151 related articles for article (PubMed ID: 31117183)
1. Fragment-Based Ligand-Protein Contact Statistics: Application to Docking Simulations.
Macari G; Toti D; Del Moro C; Polticelli F
Int J Mol Sci; 2019 May; 20(10):. PubMed ID: 31117183
[TBL] [Abstract][Full Text] [Related]
2. Comparative assessment of scoring functions on an updated benchmark: 2. Evaluation methods and general results.
Li Y; Han L; Liu Z; Wang R
J Chem Inf Model; 2014 Jun; 54(6):1717-36. PubMed ID: 24708446
[TBL] [Abstract][Full Text] [Related]
3. 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]
4. LEADS-FRAG: A Benchmark Data Set for Assessment of Fragment Docking Performance.
Chachulski L; Windshügel B
J Chem Inf Model; 2020 Dec; 60(12):6544-6554. PubMed ID: 33289563
[TBL] [Abstract][Full Text] [Related]
5. Forging the Basis for Developing Protein-Ligand Interaction Scoring Functions.
Liu Z; Su M; Han L; Liu J; Yang Q; Li Y; Wang R
Acc Chem Res; 2017 Feb; 50(2):302-309. PubMed ID: 28182403
[TBL] [Abstract][Full Text] [Related]
6. 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]
7. PLHINT: A knowledge-driven computational approach based on the intermolecular H bond interactions at the protein-ligand interface from docking solutions.
Kumar SP
J Mol Graph Model; 2018 Jan; 79():194-212. PubMed ID: 29241118
[TBL] [Abstract][Full Text] [Related]
8. Evaluation of AutoDock and AutoDock Vina on the CASF-2013 Benchmark.
Gaillard T
J Chem Inf Model; 2018 Aug; 58(8):1697-1706. PubMed ID: 29989806
[TBL] [Abstract][Full Text] [Related]
9. Local Interaction Density (LID), a Fast and Efficient Tool to Prioritize Docking Poses.
Jacquemard C; Tran-Nguyen VK; Drwal MN; Rognan D; Kellenberger E
Molecules; 2019 Jul; 24(14):. PubMed ID: 31323745
[TBL] [Abstract][Full Text] [Related]
10. Comprehensive evaluation of ten docking programs on a diverse set of protein-ligand complexes: the prediction accuracy of sampling power and scoring power.
Wang Z; Sun H; Yao X; Li D; Xu L; Li Y; Tian S; Hou T
Phys Chem Chem Phys; 2016 May; 18(18):12964-75. PubMed ID: 27108770
[TBL] [Abstract][Full Text] [Related]
11. Beware of machine learning-based scoring functions-on the danger of developing black boxes.
Gabel J; Desaphy J; Rognan D
J Chem Inf Model; 2014 Oct; 54(10):2807-15. PubMed ID: 25207678
[TBL] [Abstract][Full Text] [Related]
12. Comparative assessment of scoring functions on an updated benchmark: 1. Compilation of the test set.
Li Y; Liu Z; Li J; Han L; Liu J; Zhao Z; Wang R
J Chem Inf Model; 2014 Jun; 54(6):1700-16. PubMed ID: 24716849
[TBL] [Abstract][Full Text] [Related]
13. Ligand-Binding-Site Refinement to Generate Reliable Holo Protein Structure Conformations from Apo Structures.
Guterres H; Park SJ; Jiang W; Im W
J Chem Inf Model; 2021 Jan; 61(1):535-546. PubMed ID: 33337877
[TBL] [Abstract][Full Text] [Related]
14. Investigation of MM-PBSA rescoring of docking poses.
Thompson DC; Humblet C; Joseph-McCarthy D
J Chem Inf Model; 2008 May; 48(5):1081-91. PubMed ID: 18465849
[TBL] [Abstract][Full Text] [Related]
15. Ligand- and receptor-based docking with LiBELa.
dos Santos Muniz H; Nascimento AS
J Comput Aided Mol Des; 2015 Aug; 29(8):713-23. PubMed ID: 26141308
[TBL] [Abstract][Full Text] [Related]
16. FlexAID: Revisiting Docking on Non-Native-Complex Structures.
Gaudreault F; Najmanovich RJ
J Chem Inf Model; 2015 Jul; 55(7):1323-36. PubMed ID: 26076070
[TBL] [Abstract][Full Text] [Related]
17. Assessing protein-ligand interaction scoring functions with the CASF-2013 benchmark.
Li Y; Su M; Liu Z; Li J; Liu J; Han L; Wang R
Nat Protoc; 2018 Apr; 13(4):666-680. PubMed ID: 29517771
[TBL] [Abstract][Full Text] [Related]
18. 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]
19. Machine-learning scoring functions for identifying native poses of ligands docked to known and novel proteins.
Ashtawy HM; Mahapatra NR
BMC Bioinformatics; 2015; 16 Suppl 6(Suppl 6):S3. PubMed ID: 25916860
[TBL] [Abstract][Full Text] [Related]
20. The scoring bias in reverse docking and the score normalization strategy to improve success rate of target fishing.
Luo Q; Zhao L; Hu J; Jin H; Liu Z; Zhang L
PLoS One; 2017; 12(2):e0171433. PubMed ID: 28196116
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]