ArticleNature communications2024
SQM2.20: Semiempirical quantum-mechanical scoring function yields DFT-quality protein-ligand binding affinity predictions in minutes.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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25 citing papers in PubMed.
- Data driven selection of consensus docking pipelines for structure based hit identification.npj drug discovery · 2026Article
- FLOWR.ROOT - A flow matching-based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction.Nature communications · 2026Article
- Residue-Level Affinity Decomposition via Quantum Electron Density: A Multivariable Framework Applied to HIV-1 Protease Inhibitors.The journal of physical chemistry. B · 2026Article
- Computer-Based Design to Improve Bacillus thuringiensis Chitinase for Industrial Applications.ChemistryOpen · 2026Article
- Potent Competitive Inhibitors of Ecto-5'-nucleotidase (CD73) based on 6‑(Het)aryl-7-deazapurine Ribonucleoside 5'‑ACS pharmacology & translational science · 2026Article
- Quantum-Driven High-Throughput Docking: Advances in Molecular Scoring and Drug Discovery.Methods in molecular biology (Clifton, N.J.) · 2026Review
- Expediting hit-to-lead progression in drug discovery through reaction prediction and multi-dimensional optimization.Nature communications · 2025Article
- Evaluation of Protein-Ligand binding interactions of alkaline phosphatase inhibitors by Quantum-Mechanical methods.Journal of computer-aided molecular design · 2025Article
- Article
- Accurate and Rapid Ranking of Protein-Ligand Binding Affinities Using Density Matrix Fragmentation and Physics-Informed Machine Learning Dispersion Potentials.Chemphyschem : a European journal of chemical physics and physical chemistry · 2025Article
- Extending quantum-mechanical benchmark accuracy to biological ligand-pocket interactions.Nature communications · 2025Article
- Comparative Analysis of Quantum-Mechanical and Standard Single-Structure Protein-Ligand Scoring Functions with MD-Based Free Energy Calculations.Journal of chemical information and modeling · 2025Article
- Multiscale Computational Protocols for Accurate Residue Interactions at the Flexible Insulin-Receptor Interface.Journal of chemical information and modeling · 2025Article
- On-Resin Assembly of Macrocyclic Inhibitors ofJournal of medicinal chemistry · 2025Article
- Computation of Protein-Ligand Binding Free Energies with a Quantum Mechanics-Based Mining Minima Algorithm.Journal of chemical theory and computation · 2025Article
- Discriminating High from Low Energy Conformers of Druglike Molecules: An Assessment of Machine Learning Potentials and Quantum Chemical Methods.Chemphyschem : a European journal of chemical physics and physical chemistry · 2025Article
- The Need for Continuing Blinded Pose- and Activity Prediction Benchmarks.Journal of chemical information and modeling · 2025Review
- GRADE and X-GRADE: Unveiling Novel Protein-Ligand Interaction Fingerprints Based on GRAIL Scores.Journal of chemical information and modeling · 2025Article
- PM6-ML: The Synergy of Semiempirical Quantum Chemistry and Machine Learning Transformed into a Practical Computational Method.Journal of chemical theory and computation · 2025Article
- Rationalizing protein-ligand interactions via the effective fragment potential method and structural data from classical molecular dynamics.The Journal of chemical physics · 2025Article
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4 authors.
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Abstract
Accurate estimation of protein-ligand binding affinity is the cornerstone of computer-aided drug design. We present a universal physics-based scoring function, named SQM2.20, addressing key terms of binding free energy using semiempirical quantum-mechanical computational methods. SQM2.20 incorporates the latest methodological advances while remaining computationally efficient even for systems with thousands of atoms. To validate it rigorously, we have compiled and made available the PL-REX benchmark dataset consisting of high-resolution crystal structures and reliable experimental affinities for ten diverse protein targets. Comparative assessments demonstrate that SQM2.20 outperforms other scoring methods and reaches a level of accuracy similar to much more expensive DFT calculations. In the PL-REX dataset, it achieves excellent correlation with experimental data (average R
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