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Results: 1 to 20 of 118

1.

Toward fully automated high performance computing drug discovery: a massively parallel virtual screening pipeline for docking and molecular mechanics/generalized born surface area rescoring to improve enrichment.

Zhang X, Wong SE, Lightstone FC.

J Chem Inf Model. 2014 Jan 27;54(1):324-37. doi: 10.1021/ci4005145. Epub 2014 Jan 3.

PMID:
24358939
[PubMed - in process]
2.

Rescoring docking hit lists for model cavity sites: predictions and experimental testing.

Graves AP, Shivakumar DM, Boyce SE, Jacobson MP, Case DA, Shoichet BK.

J Mol Biol. 2008 Mar 28;377(3):914-34. doi: 10.1016/j.jmb.2008.01.049. Epub 2008 Jan 30.

PMID:
18280498
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

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. doi: 10.1021/ci700470c. Epub 2008 May 9.

PMID:
18465849
[PubMed - indexed for MEDLINE]
4.

Message passing interface and multithreading hybrid for parallel molecular docking of large databases on petascale high performance computing machines.

Zhang X, Wong SE, Lightstone FC.

J Comput Chem. 2013 Apr 30;34(11):915-27. doi: 10.1002/jcc.23214. Epub 2013 Jan 23.

PMID:
23345155
[PubMed - indexed for MEDLINE]
5.
6.

Application of docking and QM/MM-GBSA rescoring to screen for novel Myt1 kinase inhibitors.

Wichapong K, Rohe A, Platzer C, Slynko I, Erdmann F, Schmidt M, Sippl W.

J Chem Inf Model. 2014 Mar 24;54(3):881-93. doi: 10.1021/ci4007326. Epub 2014 Feb 13.

PMID:
24490903
[PubMed - in process]
7.

Binding estimation after refinement, a new automated procedure for the refinement and rescoring of docked ligands in virtual screening.

Rastelli G, Degliesposti G, Del Rio A, Sgobba M.

Chem Biol Drug Des. 2009 Mar;73(3):283-6. doi: 10.1111/j.1747-0285.2009.00780.x.

PMID:
19207463
[PubMed - indexed for MEDLINE]
8.

An efficient computational method for calculating ligand binding affinities.

Suenaga A, Okimoto N, Hirano Y, Fukui K.

PLoS One. 2012;7(8):e42846. doi: 10.1371/journal.pone.0042846. Epub 2012 Aug 20.

PMID:
22916168
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Predicting fragment binding poses using a combined MCSS MM-GBSA approach.

Haider MK, Bertrand HO, Hubbard RE.

J Chem Inf Model. 2011 May 23;51(5):1092-105. doi: 10.1021/ci100469n. Epub 2011 Apr 29.

PMID:
21528911
[PubMed - indexed for MEDLINE]
10.

Cheminformatics meets molecular mechanics: a combined application of knowledge-based pose scoring and physical force field-based hit scoring functions improves the accuracy of structure-based virtual screening.

Hsieh JH, Yin S, Wang XS, Liu S, Dokholyan NV, Tropsha A.

J Chem Inf Model. 2012 Jan 23;52(1):16-28. doi: 10.1021/ci2002507. Epub 2011 Dec 14.

PMID:
22017385
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

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]
12.

Performance evaluation of 2D fingerprint and 3D shape similarity methods in virtual screening.

Hu G, Kuang G, Xiao W, Li W, Liu G, Tang Y.

J Chem Inf Model. 2012 May 25;52(5):1103-13. doi: 10.1021/ci300030u. Epub 2012 May 11.

PMID:
22551340
[PubMed - indexed for MEDLINE]
13.

Application of a post-docking procedure based on MM-PBSA and MM-GBSA on single and multiple protein conformations.

Sgobba M, Caporuscio F, Anighoro A, Portioli C, Rastelli G.

Eur J Med Chem. 2012 Dec;58:431-40. doi: 10.1016/j.ejmech.2012.10.024. Epub 2012 Oct 25.

PMID:
23153814
[PubMed - indexed for MEDLINE]
14.

Could MM-GBSA be accurate enough for calculation of absolute protein/ligand binding free energies?

Mulakala C, Viswanadhan VN.

J Mol Graph Model. 2013 Nov;46:41-51. doi: 10.1016/j.jmgm.2013.09.005. Epub 2013 Sep 18.

PMID:
24121518
[PubMed - indexed for MEDLINE]
15.

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]
16.

Testing assumptions and hypotheses for rescoring success in protein-ligand docking.

O'Boyle NM, Liebeschuetz JW, Cole JC.

J Chem Inf Model. 2009 Aug;49(8):1871-8. doi: 10.1021/ci900164f.

PMID:
19645429
[PubMed - indexed for MEDLINE]
17.

Validation of an automated procedure for the prediction of relative free energies of binding on a set of aldose reductase inhibitors.

Ferrari AM, Degliesposti G, Sgobba M, Rastelli G.

Bioorg Med Chem. 2007 Dec 15;15(24):7865-77. Epub 2007 Aug 22.

PMID:
17870536
[PubMed - indexed for MEDLINE]
18.

Ligand-based virtual screening approach using a new scoring function.

Hamza A, Wei NN, Zhan CG.

J Chem Inf Model. 2012 Apr 23;52(4):963-74. doi: 10.1021/ci200617d. Epub 2012 Apr 9.

PMID:
22486340
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Molecular modeling study of checkpoint kinase 1 inhibitors by multiple docking strategies and prime/MM-GBSA calculation.

Du J, Sun H, Xi L, Li J, Yang Y, Liu H, Yao X.

J Comput Chem. 2011 Oct;32(13):2800-9. doi: 10.1002/jcc.21859. Epub 2011 Jun 29.

PMID:
21717478
[PubMed - indexed for MEDLINE]
20.

Optimization of compound ranking for structure-based virtual ligand screening using an established FRED-Surflex consensus approach.

Du J, Bleylevens IW, Bitorina AV, Wichapong K, Nicolaes GA.

Chem Biol Drug Des. 2014 Jan;83(1):37-51. doi: 10.1111/cbdd.12202. Epub 2013 Oct 4.

PMID:
23941463
[PubMed - indexed for MEDLINE]

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