269 related articles for article (PubMed ID: 34475217)
21. Predicting absolute ligand binding free energies to a simple model site.
Mobley DL; Graves AP; Chodera JD; McReynolds AC; Shoichet BK; Dill KA
J Mol Biol; 2007 Aug; 371(4):1118-34. PubMed ID: 17599350
[TBL] [Abstract][Full Text] [Related]
22. Flexibility and explicit solvent in molecular-dynamics-based docking of protein-glycosaminoglycan systems.
Samsonov SA; Gehrcke JP; Pisabarro MT
J Chem Inf Model; 2014 Feb; 54(2):582-92. PubMed ID: 24479827
[TBL] [Abstract][Full Text] [Related]
23. Incorporating backbone flexibility in MedusaDock improves ligand-binding pose prediction in the CSAR2011 docking benchmark.
Ding F; Dokholyan NV
J Chem Inf Model; 2013 Aug; 53(8):1871-9. PubMed ID: 23237273
[TBL] [Abstract][Full Text] [Related]
24. FlexE: efficient molecular docking considering protein structure variations.
Claussen H; Buning C; Rarey M; Lengauer T
J Mol Biol; 2001 Apr; 308(2):377-95. PubMed ID: 11327774
[TBL] [Abstract][Full Text] [Related]
25. CDOCKER and λ-dynamics for prospective prediction in D₃R Grand Challenge 2.
Ding X; Hayes RL; Vilseck JZ; Charles MK; Brooks CL
J Comput Aided Mol Des; 2018 Jan; 32(1):89-102. PubMed ID: 28884249
[TBL] [Abstract][Full Text] [Related]
26. Conformational energy range of ligands in protein crystal structures: The difficult quest for accurate understanding.
Peach ML; Cachau RE; Nicklaus MC
J Mol Recognit; 2017 Aug; 30(8):. PubMed ID: 28233410
[TBL] [Abstract][Full Text] [Related]
27. Free Energy Calculations Using the Movable Type Method with Molecular Dynamics Driven Protein-Ligand Sampling.
Liu W; Liu Z; Liu H; Westerhoff LM; Zheng Z
J Chem Inf Model; 2022 Nov; 62(22):5645-5665. PubMed ID: 36282990
[TBL] [Abstract][Full Text] [Related]
28. Effect of input differences on the results of docking calculations.
Feher M; Williams CI
J Chem Inf Model; 2009 Jul; 49(7):1704-14. PubMed ID: 19530660
[TBL] [Abstract][Full Text] [Related]
29. Crystal structure analysis, covalent docking, and molecular dynamics calculations reveal a conformational switch in PhaZ7 PHB depolymerase.
Kellici TF; Mavromoustakos T; Jendrossek D; Papageorgiou AC
Proteins; 2017 Jul; 85(7):1351-1361. PubMed ID: 28370478
[TBL] [Abstract][Full Text] [Related]
30. Improving docking results via reranking of ensembles of ligand poses in multiple X-ray protein conformations with MM-GBSA.
Greenidge PA; Kramer C; Mozziconacci JC; Sherman W
J Chem Inf Model; 2014 Oct; 54(10):2697-717. PubMed ID: 25266271
[TBL] [Abstract][Full Text] [Related]
31. The impact of molecular dynamics sampling on the performance of virtual screening against GPCRs.
Tarcsay A; Paragi G; Vass M; Jójárt B; Bogár F; Keserű GM
J Chem Inf Model; 2013 Nov; 53(11):2990-9. PubMed ID: 24116387
[TBL] [Abstract][Full Text] [Related]
32. Insights into molecular interactions between CaM and its inhibitors from molecular dynamics simulations and experimental data.
González-Andrade M; Rodríguez-Sotres R; Madariaga-Mazón A; Rivera-Chávez J; Mata R; Sosa-Peinado A; Del Pozo-Yauner L; Arias-Olguín II
J Biomol Struct Dyn; 2016; 34(1):78-91. PubMed ID: 25702612
[TBL] [Abstract][Full Text] [Related]
33. Molecular Dynamics in Mixed Solvents Reveals Protein-Ligand Interactions, Improves Docking, and Allows Accurate Binding Free Energy Predictions.
Arcon JP; Defelipe LA; Modenutti CP; López ED; Alvarez-Garcia D; Barril X; Turjanski AG; Martí MA
J Chem Inf Model; 2017 Apr; 57(4):846-863. PubMed ID: 28318252
[TBL] [Abstract][Full Text] [Related]
34. Structure-based virtual screening of the nociceptin receptor: hybrid docking and shape-based approaches for improved hit identification.
Daga PR; Polgar WE; Zaveri NT
J Chem Inf Model; 2014 Oct; 54(10):2732-43. PubMed ID: 25148595
[TBL] [Abstract][Full Text] [Related]
35. Fully automated flexible docking of ligands into flexible synthetic receptors using forward and inverse docking strategies.
Kämper A; Apostolakis J; Rarey M; Marian CM; Lengauer T
J Chem Inf Model; 2006; 46(2):903-11. PubMed ID: 16563022
[TBL] [Abstract][Full Text] [Related]
36. 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]
37. 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]
38. AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility.
Ravindranath PA; Forli S; Goodsell DS; Olson AJ; Sanner MF
PLoS Comput Biol; 2015 Dec; 11(12):e1004586. PubMed ID: 26629955
[TBL] [Abstract][Full Text] [Related]
39. HierVLS hierarchical docking protocol for virtual ligand screening of large-molecule databases.
Floriano WB; Vaidehi N; Zamanakos G; Goddard WA
J Med Chem; 2004 Jan; 47(1):56-71. PubMed ID: 14695820
[TBL] [Abstract][Full Text] [Related]
40. Protein-protein docking with multiple residue conformations and residue substitutions.
Lorber DM; Udo MK; Shoichet BK
Protein Sci; 2002 Jun; 11(6):1393-408. PubMed ID: 12021438
[TBL] [Abstract][Full Text] [Related]
[Previous] [Next] [New Search]
