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Results: 1 to 20 of 129

1.

Surflex-Dock: Docking benchmarks and real-world application.

Spitzer R, Jain AN.

J Comput Aided Mol Des. 2012 Jun;26(6):687-99. doi: 10.1007/s10822-011-9533-y. Epub 2012 May 9.

PMID:
22569590
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Comparison of several molecular docking programs: pose prediction and virtual screening accuracy.

Cross JB, Thompson DC, Rai BK, Baber JC, Fan KY, Hu Y, Humblet C.

J Chem Inf Model. 2009 Jun;49(6):1455-74. doi: 10.1021/ci900056c.

PMID:
19476350
[PubMed - indexed for MEDLINE]
3.

Docking and scoring with ICM: the benchmarking results and strategies for improvement.

Neves MA, Totrov M, Abagyan R.

J Comput Aided Mol Des. 2012 Jun;26(6):675-86. doi: 10.1007/s10822-012-9547-0. Epub 2012 May 9.

PMID:
22569591
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Pose prediction and virtual screening performance of GOLD scoring functions in a standardized test.

Liebeschuetz JW, Cole JC, Korb O.

J Comput Aided Mol Des. 2012 Jun;26(6):737-48. doi: 10.1007/s10822-012-9551-4. Epub 2012 Feb 28.

PMID:
22371207
[PubMed - indexed for MEDLINE]
5.

Effects of protein conformation in docking: improved pose prediction through protein pocket adaptation.

Jain AN.

J Comput Aided Mol Des. 2009 Jun;23(6):355-74. doi: 10.1007/s10822-009-9266-3. Epub 2009 Apr 2.

PMID:
19340588
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Variability in docking success rates due to dataset preparation.

Corbeil CR, Williams CI, Labute P.

J Comput Aided Mol Des. 2012 Jun;26(6):775-86. doi: 10.1007/s10822-012-9570-1. Epub 2012 May 8.

PMID:
22566074
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Docking performance of the glide program as evaluated on the Astex and DUD datasets: a complete set of glide SP results and selected results for a new scoring function integrating WaterMap and glide.

Repasky MP, Murphy RB, Banks JL, Greenwood JR, Tubert-Brohman I, Bhat S, Friesner RA.

J Comput Aided Mol Des. 2012 Jun;26(6):787-99. doi: 10.1007/s10822-012-9575-9. Epub 2012 May 11.

PMID:
22576241
[PubMed - indexed for MEDLINE]
8.

Nonlinear scoring functions for similarity-based ligand docking and binding affinity prediction.

Brylinski M.

J Chem Inf Model. 2013 Nov 25;53(11):3097-112. doi: 10.1021/ci400510e. Epub 2013 Nov 11.

PMID:
24171431
[PubMed - indexed for MEDLINE]
9.

Evaluation of docking performance: comparative data on docking algorithms.

Kontoyianni M, McClellan LM, Sokol GS.

J Med Chem. 2004 Jan 29;47(3):558-65.

PMID:
14736237
[PubMed - indexed for MEDLINE]
10.

Protein flexibility in ligand docking and virtual screening to protein kinases.

Cavasotto CN, Abagyan RA.

J Mol Biol. 2004 Mar 12;337(1):209-25.

PMID:
15001363
[PubMed - indexed for MEDLINE]
11.

Lead Finder docking and virtual screening evaluation with Astex and DUD test sets.

Novikov FN, Stroylov VS, Zeifman AA, Stroganov OV, Kulkov V, Chilov GG.

J Comput Aided Mol Des. 2012 Jun;26(6):725-35. doi: 10.1007/s10822-012-9549-y. Epub 2012 May 9.

PMID:
22569592
[PubMed - indexed for MEDLINE]
12.

Ensemble docking of multiple protein structures: considering protein structural variations in molecular docking.

Huang SY, Zou X.

Proteins. 2007 Feb 1;66(2):399-421.

PMID:
17096427
[PubMed - indexed for MEDLINE]
13.

Lead finder: an approach to improve accuracy of protein-ligand docking, binding energy estimation, and virtual screening.

Stroganov OV, Novikov FN, Stroylov VS, Kulkov V, Chilov GG.

J Chem Inf Model. 2008 Dec;48(12):2371-85. doi: 10.1021/ci800166p.

PMID:
19007114
[PubMed - indexed for MEDLINE]
14.

FRED and HYBRID docking performance on standardized datasets.

McGann M.

J Comput Aided Mol Des. 2012 Aug;26(8):897-906. doi: 10.1007/s10822-012-9584-8. Epub 2012 Jun 5.

PMID:
22669221
[PubMed - indexed for MEDLINE]
15.

FlexE: efficient molecular docking considering protein structure variations.

Claussen H, Buning C, Rarey M, Lengauer T.

J Mol Biol. 2001 Apr 27;308(2):377-95.

PMID:
11327774
[PubMed - indexed for MEDLINE]
16.

FINDSITE(comb): a threading/structure-based, proteomic-scale virtual ligand screening approach.

Zhou H, Skolnick J.

J Chem Inf Model. 2013 Jan 28;53(1):230-40. doi: 10.1021/ci300510n. Epub 2012 Dec 28.

PMID:
23240691
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Protein Alpha Shape (PAS) Dock: a new gaussian-based score function suitable for docking in homology modelled protein structures.

Tøndel K, Anderssen E, Drabløs F.

J Comput Aided Mol Des. 2006 Mar;20(3):131-44. Epub 2006 May 2.

PMID:
16652207
[PubMed - indexed for MEDLINE]
18.

Molecular docking of intercalators and groove-binders to nucleic acids using Autodock and Surflex.

Holt PA, Chaires JB, Trent JO.

J Chem Inf Model. 2008 Aug;48(8):1602-15. doi: 10.1021/ci800063v. Epub 2008 Jul 22.

PMID:
18642866
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Protein-ligand docking against non-native protein conformers.

Verdonk ML, Mortenson PN, Hall RJ, Hartshorn MJ, Murray CW.

J Chem Inf Model. 2008 Nov;48(11):2214-25. doi: 10.1021/ci8002254.

PMID:
18954138
[PubMed - indexed for MEDLINE]
20.

AMMOS: Automated Molecular Mechanics Optimization tool for in silico Screening.

Pencheva T, Lagorce D, Pajeva I, Villoutreix BO, Miteva MA.

BMC Bioinformatics. 2008 Oct 16;9:438. doi: 10.1186/1471-2105-9-438.

PMID:
18925937
[PubMed - indexed for MEDLINE]
Free PMC Article

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