ArticleFrontiers in molecular biosciences2022
Relative binding free energy calculations with transformato: A molecular dynamics engine-independent tool.
Article in Frontiers in molecular biosciences, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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7 citing papers in PubMed.
- Molecular Dynamics Simulation of NTO/TNPyO Co-Crystals for Targeted Acidity Regulation of NTO.Langmuir : the ACS journal of surfaces and colloids · 2026Article
- Ligand Binding Affinity Prediction for Membrane Proteins with Alchemical Free Energy Calculation Methods.Journal of chemical information and modeling · 2024Article
- Insights and Challenges in Correcting Force Field Based Solvation Free Energies Using a Neural Network Potential.The journal of physical chemistry. B · 2024Article
- Updates to Protex for Simulating Proton Transfers in an Ionic Liquid.The journal of physical chemistry. B · 2024Article
- Alchemical Free Energy Workflows for the Computation of Protein-Ligand Binding Affinities.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Calculations of Absolute Solvation Free Energies with Transformato─Application to the FreeSolv Database Using the CGenFF Force Field.Journal of chemical theory and computation · 2023Article
- Broadening the Scope of Binding Free Energy Calculations Using a Separated Topologies Approach.Journal of chemical theory and computation · 2023Article
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3 authors.
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Abstract
We present the software package transformato for the setup of large-scale relative binding free energy calculations. Transformato is written in Python as an open source project (https://github.com/wiederm/transformato); in contrast to comparable tools, it is not closely tied to a particular molecular dynamics engine to carry out the underlying simulations. Instead of alchemically transforming a ligand
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