DOVIS 2.0: an efficient and easy to use parallel virtual screening tool based on AutoDock 4.0

Jiang, Xiaohui; Kumar, Kamal; Hu, Xin; Wallqvist, Anders; Reifman, Jaques

doi:10.1186/1752-153x-2-18

Cited by 93 publications

(84 citation statements)

References 9 publications

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“…The AutoDock-based DOVIS program 51,52 was used to screen the NIH Molecular Library Small Molecule Repository (MLSMR) collection of ∼350000 compounds against the structure model of FtuFabI−NAD. The active site of the protein was defined by a grid of 60 × 60 × 60 points with a grid spacing of 0.35 Å centered at the center of mass of NAD.…”

Section: ■ Methodsmentioning

confidence: 99%

3-Substituted Indole Inhibitors Against Francisella tularensis FabI Identified by Structure-Based Virtual Screening

Compton

AbdulHameed

et al. 2013

J. Med. Chem.

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In this study, we describe novel inhibitors against Francisella tularensis SchuS4 FabI identified from structure-based in silico screening with integrated molecular dynamics simulations to account for induced fit of a flexible loop crucial for inhibitor binding. Two 3-substituted indoles, 54 and 57, preferentially bound the NAD + form of the enzyme and inhibited growth of F. tularensis SchuS4 at concentrations near that of their measured K i . While 57 was species-specific, 54 showed a broader spectrum of growth inhibition against F. tularensis, Bacillus anthracis, and Staphylococcus aureus. Binding interaction analysis in conjunction with site-directed mutagenesis revealed key residues and elements that contribute to inhibitor binding and species specificity. Mutation of Arg-96, a poorly conserved residue opposite the loop, was unexpectedly found to enhance inhibitor binding in the R96G and R96M variants. This residue may affect the stability and closure of the flexible loop to enhance inhibitor (or substrate) binding.

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Section: ■ Methodsmentioning

confidence: 99%

3-Substituted Indole Inhibitors Against Francisella tularensis FabI Identified by Structure-Based Virtual Screening

Compton

AbdulHameed

et al. 2013

J. Med. Chem.

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“…Software platforms currently used for MM docking are the Schrodinger Glide (Friesner 2004;Halgren 2004) and Autodock (Goodsell 1996) programs, which run on high performance platforms through the DOVIS (Jiang 2008) software package. Glide is a commercial package with documented performance, and the Autodock/Dovis suite is open source, with well established protocols for high performance computing.…”

Section: Componentsmentioning

confidence: 99%

Year 2 Report: Protein Function Prediction Platform

Zhou¹

2012

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Public reporting burden for this collection of information is estimated to average 1 hour per response, including the time for reviewing instructions, searching data sources, gathering and maintaining the data needed, and completing and reviewing the collection of information. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES)Lawrence Livermore National Laboratory 7000 East Avenue Livermore, CA 94550 PERFORMING ORGANIZATION REPORT NUMBER SPONSORING/MONITORING AGENCY NAME(S) AND ADDRESS(ES)DoD Chemical and Biological Defense Program (CBDP) Diagnostics and Disease Surveillance Joint Science and Technology Office (JSTO) Ft. Belvoir, VA SPONSOR/MONITOR'S ACRONYM(S)CBDT, JSTO SPONSORING/MONITORING AGENCY REPORT NUMBER DISTRIBUTION AVAILABILITY STATEMENTDistribution Statement F: Further dissemination authorized only as directed by DTRA/JSTO or higher DoD authority. Requests for this document shall be referred to DTRA/JSTO-CBI. SUPPLEMENTARY NOTES ABSTRACTUpon completion of our second year of development in a 3-year development cycle, we have completed a prototype protein structure-function annotation and function prediction system: Protein Function Prediction (PFP) platform (v.0.5). We have met our milestones for Years 1 and 2 and are positioned to continue development in completion of our original statement of work, or a reasonable modification thereof, in service to DTRA Programs involved in diagnostics and medical countermeasures research and development. SUBJECT TERMSsoftware integration, data integration, protein function prediction, functional annotation, structure modeling, mechanistic modeling, systems biology, metabolic pathway modeling, genomics, diagnostics, therapeutics, biomarkers, medical countermeasures, bioinformatics, informatics Executive SummaryUpon completion of our second year of development in a 3-year development cycle, we have completed a prototype protein structure-function annotation and function prediction system: Protein Function Prediction (PFP) platform (v.0.5). We have met our milestones for Years 1 and 2 and are positioned to continue development in completion of our original statement of work, or a reasonable modification thereof, in service to DTRA Programs involved in diagnostics and medical countermeasures research and development.

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“…Not only was the activity of chaetochromin A (1), suggested by the in silico screen, confirmed, but talaroderxines A (2) and B (3) proved to be more active in the protease assay and showed considerable protection at 20 and 2 μM in the MPNHDA. While secalonic acid (4), cephalochromin (5), and skyrin (6) were roughly comparable to chaetochromin A in the protease assay, they were devoid of activity in the MPNHDA.…”

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confidence: 99%

“…Samples of pure (≥95% by NMR) chaetochromin A (1) and several related compoundstalaroderxines A and B (2 and 3), secalonic acid A (4), cephalochromin (5), and skyrin (6) were obtained from the fungal compound collection at the University of Iowa for comparative testing. Chaetochromin A (1) was isolated from solid-substrate fermentation cultures of Chaetomium arcuatum (syn.…”

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confidence: 99%