ArticleFrontiers in chemistry2019
Refinement and Rescoring of Virtual Screening Results.
Article in Frontiers in chemistry, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers, 1 of them a synthesis that pooled it.
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Who cites it
35 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Proteins and Peptides Studied In Silico and In Vivo for the Treatment of Diabetes Mellitus: A Systematic Review.Nutrients · 2024Pooled it
- Structure-Guided Identification of GPR84 Ligand Candidates With Potential Immunomodulatory Activities.ChemMedChem · 2026Article
- From Genome Inspection to Precision Agrochemicals: A Structure-Based Antivirulence Roadmap for Sustainable Crop Protection againstJournal of agricultural and food chemistry · 2026Review
- Natural Products in Epilepsy Treatment: From Traditional Medicine Towards Computational Drug Discovery.Current issues in molecular biology · 2026Review
- Review
- Design, synthesis and biological activity of glycoconjugated ADAMTS5 exosite inhibitors: applications in osteoarthritis and ovarian cancer models.Scientific reports · 2025Article
- In silico discovery of alkaloids as VEGFR-2 inhibitors with favorable toxicity profiles: insights from molecular dynamics and MM/GBSA.In silico pharmacology · 2025Article
- In Silico Strategies to Predict Anti-aging Features of Whey Peptides.Molecular biotechnology · 2024Article
- Building shape-focused pharmacophore models for effective docking screening.Journal of cheminformatics · 2024Article
- Structure-based pharmacophore modeling for precision inhibition of mutant ESR2 in breast cancer: A systematic computational approach.Cancer medicine · 2024Article
- Efficient Refinement of Complex Structures of Flexible Histone Peptides Using Post-Docking Molecular Dynamics Protocols.International journal of molecular sciences · 2024Article
- Harnessing Brazilian biodiversity database: identification of flavonoids as potential inhibitors of SARS-CoV-2 main protease using computational approaches and all-atom molecular dynamics simulation.Frontiers in chemistry · 2024Article
- Structure-Based Discovery of Mouse Trace Amine-Associated Receptor 5 Antagonists.Journal of chemical information and modeling · 2023Article
- In silico analysis and molecular docking studies of natural compounds of Withania somnifera against bovine NLRP9.Journal of molecular modeling · 2023Article
- Past, Present, and Future Perspectives on Computer-Aided Drug Design Methodologies.Molecules (Basel, Switzerland) · 2023Review
- Strategies for Competitive Activity-Based Protein Profiling in Small Molecule Inhibitor Discovery and Characterization.Israel journal of chemistry · 2023Article
- AI-accelerated protein-ligand docking for SARS-CoV-2 is 100-fold faster with no significant change in detection.Scientific reports · 2023Article
- Application of Computational Biology and Artificial Intelligence in Drug Design.International journal of molecular sciences · 2022Review
- Protocol for iterative optimization of modified peptides bound to protein targets.Journal of computer-aided molecular design · 2022Article
- An Electrostatically-steered Conformational Selection Mechanism Promotes SARS-CoV-2 Spike Protein Variation.Journal of molecular biology · 2022Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-throughput docking is an established computational screening approach in drug design. This methodology enables a rapid identification of biologically active hit compounds, providing an efficient and cost-effective complement or alternative to experimental high-throughput screenings. However, limitations inherent to the methodology make docking results inevitably approximate. Two major Achille's heels include the use of approximated scoring functions and the limited sampling of the ligand-target complexes. Therefore, docking results require careful evaluation and further post-docking analyses. In this article, we will overview our approach to post-docking analysis in virtual screenings. BEAR (Binding Estimation After Refinement) was developed as a post-docking processing tool that refines docking poses by means of molecular dynamics (MD) and then rescores the ligands based on more accurate scoring functions (MM-PB(GB)SA). The tool has been validated and used prospectively in drug discovery applications. Future directions regarding refinement and rescoring in virtual screening are discussed.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.