ArticleJournal of computational chemistry2010
Q-Dock(LHM): Low-resolution refinement for ligand comparative modeling.
Article in Journal of computational chemistry, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Implications of the Essential Role of Small Molecule Ligand Binding Pockets in Protein-Protein Interactions.The journal of physical chemistry. B · 2022Article
- FRAGSITE: A Fragment-Based Approach for Virtual Ligand Screening.Journal of chemical information and modeling · 2021Article
- FINDSITEJournal of chemical information and modeling · 2018Article
- Assessing the similarity of ligand binding conformations with the Contact Mode Score.Computational biology and chemistry · 2016Article
- Implications of the small number of distinct ligand binding pockets in proteins for drug discovery, evolution and biochemical function.Bioorganic & medicinal chemistry letters · 2015Review
- Protein models: the Grand Challenge of protein docking.Proteins · 2014Article
- Low-resolution structural modeling of protein interactome.Current opinion in structural biology · 2013Review
- Are predicted protein structures of any value for binding site prediction and virtual ligand screening?Current opinion in structural biology · 2013Review
- FINDSITE(comb): a threading/structure-based, proteomic-scale virtual ligand screening approach.Journal of chemical information and modeling · 2013Article
- FINDSITE(X): a structure-based, small molecule virtual screening approach with application to all identified human GPCRs.Molecular pharmaceutics · 2012Article
- Article
- eThread: a highly optimized machine learning-based approach to meta-threading and the modeling of protein tertiary structures.PloS one · 2012Article
- BSP-SLIM: a blind low-resolution ligand-protein docking approach using predicted protein structures.Proteins · 2012Article
- Structure-based systems biology for analyzing off-target binding.Current opinion in structural biology · 2011Review
- The utility of geometrical and chemical restraint information extracted from predicted ligand-binding sites in protein structure refinement.Journal of structural biology · 2011Article
- Cross-reactivity virtual profiling of the human kinome by X-react(KIN): a chemical systems biology approach.Molecular pharmaceutics · 2010Article
- Comprehensive structural and functional characterization of the human kinome by protein structure modeling and ligand virtual screening.Journal of chemical information and modeling · 2010Article
- 3D structural analysis of proteins using electrostatic surfaces based on image segmentation.Journal of molecular biochemistryArticle
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2 authors.
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Abstract
The success of ligand docking calculations typically depends on the quality of the receptor structure. Given improvements in protein structure prediction approaches, approximate protein models now can be routinely obtained for the majority of gene products in a given proteome. Structure-based virtual screening of large combinatorial libraries of lead candidates against theoretically modeled receptor structures requires fast and reliable docking techniques capable of dealing with structural inaccuracies in protein models. Here, we present Q-Dock(LHM), a method for low-resolution refinement of binding poses provided by FINDSITE(LHM), a ligand homology modeling approach. We compare its performance to that of classical ligand docking approaches in ligand docking against a representative set of experimental (both holo and apo) as well as theoretically modeled receptor structures. Docking benchmarks reveal that unlike all-atom docking, Q-Dock(LHM) exhibits the desired tolerance to the receptor's structure deformation. Our results suggest that the use of an evolution-based approach to ligand homology modeling followed by fast low-resolution refinement is capable of achieving satisfactory performance in ligand-binding pose prediction with promising applicability to proteome-scale applications.
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