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Items: 1 to 20 of 149

1.

FReDoWS: a method to automate molecular docking simulations with explicit receptor flexibility and snapshots selection.

Machado KS, Schroeder EK, Ruiz DD, Cohen EM, de Souza ON.

BMC Genomics. 2011 Dec 22;12 Suppl 4:S6. doi: 10.1186/1471-2164-12-S4-S6. Epub 2011 Dec 22.

2.

Effect of the explicit flexibility of the InhA enzyme from Mycobacterium tuberculosis in molecular docking simulations.

Cohen EM, Machado KS, Cohen M, de Souza ON.

BMC Genomics. 2011 Dec 22;12 Suppl 4:S7. doi: 10.1186/1471-2164-12-S4-S7. Epub 2011 Dec 22.

3.

Mining flexible-receptor docking experiments to select promising protein receptor snapshots.

Machado KS, Winck AT, Ruiz DD, de Souza ON.

BMC Genomics. 2010 Dec 22;11 Suppl 5:S6. doi: 10.1186/1471-2164-11-S5-S6.

4.

Automatic design of decision-tree induction algorithms tailored to flexible-receptor docking data.

Barros RC, Winck AT, Machado KS, Basgalupp MP, de Carvalho AC, Ruiz DD, de Souza ON.

BMC Bioinformatics. 2012 Nov 21;13:310. doi: 10.1186/1471-2105-13-310.

5.

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
6.

Discovery of new inhibitors of Mycobacterium tuberculosis InhA enzyme using virtual screening and a 3D-pharmacophore-based approach.

Pauli I, dos Santos RN, Rostirolla DC, Martinelli LK, Ducati RG, Timmers LF, Basso LA, Santos DS, Guido RV, Andricopulo AD, Norberto de Souza O.

J Chem Inf Model. 2013 Sep 23;53(9):2390-401. doi: 10.1021/ci400202t. Epub 2013 Aug 20.

PMID:
23889525
7.

On the use of molecular dynamics receptor conformations for virtual screening.

Nichols SE, Baron R, McCammon JA.

Methods Mol Biol. 2012;819:93-103. doi: 10.1007/978-1-61779-465-0_7.

PMID:
22183532
8.

Molecular docking of balanol to dynamics snapshots of protein kinase A.

Wong CF, Kua J, Zhang Y, Straatsma TP, McCammon JA.

Proteins. 2005 Dec 1;61(4):850-8.

PMID:
16245317
9.

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.

10.

Cross-docking study on InhA inhibitors: a combination of Autodock Vina and PM6-DH2 simulations to retrieve bio-active conformations.

Stigliani JL, Bernardes-GĂ©nisson V, Bernadou J, Pratviel G.

Org Biomol Chem. 2012 Aug 21;10(31):6341-9. doi: 10.1039/c2ob25602a. Epub 2012 Jun 29.

PMID:
22751934
11.

wFReDoW: a cloud-based web environment to handle molecular docking simulations of a fully flexible receptor model.

De Paris R, Frantz FA, de Souza ON, Ruiz DD.

Biomed Res Int. 2013;2013:469363. doi: 10.1155/2013/469363. Epub 2013 Apr 11.

13.

FDS: flexible ligand and receptor docking with a continuum solvent model and soft-core energy function.

Taylor RD, Jewsbury PJ, Essex JW.

J Comput Chem. 2003 Oct;24(13):1637-56.

PMID:
12926007
14.
15.

Multiple automatic base selection: protein-ligand docking based on incremental construction without manual intervention.

Rarey M, Kramer B, Lengauer T.

J Comput Aided Mol Des. 1997 Jul;11(4):369-84.

PMID:
9334903
16.

Probing the structure of Mycobacterium tuberculosis MbtA: model validation using molecular dynamics simulations and docking studies.

Maganti L, Open Source Drug Discovery Consortium, Ghoshal N.

J Biomol Struct Dyn. 2014;32(2):273-88. doi: 10.1080/07391102.2012.762752. Epub 2013 Mar 25.

PMID:
23527569
17.

Elucidating isoniazid resistance using molecular modeling.

Wahab HA, Choong YS, Ibrahim P, Sadikun A, Scior T.

J Chem Inf Model. 2009 Jan;49(1):97-107. doi: 10.1021/ci8001342.

PMID:
19067649
18.

An Effective Approach for Clustering InhA Molecular Dynamics Trajectory Using Substrate-Binding Cavity Features.

De Paris R, Quevedo CV, Ruiz DD, Norberto de Souza O.

PLoS One. 2015 Jul 28;10(7):e0133172. doi: 10.1371/journal.pone.0133172. eCollection 2015.

19.
20.

Receptor flexibility in de novo ligand design and docking.

Alberts IL, Todorov NP, Dean PM.

J Med Chem. 2005 Oct 20;48(21):6585-96.

PMID:
16220975

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