dec; 112(48):15355-60. PubMed ID: 18991438
[TBL] [Abstract][Full Text] [Related]
35. Solvation studies of DMP323 and A76928 bound to HIV protease: analysis of water sites using grand canonical Monte Carlo simulations.
Marrone TJ; Resat H; Hodge CN; Chang CH; McCammon JA
Protein Sci; 1998 Mar; 7(3):573-9. PubMed ID: 9541388
[TBL] [Abstract][Full Text] [Related]
36. Water at biomolecular binding interfaces.
Li Z; Lazaridis T
Phys Chem Chem Phys; 2007 Feb; 9(5):573-81. PubMed ID: 17242738
[TBL] [Abstract][Full Text] [Related]
37. Nonequilibrium, multiple-timescale simulations of ligand-receptor interactions in structured protein systems.
Zhang Y; Peters MH; Li Y
Proteins; 2003 Aug; 52(3):339-48. PubMed ID: 12866048
[TBL] [Abstract][Full Text] [Related]
38. Calculation of affinities of peptides for proteins.
Donnini S; Juffer AH
J Comput Chem; 2004 Feb; 25(3):393-411. PubMed ID: 14696074
[TBL] [Abstract][Full Text] [Related]
39. Accurate predictions of nonpolar solvation free energies require explicit consideration of binding-site hydration.
Genheden S; Mikulskis P; Hu L; Kongsted J; Söderhjelm P; Ryde U
J Am Chem Soc; 2011 Aug; 133(33):13081-92. PubMed ID: 21728337
[TBL] [Abstract][Full Text] [Related]
40. Exhaustive docking of molecular fragments with electrostatic solvation.
Majeux N; Scarsi M; Apostolakis J; Ehrhardt C; Caflisch A
Proteins; 1999 Oct; 37(1):88-105. PubMed ID: 10451553
[TBL] [Abstract][Full Text] [Related]
[Previous] [Next] [New Search]