ArticleJournal of computer-aided molecular design2016
Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations.
Article in Journal of computer-aided molecular design, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 49 citations in OpenAlex.
- Fully Automatable Relative Binding Free Energy Calculations with Enhanced Sampling Using FAST/MBAR.Journal of chemical theory and computation · 2026Article
- Quantum Mechanics in Drug Discovery: A Comprehensive Review of Methods, Applications, and Future Directions.International journal of molecular sciences · 2025Review
- Molecular docking and dynamics studies to identify novel active compounds targeting potential breast cancer receptor proteins from an indigenous herbF1000Research · 2024Article
- Prioritizing Small Sets of Molecules for Synthesis through in-silico Tools: A Comparison of Common Ranking Methods.ChemMedChem · 2023Article
- Phytochemical Compound Screening to Identify Novel Small Molecules against Dengue Virus: A Docking and Dynamics Study.Molecules (Basel, Switzerland) · 2022Article
- Profiling of phytochemical and antioxidant activity of wild mushrooms: Evidence from the in vitro study and phytoconstituent's binding affinity to the human erythrocyte catalase and human glutathione reductase.Food science & nutrition · 2022Article
- Identification of Drug Combination Therapies for SARS-CoV-2: A Molecular Dynamics Simulations Approach.Drug design, development and therapy · 2022Article
- Molecular Docking and Molecular Dynamics Simulation of Fisetin, Galangin, Hesperetin, Hesperidin, Myricetin, and Naringenin against Polymerase of Dengue Virus.Journal of tropical medicine · 2022Article
- Kidney injury molecule-1 is a potential receptor for SARS-CoV-2.Journal of molecular cell biology · 2021Article
- DockingApp RF: A State-of-the-Art Novel Scoring Function for Molecular Docking in a User-Friendly Interface to AutoDock Vina.International journal of molecular sciences · 2020Article
- Thermodynamic Integration in 3n Dimensions without Biases or Alchemy for Protein Interactions.Frontiers in physics · 2020Article
- Water structure in solution and crystal molecular dynamics simulations compared to protein crystal structures.RSC advances · 2020Article
- D3R Grand Challenge 4: ligand similarity and MM-GBSA-based pose prediction and affinity ranking for BACE-1 inhibitors.Journal of computer-aided molecular design · 2020Article
- Comparison of affinity ranking using AutoDock-GPU and MM-GBSA scores for BACE-1 inhibitors in the D3R Grand Challenge 4.Journal of computer-aided molecular design · 2019Article
- Improving small molecule virtual screening strategies for the next generation of therapeutics.Current opinion in chemical biology · 2018Review
- Quantum Chemical Approaches in Structure-Based Virtual Screening and Lead Optimization.Frontiers in chemistry · 2018Review
- Using physics-based pose predictions and free energy perturbation calculations to predict binding poses and relative binding affinities for FXR ligands in the D3R Grand Challenge 2.Journal of computer-aided molecular design · 2018Article
- Optimal affinity ranking for automated virtual screening validated in prospective D3R grand challenges.Journal of computer-aided molecular design · 2018Article
- Docking of small molecules to farnesoid X receptors using AutoDock Vina with the Convex-PL potential: lessons learned from D3R Grand Challenge 2.Journal of computer-aided molecular design · 2018Article
- Binding affinities of the farnesoid X receptor in the D3R Grand Challenge 2 estimated by free-energy perturbation and docking.Journal of computer-aided molecular design · 2018Article
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We have estimated the binding affinity of three sets of ligands of the heat-shock protein 90 in the D3R grand challenge blind test competition. We have employed four different methods, based on five different crystal structures: first, we docked the ligands to the proteins with induced-fit docking with the Glide software and calculated binding affinities with three energy functions. Second, the docked structures were minimised in a continuum solvent and binding affinities were calculated with the MM/GBSA method (molecular mechanics combined with generalised Born and solvent-accessible surface area solvation). Third, the docked structures were re-optimised by combined quantum mechanics and molecular mechanics (QM/MM) calculations. Then, interaction energies were calculated with quantum mechanical calculations employing 970-1160 atoms in a continuum solvent, combined with energy corrections for dispersion, zero-point energy and entropy, ligand distortion, ligand solvation, and an increase of the basis set to quadruple-zeta quality. Fourth, relative binding affinities were estimated by free-energy simulations, using the multi-state Bennett acceptance-ratio approach. Unfortunately, the results were varying and rather poor, with only one calculation giving a correlation to the experimental affinities larger than 0.7, and with no consistent difference in the quality of the predictions from the various methods. For one set of ligands, the results could be strongly improved (after experimental data were revealed) if it was recognised that one of the ligands displaced one or two water molecules. For the other two sets, the problem is probably that the ligands bind in different modes than in the crystal structures employed or that the conformation of the ligand-binding site or the whole protein changes.
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