ArticleJournal of cheminformatics2019
QligFEP: an automated workflow for small molecule free energy calculations in Q.
Article in Journal of cheminformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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41 citing papers in PubMed, 84 citations in OpenAlex.
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- NEMAT: An Automated Nonequilibrium Free-Energy Framework for Predicting Ligand Affinity in Membrane Proteins.Journal of chemical information and modeling · 2026Article
- Accelerated Combinatorial Drug Design for Human Immunodeficiency Virus Resistance through Seeded Multisite λ-Dynamics.Journal of chemical theory and computation · 2026Article
- Doing More with Less: Accurate and Scalable Ligand Free Energy Calculations by Focusing on the Binding Site.Journal of chemical information and modeling · 2026Article
- The Open Molecular Software Foundation (OMSF) and the Growing Role of Open Source Software in Molecular Modeling.Journal of chemical information and modeling · 2026Review
- BindFlow: A Free, User-Friendly Pipeline for Absolute Binding Free Energy Calculations Using Free Energy Perturbation or MM(PB/GB)SA.Journal of chemical theory and computation · 2026Article
- Accurate predictions of protein mutational effects accelerated with a hybrid-topology free energy protocol.Communications chemistry · 2025Article
- Integrating Machine Learning into Free Energy Perturbation Workflows.Journal of chemical information and modeling · 2025Review
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- Ligand and Residue Free Energy Perturbations Solve the Dual Binding Mode Proposal for an AThe journal of physical chemistry. B · 2025Article
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- Konnektor: A Framework for Using Graph Theory to Plan Networks for Free Energy Calculations.Journal of chemical information and modeling · 2024Article
- How to Sample Dozens of Substitutions per Site with λ Dynamics.Journal of chemical theory and computation · 2024Article
- Kartograf: A Geometrically Accurate Atom Mapper for Hybrid-Topology Relative Free Energy Calculations.Journal of chemical theory and computation · 2024Article
- phbuilder: A Tool for Efficiently Setting up Constant pH Molecular Dynamics Simulations in GROMACS.Journal of chemical information and modeling · 2024Article
- Alchemical Free Energy Workflows for the Computation of Protein-Ligand Binding Affinities.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Accelerating Alchemical Free Energy Prediction Using a Multistate Method: Application to Multiple Kinases.Journal of chemical information and modeling · 2023Article
- The maximal and current accuracy of rigorous protein-ligand binding free energy calculations.Communications chemistry · 2023Article
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Authors and funding
4 authors at 1 institution in 1 country.
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Abstract
The process of ligand binding to a biological target can be represented as the equilibrium between the relevant solvated and bound states of the ligand. This which is the basis of structure-based, rigorous methods such as the estimation of relative binding affinities by free energy perturbation (FEP). Despite the growing capacity of computing power and the development of more accurate force fields, a high throughput application of FEP is currently hampered due to the need, in the current schemes, of an expert user definition of the "alchemical" transformations between molecules in the series explored. Here, we present QligFEP, a solution to this problem using an automated workflow for FEP calculations based on a dual topology approach. In this scheme, the starting poses of each of the two ligands, for which the relative affinity is to be calculated, are explicitly present in the MD simulations associated with the (dual topology) FEP transformation, making the perturbation pathway between the two ligands univocal. We show that this generalized method can be applied to accurately estimate solvation free energies for amino acid sidechain mimics, as well as the binding affinity shifts due to the chemical changes typical of lead optimization processes. This is illustrated in a number of protein systems extracted from other FEP studies in the literature: inhibitors of CDK2 kinase and a series of A
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