224 related articles for article (PubMed ID: 32383873)
1. Higher Accuracy Achieved for Protein-Ligand Binding Pose Prediction by Elastic Network Model-Based Ensemble Docking.
Wang A; Zhang Y; Chu H; Liao C; Zhang Z; Li G
J Chem Inf Model; 2020 Jun; 60(6):2939-2950. PubMed ID: 32383873
[TBL] [Abstract][Full Text] [Related]
2. 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]
3. Plasticity of the Binding Site of Renin: Optimized Selection of Protein Structures for Ensemble Docking.
Strecker C; Meyer B
J Chem Inf Model; 2018 May; 58(5):1121-1131. PubMed ID: 29683661
[TBL] [Abstract][Full Text] [Related]
4. Improving the Accuracy of Protein-Ligand Binding Mode Prediction Using a Molecular Dynamics-Based Pocket Generation Approach.
Araki M; Iwata H; Ma B; Fujita A; Terayama K; Sagae Y; Ono F; Tsuda K; Kamiya N; Okuno Y
J Comput Chem; 2018 Dec; 39(32):2679-2689. PubMed ID: 30515903
[TBL] [Abstract][Full Text] [Related]
5. Holo-like and Druggable Protein Conformations from Enhanced Sampling of Binding Pocket Volume and Shape.
Basciu A; Malloci G; Pietrucci F; Bonvin AMJJ; Vargiu AV
J Chem Inf Model; 2019 Apr; 59(4):1515-1528. PubMed ID: 30883122
[TBL] [Abstract][Full Text] [Related]
6. Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach.
Lam PC; Abagyan R; Totrov M
J Comput Aided Mol Des; 2018 Jan; 32(1):187-198. PubMed ID: 28887659
[TBL] [Abstract][Full Text] [Related]
7. 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]
8. Ensemble docking of multiple protein structures: considering protein structural variations in molecular docking.
Huang SY; Zou X
Proteins; 2007 Feb; 66(2):399-421. PubMed ID: 17096427
[TBL] [Abstract][Full Text] [Related]
9. Flexible CDOCKER: Hybrid Searching Algorithm and Scoring Function with Side Chain Conformational Entropy.
Wu Y; Brooks CL
J Chem Inf Model; 2021 Nov; 61(11):5535-5549. PubMed ID: 34704754
[TBL] [Abstract][Full Text] [Related]
10. Ligand Docking to Intermediate and Close-To-Bound Conformers Generated by an Elastic Network Model Based Algorithm for Highly Flexible Proteins.
Kurkcuoglu Z; Doruker P
PLoS One; 2016; 11(6):e0158063. PubMed ID: 27348230
[TBL] [Abstract][Full Text] [Related]
11. Ensemble learning from ensemble docking: revisiting the optimum ensemble size problem.
Mohammadi S; Narimani Z; Ashouri M; Firouzi R; Karimi-Jafari MH
Sci Rep; 2022 Jan; 12(1):410. PubMed ID: 35013496
[TBL] [Abstract][Full Text] [Related]
12. 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]
13. 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]
14. A flexible-protein molecular docking study of the binding of ruthenium complex compounds to PIM1, GSK-3β, and CDK2/Cyclin A protein kinases.
Liu Y; Agrawal NJ; Radhakrishnan R
J Mol Model; 2013 Jan; 19(1):371-82. PubMed ID: 22926267
[TBL] [Abstract][Full Text] [Related]
15. Dynamic Docking of Macrocycles in Bound and Unbound Protein Structures with DynaDock.
Meixner M; Zachmann M; Metzler S; Scheerer J; Zacharias M; Antes I
J Chem Inf Model; 2022 Jul; 62(14):3426-3441. PubMed ID: 35796228
[TBL] [Abstract][Full Text] [Related]
16. Boosted neural networks scoring functions for accurate ligand docking and ranking.
Ashtawy HM; Mahapatra NR
J Bioinform Comput Biol; 2018 Apr; 16(2):1850004. PubMed ID: 29495922
[TBL] [Abstract][Full Text] [Related]
17. GWOVina: A grey wolf optimization approach to rigid and flexible receptor docking.
Wong KM; Tai HK; Siu SWI
Chem Biol Drug Des; 2021 Jan; 97(1):97-110. PubMed ID: 32679606
[TBL] [Abstract][Full Text] [Related]
18. Assessing an ensemble docking-based virtual screening strategy for kinase targets by considering protein flexibility.
Tian S; Sun H; Pan P; Li D; Zhen X; Li Y; Hou T
J Chem Inf Model; 2014 Oct; 54(10):2664-79. PubMed ID: 25233367
[TBL] [Abstract][Full Text] [Related]
19. 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]
20. GalaxyDock: protein-ligand docking with flexible protein side-chains.
Shin WH; Seok C
J Chem Inf Model; 2012 Dec; 52(12):3225-32. PubMed ID: 23198780
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
