ArticleJournal of computer-aided molecular design2019
Calculate protein-ligand binding affinities with the extended linear interaction energy method: application on the Cathepsin S set in the D3R Grand Challenge 3.
Article in Journal of computer-aided molecular design, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Steric control of signaling bias in the immunometabolic receptor GPR84.Nature communications · 2026Article
- A Comparative Study of Deep Learning and Classical Modeling Approaches for Protein-Ligand Binding Pose and Affinity Prediction in Coronavirus Main Proteases.Journal of chemical information and modeling · 2026Article
- Neuroprotective Potential of Indole-Based Compounds: A Biochemical Study on Antioxidant Properties and Amyloid Disaggregation in Neuroblastoma Cells.Antioxidants (Basel, Switzerland) · 2024Article
- Human Antigen R -mediated modulation of Transforming Growth Factor Beta 1 expression in retinal pathological milieu.Biochemistry and biophysics reports · 2024Article
- The SAMPL9 host-guest blind challenge: an overview of binding free energy predictive accuracy.Physical chemistry chemical physics : PCCP · 2024Article
- Structural basis for the ligand recognition and signaling of free fatty acid receptors.Science advances · 2024Article
- Drug repurposing against fucosyltransferase-2 via docking, STD-NMR, and molecular dynamic simulation studies.PloS one · 2024Article
- Semi-Rational Design of L-Isoleucine Dioxygenase Generated Its Activity for Aromatic Amino Acid Hydroxylation.Molecules (Basel, Switzerland) · 2023Article
- Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host-guest binding: II. regression and dielectric constant.Journal of computer-aided molecular design · 2022Article
- Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host-guest binding: I. Standard procedure.Journal of computer-aided molecular design · 2022Article
- Affinity prediction using deep learning based on SMILES input for D3R grand challenge 4.Journal of computer-aided molecular design · 2022Article
- Machine learning on ligand-residue interaction profiles to significantly improve binding affinity prediction.Briefings in bioinformatics · 2021Article
- Incorporating structural similarity into a scoring function to enhance the prediction of binding affinities.Journal of cheminformatics · 2021Article
- Recent Developments in Free Energy Calculations for Drug Discovery.Frontiers in molecular biosciences · 2021Review
- A fast and high-quality charge model for the next generation general AMBER force field.The Journal of chemical physics · 2020Article
- How Good is Jarzynski's Equality for Computer-Aided Drug Design?The journal of physical chemistry. B · 2020Article
- Article
- D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.Journal of computer-aided molecular design · 2020Article
- Docking rigid macrocycles using Convex-PL, AutoDock Vina, and RDKit in the D3R Grand Challenge 4.Journal of computer-aided molecular design · 2020Article
- Correlation of cathepsin S with coronary stenosis degree, carotid thickness, blood pressure, glucose and lipid metabolism and vascular endothelial function in atherosclerosis.Experimental and therapeutic medicine · 2020Article
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5 authors.
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Abstract
We participated in the Cathepsin S (CatS) sub-challenge of the Drug Design Data Resource (D3R) Grand Challenge 3 (GC3) in 2017 to blindly predict the binding poses of 24 CatS-bound ligands, the binding affinity ranking of 136 ligands, and the binding free energies of a subset of 33 ligands in Stage 1A and Stage 2. Our submitted predictions ranked relatively well compared to the submissions from other participants. Here we present our methodologies used in the challenge. For the binding pose prediction, we employed the Glide module in the Schrodinger Suite 2017 and AutoDock Vina. For the binding affinity/free energy prediction, we carried out molecular dynamics simulations of the complexes in explicit water solvent with counter ions, and then estimated the binding free energies with our newly developed model of extended linear interaction energy (ELIE), which is inspired by two other popular end-point approaches: the linear interaction energy (LIE) method, and the molecular mechanics with Poisson-Boltzmann surface area solvation method (MM/PBSA). Our studies suggest that ELIE is a good trade-off between efficiency and accuracy, and it is appropriate for filling the gap between the high-throughput docking and scoring methods and the rigorous but much more computationally demanding methods like free energy perturbation (FEP) or thermodynamics integration (TI) in computer-aided drug design (CADD) projects.
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