ReviewFrontiers in molecular biosciences2021
Recent Developments in Free Energy Calculations for Drug Discovery.
Review in Frontiers in molecular biosciences, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.
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Who cites it
64 citing papers in PubMed.
- AntiLipo: A Comprehensive Database, Deep Learning-Based Prediction Model, and Computational Study of Anti-Hyperlipidemic Peptides.Interdisciplinary sciences, computational life sciences · 2026Article
- The Effect of CuACS chemical neuroscience · 2026Article
- ModBindProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Reproducibility, validation, and failure modes across classical and AI-driven molecular docking.Journal of computer-aided molecular design · 2026Review
- Understanding the structural stability and plasticity of VPS34 protein determined by selective/nonselective inhibitors: insights from molecular dynamics simulations.Molecular diversity · 2026Article
- Floridoside as a Hinge-Targeted Inhibitor of MAPK13: Atomistic Insights from Molecular Dynamics Simulations.Marine drugs · 2026Article
- Efficient Binding Affinity Estimation for Fragment-Based Compounds Using a Separated Topologies Approach.Journal of chemical information and modeling · 2026Article
- Enhancing mutation impact prediction in protein-protein interactions through interpretable graph-based multi-level feature interactions.Bioinformatics (Oxford, England) · 2026Article
- Free energy calculations in molecular modeling: from classical methods to machine learning.Journal of molecular modeling · 2026Review
- Molecular dynamics simulations of temperature-dependent PET binding in PETase, ThermoPETase, and FAST-PETase.RSC advances · 2026Article
- In Silico Profiling of Phytochemicals for Modulating Amyloid Beta-Mediated Immune Regulation and Neuroinflammation in Alzheimer's Disease.ACS omega · 2026Article
- Stacked ensemble learning and in-silico profiling reveal dual DPP-IV and SGLT2 inhibitors from Moringa oleifera metabolites.Scientific reports · 2026Article
- Hybrid Computational Framework Integrating Ensemble Learning, Molecular Docking, and Dynamics for Predicting Antimalarial Efficacy of Malaria Box Compounds.International journal of molecular sciences · 2026Article
- A Relative Binding Free Energy Framework for Structurally Dissimilar Molecules.Journal of chemical information and modeling · 2026Article
- Membrane insertion and dimerization of glycophorin-A mutations studied by free energy simulations.Biophysical journal · 2026Article
- Computer Simulations of Multidrug Efflux Pumps of the Resistance-Nodulation-Cell Division Superfamily.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Can AI-Predicted Complexes Teach Machine Learning to Compute Drug Binding Affinity?Journal of chemical information and modeling · 2025Article
- In silico-driven protocol for hit-to-lead optimization: a case study on PDE9A inhibitors.Journal of computer-aided molecular design · 2025Article
- Data-Efficient Equivariant NNPs Enable DFT-Accurate Simulations and Implicit Solvation Free Energies.The journal of physical chemistry. B · 2025Article
- Investigation of the Substrate Selection Mechanism of Poly (A) Polymerase Based on Molecular Dynamics Simulations and Markov State Model.International journal of molecular sciences · 2025Article
4 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
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Abstract
The grand challenge in structure-based drug design is achieving accurate prediction of binding free energies. Molecular dynamics (MD) simulations enable modeling of conformational changes critical to the binding process, leading to calculation of thermodynamic quantities involved in estimation of binding affinities. With recent advancements in computing capability and predictive accuracy, MD based virtual screening has progressed from the domain of theoretical attempts to real application in drug development. Approaches including the Molecular Mechanics Poisson Boltzmann Surface Area (MM-PBSA), Linear Interaction Energy (LIE), and alchemical methods have been broadly applied to model molecular recognition for drug discovery and lead optimization. Here we review the varied methodology of these approaches, developments enhancing simulation efficiency and reliability, remaining challenges hindering predictive performance, and applications to problems in the fields of medicine and biochemistry.
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