ArticleFrontiers in chemistry2020
High-Throughput Docking Using Quantum Mechanical Scoring.
Article in Frontiers in chemistry, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Assessing the ligand native-like pose using a quantum mechanical-derived hydropathic score for protein-ligand complementarity.npj drug discovery · 2026Article
- Pangenomics insights of enterococcus faecium human isolates and identification of novel therapeutic targets by in silico subtractive genomics.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2026Article
- Quantum-Driven High-Throughput Docking: Advances in Molecular Scoring and Drug Discovery.Methods in molecular biology (Clifton, N.J.) · 2026Review
- The physics-AI dialogue in drug design.RSC medicinal chemistry · 2025Review
- Molecular Docking in Drug Discovery: Techniques, Applications, and Advancements.Current medicinal chemistry · 2025Review
- Combining the Fragment Molecular Orbital and GRID Approaches for the Prediction of Ligand-Metalloenzyme Binding Affinity: The Case Study of hCA II Inhibitors.Molecules (Basel, Switzerland) · 2024Article
- The Advances and Limitations of the Determination and Applications of Water Structure in Molecular Engineering.International journal of molecular sciences · 2023Review
- Article
- HINT, a code for understanding the interaction between biomolecules: a tribute to Donald J. Abraham.Frontiers in molecular biosciences · 2023Review
- Emerging frontiers in virtual drug discovery: From quantum mechanical methods to deep learning approaches.Current opinion in chemical biology · 2022Review
- Systemic evolutionary chemical space exploration for drug discovery.Journal of cheminformatics · 2022Article
- Combination of pose and rank consensus in docking-based virtual screening: the best of both worlds.RSC advances · 2021Article
- A critical overview of computational approaches employed for COVID-19 drug discovery.Chemical Society reviews · 2021Review
- Functional and druggability analysis of the SARS-CoV-2 proteome.European journal of pharmacology · 2021Article
- Docking-generated multiple ligand poses for bootstrapping bioactivity classifying Machine Learning: Repurposing covalent inhibitors for COVID-19-related TMPRSS2 as case study.Computational and structural biotechnology journal · 2021Article
- A Machine Learning Model to Predict Drug Transfer Across the Human Placenta Barrier.Frontiers in chemistry · 2021Article
- Resources and computational strategies to advance small molecule SARS-CoV-2 discovery: Lessons from the pandemic and preparing for future health crises.Computational and structural biotechnology journal · 2021Review
- 3D-QSAR Studies of 1,2,4-Oxadiazole Derivatives as Sortase A Inhibitors.BioMed research international · 2021Article
- Merging Ligand-Based and Structure-Based Methods in Drug Discovery: An Overview of Combined Virtual Screening Approaches.Molecules (Basel, Switzerland) · 2020Review
- Flexi-pharma: a molecule-ranking strategy for virtual screening using pharmacophores from ligand-free conformational ensembles.Journal of computer-aided molecular design · 2020Article
Corrections and comments
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2 authors.
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Abstract
Today high-throughput docking is one of the most commonly used computational tools in drug lead discovery. While there has been an impressive methodological improvement in docking accuracy, docking scoring still remains an open challenge. Most docking programs are rooted in classical molecular mechanics. However, to better characterize protein-ligand interactions, the use of a more accurate quantum mechanical (QM) description would be necessary. In this work, we introduce a QM-based docking scoring function for high-throughput docking and evaluate it on 10 protein systems belonging to diverse protein families, and with different binding site characteristics. Outstanding results were obtained, with our QM scoring function displaying much higher enrichment (screening power) than a traditional docking method. It is acknowledged that developments in quantum mechanics theory, algorithms and computer hardware throughout the upcoming years will allow semi-empirical (or low-cost) quantum mechanical methods to slowly replace force-field calculations. It is thus urgently needed to develop and validate novel quantum mechanical-based scoring functions for high-throughput docking toward more accurate methods for the identification and optimization of modulators of pharmaceutically relevant targets.
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Registered trials
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