ArticleMethods (San Diego, Calif.)2015
Protein structure prediction provides comparable performance to crystallographic structures in docking-based virtual screening.
Article in Methods (San Diego, Calif.), 2015. 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.
- TruMPET: A New Method for Protein Secondary Structure Prediction Using Neural Networks Trained on Multiple Pre-Selected Physicochemical and Structural Features.International journal of molecular sciences · 2025Article
- Exploring the Potential of Malvidin and Echiodinin as Probable Antileishmanial Agents Through In Silico Analysis and In Vitro Efficacy.Molecules (Basel, Switzerland) · 2025Article
- Fragment-Based Drug Discovery against Mycobacteria: The Success and Challenges.International journal of molecular sciences · 2022Review
- Structure-Based Design of First-Generation Small Molecule Inhibitors Targeting the Catalytic Pockets of AID, APOBEC3A, and APOBEC3B.ACS pharmacology & translational science · 2021Article
- Comparison of structure- and ligand-based scoring functions for deep generative models: a GPCR case study.Journal of cheminformatics · 2021Article
- Prediction of Functional Consequences of Missense Mutations in ANO4 Gene.International journal of molecular sciences · 2021Article
- Computational Prediction of Chemical Tools for Identification and Validation of Synthetic Lethal Interaction Networks.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Protein X-ray Crystallography and Drug Discovery.Molecules (Basel, Switzerland) · 2020Review
- Rational design of agonists for bitter taste receptor TAS2R14: from modeling to bench and back.Cellular and molecular life sciences : CMLS · 2020Article
- In silico prediction of prolactin molecules as a tool for equine genomics reproduction.Molecular diversity · 2019Article
- A Chemosensory GPCR as a Potential Target to Control the Root-Knot NematodeMolecules (Basel, Switzerland) · 2019Article
- Homology Model and Docking-Based Virtual Screening for Ligands of Human Dyskerin as New Inhibitors of Telomerase for Cancer Treatment.International journal of molecular sciences · 2018Article
- GPCRs from fusarium graminearum detection, modeling and virtual screening - the search for new routes to control head blight disease.BMC bioinformatics · 2016Article
- Identification of novel Trypanosoma cruzi prolyl oligopeptidase inhibitors by structure-based virtual screening.Journal of computer-aided molecular design · 2016Article
- Computational modelling of the binding of arachidonic acid to the human monooxygenase CYP2J2.Journal of molecular modeling · 2016Article
- The Hevea brasiliensis XIP aquaporin subfamily: genomic, structural and functional characterizations with relevance to intensive latex harvesting.Plant molecular biology · 2016Article
- Illustrating and homology modeling the proteins of the Zika virus.F1000Research · 2016Article
- Computational protein structure refinement: Almost there, yet still so far to go.Wiley interdisciplinary reviews. Computational molecular scienceArticle
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4 authors.
Funding
Abstract
Structure based virtual screening has largely been limited to protein targets for which either an experimental structure is available or a strongly homologous template exists so that a high-resolution model can be constructed. The performance of state of the art protein structure predictions in virtual screening in systems where only weakly homologous templates are available is largely untested. Using the challenging DUD database of structural decoys, we show here that even using templates with only weak sequence homology (<30% sequence identity) structural models can be constructed by I-TASSER which achieve comparable enrichment rates to using the experimental bound crystal structure in the majority of the cases studied. For 65% of the targets, the I-TASSER models, which are constructed essentially in the apo conformations, reached 70% of the virtual screening performance of using the holo-crystal structures. A correlation was observed between the success of I-TASSER in modeling the global fold and local structures in the binding pockets of the proteins versus the relative success in virtual screening. The virtual screening performance can be further improved by the recognition of chemical features of the ligand compounds. These results suggest that the combination of structure-based docking and advanced protein structure modeling methods should be a valuable approach to the large-scale drug screening and discovery studies, especially for the proteins lacking crystallographic structures.
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