283 related articles for article (PubMed ID: 18280498)
21. Testing inhomogeneous solvation theory in structure-based ligand discovery.
Balius TE; Fischer M; Stein RM; Adler TB; Nguyen CN; Cruz A; Gilson MK; Kurtzman T; Shoichet BK
Proc Natl Acad Sci U S A; 2017 Aug; 114(33):E6839-E6846. PubMed ID: 28760952
[TBL] [Abstract][Full Text] [Related]
22. Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking.
Hou T; Wang J; Li Y; Wang W
J Comput Chem; 2011 Apr; 32(5):866-77. PubMed ID: 20949517
[TBL] [Abstract][Full Text] [Related]
23. Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations.
Misini Ignjatović M; Caldararu O; Dong G; Muñoz-Gutierrez C; Adasme-Carreño F; Ryde U
J Comput Aided Mol Des; 2016 Sep; 30(9):707-730. PubMed ID: 27565797
[TBL] [Abstract][Full Text] [Related]
24. Rescoring of docking poses under Occam's Razor: are there simpler solutions?
Zhenin M; Bahia MS; Marcou G; Varnek A; Senderowitz H; Horvath D
J Comput Aided Mol Des; 2018 Sep; 32(9):877-888. PubMed ID: 30173397
[TBL] [Abstract][Full Text] [Related]
25. Negative Image-Based Rescoring: Using Cavity Information to Improve Docking Screening.
Pentikäinen OT; Postila PA
Methods Mol Biol; 2021; 2266():141-154. PubMed ID: 33759125
[TBL] [Abstract][Full Text] [Related]
26. Application of a post-docking procedure based on MM-PBSA and MM-GBSA on single and multiple protein conformations.
Sgobba M; Caporuscio F; Anighoro A; Portioli C; Rastelli G
Eur J Med Chem; 2012 Dec; 58():431-40. PubMed ID: 23153814
[TBL] [Abstract][Full Text] [Related]
27. Postprocessing of docked protein-ligand complexes using implicit solvation models.
Lindström A; Edvinsson L; Johansson A; Andersson CD; Andersson IE; Raubacher F; Linusson A
J Chem Inf Model; 2011 Feb; 51(2):267-82. PubMed ID: 21309544
[TBL] [Abstract][Full Text] [Related]
28. Binding estimation after refinement, a new automated procedure for the refinement and rescoring of docked ligands in virtual screening.
Rastelli G; Degliesposti G; Del Rio A; Sgobba M
Chem Biol Drug Des; 2009 Mar; 73(3):283-6. PubMed ID: 19207463
[TBL] [Abstract][Full Text] [Related]
29. Docking pose selection by interaction pattern graph similarity: application to the D3R grand challenge 2015.
Slynko I; Da Silva F; Bret G; Rognan D
J Comput Aided Mol Des; 2016 Sep; 30(9):669-683. PubMed ID: 27480696
[TBL] [Abstract][Full Text] [Related]
30. Application of docking and QM/MM-GBSA rescoring to screen for novel Myt1 kinase inhibitors.
Wichapong K; Rohe A; Platzer C; Slynko I; Erdmann F; Schmidt M; Sippl W
J Chem Inf Model; 2014 Mar; 54(3):881-93. PubMed ID: 24490903
[TBL] [Abstract][Full Text] [Related]
31. Comparative docking of dual conformations in human fatty acid synthase thioesterase domain reveals potential binding cavity for virtual screening of ligands.
John A; Vetrivel U; Subramanian K; Deepa PR
J Biomol Struct Dyn; 2017 May; 35(6):1350-1366. PubMed ID: 27145135
[TBL] [Abstract][Full Text] [Related]
32. Efficient conformational sampling and weak scoring in docking programs? Strategy of the wisdom of crowds.
Chaput L; Mouawad L
J Cheminform; 2017 Jun; 9(1):37. PubMed ID: 29086077
[TBL] [Abstract][Full Text] [Related]
33. Predicting fragment binding poses using a combined MCSS MM-GBSA approach.
Haider MK; Bertrand HO; Hubbard RE
J Chem Inf Model; 2011 May; 51(5):1092-105. PubMed ID: 21528911
[TBL] [Abstract][Full Text] [Related]
34. farPPI: a webserver for accurate prediction of protein-ligand binding structures for small-molecule PPI inhibitors by MM/PB(GB)SA methods.
Wang Z; Wang X; Li Y; Lei T; Wang E; Li D; Kang Y; Zhu F; Hou T
Bioinformatics; 2019 May; 35(10):1777-1779. PubMed ID: 30329012
[TBL] [Abstract][Full Text] [Related]
35. A statistical rescoring scheme for protein-ligand docking: Consideration of entropic effect.
Lee J; Seok C
Proteins; 2008 Feb; 70(3):1074-83. PubMed ID: 18076034
[TBL] [Abstract][Full Text] [Related]
36. Evaluation of docking performance: comparative data on docking algorithms.
Kontoyianni M; McClellan LM; Sokol GS
J Med Chem; 2004 Jan; 47(3):558-65. PubMed ID: 14736237
[TBL] [Abstract][Full Text] [Related]
37. Assessing the performance of MM/PBSA and MM/GBSA methods. 9. Prediction reliability of binding affinities and binding poses for protein-peptide complexes.
Weng G; Wang E; Chen F; Sun H; Wang Z; Hou T
Phys Chem Chem Phys; 2019 May; 21(19):10135-10145. PubMed ID: 31062799
[TBL] [Abstract][Full Text] [Related]
38. Development of Effective Therapeutic Molecule from Natural Sources against Coronavirus Protease.
Fadaka AO; Sibuyi NRS; Martin DR; Klein A; Madiehe A; Meyer M
Int J Mol Sci; 2021 Aug; 22(17):. PubMed ID: 34502340
[TBL] [Abstract][Full Text] [Related]
39. Ligand-Enhanced Negative Images Optimized for Docking Rescoring.
Kurkinen ST; Lehtonen JV; Pentikäinen OT; Postila PA
Int J Mol Sci; 2022 Jul; 23(14):. PubMed ID: 35887220
[TBL] [Abstract][Full Text] [Related]
40. Roles for ordered and bulk solvent in ligand recognition and docking in two related cavities.
Barelier S; Boyce SE; Fish I; Fischer M; Goodin DB; Shoichet BK
PLoS One; 2013; 8(7):e69153. PubMed ID: 23874896
[TBL] [Abstract][Full Text] [Related]
[Previous] [Next] [New Search]