ArticleJournal of computer-aided molecular design2021
Improving virtual screening results with MM/GBSA and MM/PBSA rescoring.
Article in Journal of computer-aided molecular design, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
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- Computational Pipeline for Accelerating the Design of Glycomimetics.Journal of chemical information and modeling · 2025Article
- Enhancing aptamer selection in alzheimer's disease: integrating structure prediction and molecular dynamics simulations.Scientific reports · 2025Article
- The Quasi-Bound State as a Predictor of Relative Binding Free Energy.Journal of chemical information and modeling · 2025Article
- Suppressing Mycobacterium tuberculosis virulence and drug resistance by targeting Eis protein through computational drug discovery.Molecular diversity · 2025Article
- Aotaphenazine, a rare hydrophenazine, targets topoisomerase II with anticancer efficacy: In silico to in vitro evidence.PloS one · 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
- The potential ofJournal of integrative bioinformatics · 2024Article
- Antibiotic resistance challenge: evaluating anthraquinones as rifampicin monooxygenase inhibitors through integrated bioinformatics analysis.Genomics & informatics · 2024Article
- 3D-QSAR, Scaffold Hopping, Virtual Screening, and Molecular Dynamics Simulations of Pyridin-2-one as mIDH1 Inhibitors.International journal of molecular sciences · 2024Article
- Understanding the impact of binding free energy and kinetics calculations in modern drug discovery.Expert opinion on drug discovery · 2024Review
- In Silico Search for Drug Candidates Targeting the PAX8-PPARγ Fusion Protein in Thyroid Cancer.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
- Identification of TBK1 inhibitors against breast cancer using a computational approach supported by machine learning.Frontiers in pharmacology · 2024Article
- Identification of potent anti-Candida metabolites produced by the soft coral associated Streptomyces sp. HC14 using chemoinformatics.Scientific reports · 2023Article
- A cheminformatics-biophysics correlate to identify promising lead molecules against matrix metalloproteinase-2 (MMP-2) enzyme: A promising anti-cancer target.Saudi pharmaceutical journal : SPJ : the official publication of the Saudi Pharmaceutical Society · 2023Article
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1 author.
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Abstract
Virtual screening (VS) based on molecular docking is one of the most useful methods in computer-aided drug design. By allowing to identify computationally putative ligands binding to the proteins of interest, VS dramatically reduces the time and expense of the development of novel therapeutics. Among the limitations of the VS approaches is the low accuracy of scoring functions implemented in docking methods for assessing binding affinity. Many such scoring functions are developed for rapid, high-throughput evaluation of binding energy of multiple conformations generated by a searching algorithm. The methods for more rigorous calculation of binding affinity calculation are generally time-consuming. Even so, in many studies more accurate methods were used for rescoring of the final poses and false-positive hits evaluation. We performed VS for three benchmark sets and used energy minimization with MM/PB(GB)SA methods (molecular mechanics energies combined with the Poisson-Boltzmann or generalized Born and surface area) to rescore binding affinities. The comparison of the area under the curve (AUC), enrichment factor (EF), and Boltzmann-enhanced discrimination of receiver operating characteristics (BEDROC) showed essential improvements in the binding energy prediction after the rescoring. Finally, we provide a program for minimization and rescoring VS results based on freely available AmberTools. The code requires just the final binding poses of the ligand as the input and can be used with any docking program.
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