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Automated Docking Screens: A Feasibility Study
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DOI：10.1021/jm9006966.png)
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摘要
En 中文
Molecular docking is the most practical approach to leverage protein structure for ligand discovery, but the technique retains important liabilities that make it challenging to deploy on a large scale. We have therefore created an expert system, DOCK Blaster, to investigate the feasibility of full automation. The method requires a PDB code, sometimes with a ligand structure, and from that alone can launch a full screen of large libraries. A critical feature is self-assessment, which estimates the anticipated reliability of the automated screening results using pose fidelity and enrichment. Against common benchmarks, DOCK Blaster recapitulates the crystal ligand pose within 2 angstrom rmsd 50-60% of the time; inferior to an expert, but respectrable. Half the time the ligand also ranked among the top 5% of 100 physically matched decoys chosen on the fly. Further tests were undertaken culminating in a study of 7755 eligible PDB structures. In 1398 cases, the redocked ligand ranked in the top 5% of 100 property-matched decoys while also posing within 2 angstrom rmsd, suggesting that unsupervised prospective docking is viable. DOCK Blaster is available at http://blaster.docking.org.
Keyword:
STRUCTURE-BASED DISCOVERY
PROTEIN-LIGAND DOCKING
MOLECULAR DOCKING
SCORING FUNCTIONS
RECEPTOR LIGANDS
FLEXIBLE DOCKING
HIGH-THROUGHPUT
BETA-LACTAMASE
LEAD DISCOVERY
DRUG DESIGN
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期刊
IF:
6.8
论文数:
2.7W
被引数:
9.4W
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引用论文
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Development and validation of a modular, extensible docking program: DOCK 5开发和验证模块化、可扩展的对接程序: DOCK 5
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