ArticleThe journal of physical chemistry. B2020
How Good is Jarzynski's Equality for Computer-Aided Drug Design?
Article in The journal of physical chemistry. B, 2020. 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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Who cites it
7 citing papers in PubMed, 22 citations in OpenAlex.
- Differentiation of RNA-protein docking structures through molecular dynamics simulation and machine learning methods.Briefings in bioinformatics · 2026Article
- Multisite λ-Dynamics for Protein-DNA Binding Affinity Prediction.Journal of chemical theory and computation · 2025Article
- Treatment of flexibility of protein backbone in simulations of protein-ligand interactions using steered molecular dynamics.Scientific reports · 2024Article
- Crystallographic and Computational Insights into Isoform-Selective Dynamics in Nitric Oxide Synthase.Biochemistry · 2024Article
- Fluctuation Relations to Calculate Protein Redox Potentials from Molecular Dynamics Simulations.Journal of chemical theory and computation · 2024Article
- Nonspecific vs. specific DNA binding free energetics of a transcription factor domain protein.Biophysical journal · 2023Article
- Dependence of Work on the Pulling Speed in Mechanical Ligand Unbinding.The journal of physical chemistry. B · 2021Article
Corrections and comments
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Authors and funding
3 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Accurate determination of the binding affinity of the ligand to the receptor remains a difficult problem in computer-aided drug design. Here, we study and compare the efficiency of Jarzynski's equality (JE) combined with steered molecular dynamics and the linear interaction energy (LIE) method by assessing the binding affinity of 23 small compounds to six receptors, including β-lactamase, thrombin, factor Xa, HIV-1 protease (HIV), myeloid cell leukemia-1, and cyclin-dependent kinase 2 proteins. It was shown that Jarzynski's nonequilibrium binding free energy Δ
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