111 related articles for article (PubMed ID: 26352326)
1. Enhanced molecular dynamics sampling of drug target conformations.
Rodriguez-Bussey IG; Doshi U; Hamelberg D
Biopolymers; 2016 Jan; 105(1):35-42. PubMed ID: 26352326
[TBL] [Abstract][Full Text] [Related]
2. Towards fast, rigorous and efficient conformational sampling of biomolecules: Advances in accelerated molecular dynamics.
Doshi U; Hamelberg D
Biochim Biophys Acta; 2015 May; 1850(5):878-888. PubMed ID: 25153688
[TBL] [Abstract][Full Text] [Related]
3. Improved Statistical Sampling and Accuracy with Accelerated Molecular Dynamics on Rotatable Torsions.
Doshi U; Hamelberg D
J Chem Theory Comput; 2012 Nov; 8(11):4004-12. PubMed ID: 26605567
[TBL] [Abstract][Full Text] [Related]
4. Cyclophilin A inhibition: targeting transition-state-bound enzyme conformations for structure-based drug design.
Nagaraju M; McGowan LC; Hamelberg D
J Chem Inf Model; 2013 Feb; 53(2):403-10. PubMed ID: 23312027
[TBL] [Abstract][Full Text] [Related]
5. Achieving Rigorous Accelerated Conformational Sampling in Explicit Solvent.
Doshi U; Hamelberg D
J Phys Chem Lett; 2014 Apr; 5(7):1217-24. PubMed ID: 26274474
[TBL] [Abstract][Full Text] [Related]
6. Protein flexibility in ligand docking and virtual screening to protein kinases.
Cavasotto CN; Abagyan RA
J Mol Biol; 2004 Mar; 337(1):209-25. PubMed ID: 15001363
[TBL] [Abstract][Full Text] [Related]
7. Ensemble-based docking using biased molecular dynamics.
Campbell AJ; Lamb ML; Joseph-McCarthy D
J Chem Inf Model; 2014 Jul; 54(7):2127-38. PubMed ID: 24881672
[TBL] [Abstract][Full Text] [Related]
8. 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]
9. Modeling correlated main-chain motions in proteins for flexible molecular recognition.
Zavodszky MI; Lei M; Thorpe MF; Day AR; Kuhn LA
Proteins; 2004 Nov; 57(2):243-61. PubMed ID: 15340912
[TBL] [Abstract][Full Text] [Related]
10. Integrating Molecular Docking and Molecular Dynamics Simulations.
Santos LHS; Ferreira RS; Caffarena ER
Methods Mol Biol; 2019; 2053():13-34. PubMed ID: 31452096
[TBL] [Abstract][Full Text] [Related]
11. Shape-based virtual screening, docking, and molecular dynamics simulations to identify Mtb-ASADH inhibitors.
Kumar R; Garg P; Bharatam PV
J Biomol Struct Dyn; 2015; 33(5):1082-93. PubMed ID: 24875451
[TBL] [Abstract][Full Text] [Related]
12. Tackling the conformational sampling of larger flexible compounds and macrocycles in pharmacology and drug discovery.
Chen IJ; Foloppe N
Bioorg Med Chem; 2013 Dec; 21(24):7898-920. PubMed ID: 24184215
[TBL] [Abstract][Full Text] [Related]
13. Discovering potent small molecule inhibitors of cyclophilin A using de novo drug design approach.
Ni S; Yuan Y; Huang J; Mao X; Lv M; Zhu J; Shen X; Pei J; Lai L; Jiang H; Li J
J Med Chem; 2009 Sep; 52(17):5295-8. PubMed ID: 19691347
[TBL] [Abstract][Full Text] [Related]
14. Molecular dynamics in drug design.
Zhao H; Caflisch A
Eur J Med Chem; 2015 Feb; 91():4-14. PubMed ID: 25108504
[TBL] [Abstract][Full Text] [Related]
15. Accelerated molecular dynamics in computational drug design.
Wereszczynski J; McCammon JA
Methods Mol Biol; 2012; 819():515-24. PubMed ID: 22183555
[TBL] [Abstract][Full Text] [Related]
16. Computational sampling of a cryptic drug binding site in a protein receptor: explicit solvent molecular dynamics and inhibitor docking to p38 MAP kinase.
Frembgen-Kesner T; Elcock AH
J Mol Biol; 2006 May; 359(1):202-14. PubMed ID: 16616932
[TBL] [Abstract][Full Text] [Related]
17. Protein Flexibility in Docking-Based Virtual Screening: Discovery of Novel Lymphoid-Specific Tyrosine Phosphatase Inhibitors Using Multiple Crystal Structures.
Hou X; Li K; Yu X; Sun JP; Fang H
J Chem Inf Model; 2015 Sep; 55(9):1973-83. PubMed ID: 26360643
[TBL] [Abstract][Full Text] [Related]
18. 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]
19. On the use of molecular dynamics receptor conformations for virtual screening.
Nichols SE; Baron R; McCammon JA
Methods Mol Biol; 2012; 819():93-103. PubMed ID: 22183532
[TBL] [Abstract][Full Text] [Related]
20. Enrichment of druggable conformations from apo protein structures using cosolvent-accelerated molecular dynamics.
Kalenkiewicz A; Grant BJ; Yang CY
Biology (Basel); 2015 Apr; 4(2):344-66. PubMed ID: 25906084
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
