ArticleJournal of chemical theory and computation2020
Multidimensional Global Optimization and Robustness Analysis in the Context of Protein-Ligand Binding.
Article in Journal of chemical theory and computation, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Multi-Objective Loss Function For Free Energy Calculations.ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine · 2025Article
- Optimal Dielectric Boundary for Binding Free Energy Estimates in the Implicit Solvent.Journal of chemical information and modeling · 2024Article
- Inclusion of Water Multipoles into the Implicit Solvation Framework Leads to Accuracy Gains.The journal of physical chemistry. B · 2024Article
- AmberTools.Journal of chemical information and modeling · 2023Article
- Physics-Guided Deep Generative Model for New Ligand Discovery.ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine · 2023Article
- Molecular dynamics simulations, docking and MMGBSA studies of newly designed peptide-conjugated glucosyloxy stilbene derivatives with tumor cell receptors.Molecular diversity · 2022Article
- A Physics-Guided Neural Network for Predicting Protein-Ligand Binding Free Energy: From Host-Guest Systems to the PDBbind Database.Biomolecules · 2022Article
- An Effective MM/GBSA Protocol for Absolute Binding Free Energy Calculations: A Case Study on SARS-CoV-2 Spike Protein and the Human ACE2 Receptor.Molecules (Basel, Switzerland) · 2021Article
- MMGB/SA Consensus Estimate of the Binding Free Energy Between the Novel Coronavirus Spike Protein to the Human ACE2 Receptor.bioRxiv : the preprint server for biology · 2020Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Accuracy of protein-ligand binding free energy calculations utilizing implicit solvent models is critically affected by parameters of the underlying dielectric boundary, specifically, the atomic and water probe radii. Here, a global multidimensional optimization pipeline is developed to find optimal atomic radii specifically for protein-ligand binding calculations in implicit solvent. The computational pipeline has these three key components: (1) a massively parallel implementation of a deterministic global optimization algorithm (VTDIRECT95), (2) an accurate yet reasonably fast generalized Born implicit solvent model (GBNSR6), and (3) a novel robustness metric that helps distinguish between nearly degenerate local minima via a postprocessing step of the optimization. A graph-based "
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.