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Results: 1 to 20 of 28

1.

PharmDock: a pharmacophore-based docking program.

Hu B, Lill MA.

J Cheminform. 2014 Apr 16;6:14. doi: 10.1186/1758-2946-6-14. eCollection 2014.

PMID:
24739488
[PubMed]
Free PMC Article
2.

Assessing hERG pore models as templates for drug docking using published experimental constraints: the inactivated state in the context of drug block.

Dempsey CE, Wright D, Colenso CK, Sessions RB, Hancox JC.

J Chem Inf Model. 2014 Feb 24;54(2):601-12. doi: 10.1021/ci400707h. Epub 2014 Feb 6.

PMID:
24471705
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Exploring the potential of protein-based pharmacophore models in ligand pose prediction and ranking.

Hu B, Lill MA.

J Chem Inf Model. 2013 May 24;53(5):1179-90. doi: 10.1021/ci400143r. Epub 2013 May 13.

PMID:
23621564
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Prospecting for novel plant-derived molecules of Rauvolfia serpentina as inhibitors of Aldose Reductase, a potent drug target for diabetes and its complications.

Pathania S, Randhawa V, Bagler G.

PLoS One. 2013 Apr 17;8(4):e61327. doi: 10.1371/journal.pone.0061327. Print 2013.

PMID:
23613832
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

CSAR benchmark exercise 2011-2012: evaluation of results from docking and relative ranking of blinded congeneric series.

Damm-Ganamet KL, Smith RD, Dunbar JB Jr, Stuckey JA, Carlson HA.

J Chem Inf Model. 2013 Aug 26;53(8):1853-70. doi: 10.1021/ci400025f. Epub 2013 May 10.

PMID:
23548044
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Binding pocket optimization by computational protein design.

Malisi C, Schumann M, Toussaint NC, Kageyama J, Kohlbacher O, Höcker B.

PLoS One. 2012;7(12):e52505. doi: 10.1371/journal.pone.0052505. Epub 2012 Dec 27.

PMID:
23300688
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Construction and test of ligand decoy sets using MDock: community structure-activity resource benchmarks for binding mode prediction.

Huang SY, Zou X.

J Chem Inf Model. 2011 Sep 26;51(9):2107-14. doi: 10.1021/ci200080g. Epub 2011 Aug 3.

PMID:
21755952
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Advances and challenges in protein-ligand docking.

Huang SY, Zou X.

Int J Mol Sci. 2010 Aug 18;11(8):3016-34. doi: 10.3390/ijms11083016. Review.

PMID:
21152288
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Relating the shape of protein binding sites to binding affinity profiles: is there an association?

Simon Z, Vigh-Smeller M, Peragovics A, Csukly G, Zahoránszky-Kohalmi G, Rauscher AA, Jelinek B, Hári P, Bitter I, Málnási-Csizmadia A, Czobor P.

BMC Struct Biol. 2010 Oct 5;10:32. doi: 10.1186/1472-6807-10-32.

PMID:
20923553
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

SimiCon: a web tool for protein-ligand model comparison through calculation of equivalent atomic contacts.

Rueda M, Katritch V, Raush E, Abagyan R.

Bioinformatics. 2010 Nov 1;26(21):2784-5. doi: 10.1093/bioinformatics/btq504. Epub 2010 Sep 24.

PMID:
20871105
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Targeting the chromosome partitioning protein ParA in tuberculosis drug discovery.

Nisa S, Blokpoel MC, Robertson BD, Tyndall JD, Lun S, Bishai WR, O'Toole R.

J Antimicrob Chemother. 2010 Nov;65(11):2347-58. doi: 10.1093/jac/dkq311. Epub 2010 Sep 1.

PMID:
20810423
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Conformer generation with OMEGA: algorithm and validation using high quality structures from the Protein Databank and Cambridge Structural Database.

Hawkins PC, Skillman AG, Warren GL, Ellingson BA, Stahl MT.

J Chem Inf Model. 2010 Apr 26;50(4):572-84. doi: 10.1021/ci100031x.

PMID:
20235588
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Comparison of current docking tools for the simulation of inhibitor binding by the transmembrane domain of the sarco/endoplasmic reticulum calcium ATPase.

Lape M, Elam C, Paula S.

Biophys Chem. 2010 Aug;150(1-3):88-97. doi: 10.1016/j.bpc.2010.01.011. Epub 2010 Feb 4.

PMID:
20167416
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Recipes for the selection of experimental protein conformations for virtual screening.

Rueda M, Bottegoni G, Abagyan R.

J Chem Inf Model. 2010 Jan;50(1):186-93. doi: 10.1021/ci9003943.

PMID:
20000587
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Q-Dock(LHM): Low-resolution refinement for ligand comparative modeling.

Brylinski M, Skolnick J.

J Comput Chem. 2010 Apr 15;31(5):1093-105. doi: 10.1002/jcc.21395.

PMID:
19827144
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

A statistical framework to evaluate virtual screening.

Zhao W, Hevener KE, White SW, Lee RE, Boyett JM.

BMC Bioinformatics. 2009 Jul 20;10:225. doi: 10.1186/1471-2105-10-225.

PMID:
19619306
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Carborane clusters in computational drug design: a comparative docking evaluation using AutoDock, FlexX, Glide, and Surflex.

Tiwari R, Mahasenan K, Pavlovicz R, Li C, Tjarks W.

J Chem Inf Model. 2009 Jun;49(6):1581-9. doi: 10.1021/ci900031y.

PMID:
19449853
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Validation of molecular docking programs for virtual screening against dihydropteroate synthase.

Hevener KE, Zhao W, Ball DM, Babaoglu K, Qi J, White SW, Lee RE.

J Chem Inf Model. 2009 Feb;49(2):444-60. doi: 10.1021/ci800293n.

PMID:
19434845
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

A structure-based approach to ligand discovery for 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase: a target for antimicrobial therapy.

Ramsden NL, Buetow L, Dawson A, Kemp LA, Ulaganathan V, Brenk R, Klebe G, Hunter WN.

J Med Chem. 2009 Apr 23;52(8):2531-42. doi: 10.1021/jm801475n.

PMID:
19320487
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Molecular docking studies of dithionitrobenzoic acid and its related compounds to protein disulfide isomerase: computational screening of inhibitors to HIV-1 entry.

Gowthaman U, Jayakanthan M, Sundar D.

BMC Bioinformatics. 2008 Dec 12;9 Suppl 12:S14. doi: 10.1186/1471-2105-9-S12-S14.

PMID:
19091013
[PubMed - indexed for MEDLINE]
Free PMC Article

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