1
|
Hamza A, Wei NN, Zhan CG. Ligand-based virtual screening approach using a new scoring function. J Chem Inf Model 2012; 52:963-74. [PMID: 22486340 DOI: 10.1021/ci200617d] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
In this study, we aimed to develop a new ligand-based virtual screening approach using an effective shape-overlapping procedure and a more robust scoring function (denoted by the HWZ score for convenience). The HWZ score-based virtual screening approach was tested against the compounds for 40 protein targets available in the Database of Useful Decoys (DUD; dud.docking.org/jahn/ ), and the virtual screening performance was evaluated in terms of the area under the receiver operator characteristic (ROC) curve (AUC), enrichment factor (EF), and hit rate (HR), demonstrating an improved overall performance compared to other popularly used approaches examined. In particular, the HWZ score-based virtual screening led to an average AUC value of 0.84 ± 0.02 (95% confidence interval) for the 40 targets. The average HR values at the top 1% and 10% of the active compounds for the 40 targets were 46.3% ± 6.7% and 59.2% ± 4.7%, respectively. In addition, the performance of the HWZ score-based virtual screening approach is less sensitive to the choice of the target.
Collapse
Affiliation(s)
- Adel Hamza
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , 789 South Limestone Street, Lexington, Kentucky 40536, United States
| | | | | |
Collapse
|
2
|
Bielińska-Wąż D. Graphical and numerical representations of DNA sequences: statistical aspects of similarity. JOURNAL OF MATHEMATICAL CHEMISTRY 2011; 49:2345. [PMID: 32214591 PMCID: PMC7087963 DOI: 10.1007/s10910-011-9890-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Accepted: 07/22/2011] [Indexed: 05/10/2023]
Abstract
New approaches aiming at a detailed similarity/dissimilarity analysis of DNA sequences are formulated. Several corrections that enrich the information which may be derived from the alignment methods are proposed. The corrections take into account the distributions along the sequences of the aligned bases (neglected in the standard alignment methods). As a consequence, different aspects of similarity, as for example asymmetry of the gene structure, may be studied either using new similarity measures associated with four-component spectral representation of the DNA sequences or using alignment methods with corrections introduced in this paper. The corrections to the alignment methods and the statistical distribution moment-based descriptors derived from the four-component spectral representation of the DNA sequences are applied to similarity/dissimilarity studies of β-globin gene across species. The studies are supplemented by detailed similarity studies for histones H1 and H4 coding sequences. The data are described according to the latest version of the EMBL database. The work is supplemented by a concise review of the state-of-art graphical representations of DNA sequences.
Collapse
Affiliation(s)
- Dorota Bielińska-Wąż
- Instytut Fizyki, Uniwersytet Mikołaja Kopernika, Grudziądzka 5, 87-100 Toruń, Poland
| |
Collapse
|
4
|
Kirchmair J, Distinto S, Markt P, Schuster D, Spitzer GM, Liedl KR, Wolber G. How To Optimize Shape-Based Virtual Screening: Choosing the Right Query and Including Chemical Information. J Chem Inf Model 2009; 49:678-92. [DOI: 10.1021/ci8004226] [Citation(s) in RCA: 160] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Johannes Kirchmair
- Department of Pharmaceutical Chemistry, Faculty of Chemistry and Pharmacy and Center for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 52, A-6020 Innsbruck, Austria, Inte:Ligand Software-Entwicklungs- and Consulting GmbH, Clemens Maria Hofbauer-Gasse 6, A-2344 Maria Enzersdorf, Austria, and Institute of Theoretical Chemistry, Faculty of Chemistry and Pharmacy and Center for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 52, A-6020 Innsbruck, Austria
| | - Simona Distinto
- Department of Pharmaceutical Chemistry, Faculty of Chemistry and Pharmacy and Center for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 52, A-6020 Innsbruck, Austria, Inte:Ligand Software-Entwicklungs- and Consulting GmbH, Clemens Maria Hofbauer-Gasse 6, A-2344 Maria Enzersdorf, Austria, and Institute of Theoretical Chemistry, Faculty of Chemistry and Pharmacy and Center for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 52, A-6020 Innsbruck, Austria
| | - Patrick Markt
- Department of Pharmaceutical Chemistry, Faculty of Chemistry and Pharmacy and Center for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 52, A-6020 Innsbruck, Austria, Inte:Ligand Software-Entwicklungs- and Consulting GmbH, Clemens Maria Hofbauer-Gasse 6, A-2344 Maria Enzersdorf, Austria, and Institute of Theoretical Chemistry, Faculty of Chemistry and Pharmacy and Center for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 52, A-6020 Innsbruck, Austria
| | - Daniela Schuster
- Department of Pharmaceutical Chemistry, Faculty of Chemistry and Pharmacy and Center for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 52, A-6020 Innsbruck, Austria, Inte:Ligand Software-Entwicklungs- and Consulting GmbH, Clemens Maria Hofbauer-Gasse 6, A-2344 Maria Enzersdorf, Austria, and Institute of Theoretical Chemistry, Faculty of Chemistry and Pharmacy and Center for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 52, A-6020 Innsbruck, Austria
| | - Gudrun M. Spitzer
- Department of Pharmaceutical Chemistry, Faculty of Chemistry and Pharmacy and Center for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 52, A-6020 Innsbruck, Austria, Inte:Ligand Software-Entwicklungs- and Consulting GmbH, Clemens Maria Hofbauer-Gasse 6, A-2344 Maria Enzersdorf, Austria, and Institute of Theoretical Chemistry, Faculty of Chemistry and Pharmacy and Center for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 52, A-6020 Innsbruck, Austria
| | - Klaus R. Liedl
- Department of Pharmaceutical Chemistry, Faculty of Chemistry and Pharmacy and Center for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 52, A-6020 Innsbruck, Austria, Inte:Ligand Software-Entwicklungs- and Consulting GmbH, Clemens Maria Hofbauer-Gasse 6, A-2344 Maria Enzersdorf, Austria, and Institute of Theoretical Chemistry, Faculty of Chemistry and Pharmacy and Center for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 52, A-6020 Innsbruck, Austria
| | - Gerhard Wolber
- Department of Pharmaceutical Chemistry, Faculty of Chemistry and Pharmacy and Center for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 52, A-6020 Innsbruck, Austria, Inte:Ligand Software-Entwicklungs- and Consulting GmbH, Clemens Maria Hofbauer-Gasse 6, A-2344 Maria Enzersdorf, Austria, and Institute of Theoretical Chemistry, Faculty of Chemistry and Pharmacy and Center for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 52, A-6020 Innsbruck, Austria
| |
Collapse
|