ReviewAnnual review of biophysics2017
Predicting Binding Free Energies: Frontiers and Benchmarks.
Review in Annual review of biophysics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 175 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
175 citing papers in PubMed.
- Benchmarking Boltz-2 for relative kinase-inhibitor interaction patterns across conformational states and resistance mutations.npj drug discovery · 2026Article
- Evaluating molecular docking for binding affinity predictions: a systematic analysis of key parameters and the utility of AlphaFold2 structures for the Schrödinger dataset.Journal of computer-aided molecular design · 2026Article
- One Blob to Rule Them All: A Universal Dual-Topology Nonequilibrium Framework for Relative and Absolute Binding Free Energies via a Lennard-Jones Blob Reference.Journal of chemical theory and computation · 2026Article
- ARG128-associated recognition of nobiletin by BACE1 revealed by triplicate molecular dynamics, MM-GBSA, and residue-level decomposition.Molecular diversity · 2026Article
- 3DICE: interpretable 3D cross-modal learning for drug-target interaction prediction and large-scale drug discovery.Bioinformatics (Oxford, England) · 2026Article
- PrimaDORAC: An improved Web Interface for Rapid GAFF2 Parameter Assignment with ABCG2 Charge Models for Drug Design Applications.Journal of computational chemistry · 2026Article
- Evaluating AI-Generated Molecules for Drug Discovery: From Generic Metrics to Translational Readiness.International journal of molecular sciences · 2026Review
- The deformation energy gap in computational drug design: why interaction energy alone cannot rank drug candidates and a thermodynamic correction protocol.Journal of molecular modeling · 2026Article
- Molecular Quantum Computations on a Protein.Journal of chemical theory and computation · 2026Article
- MotifLeadDB: A Hierarchical Structural Data Set for Congeneric Ligand Binding Activity Change.Journal of chemical information and modeling · 2026Article
- An Automated Workflow for Diagnosing Sampling Issues Caused by Slow Torsional Motions in Molecular Simulations.Journal of chemical information and modeling · 2026Article
- A Risk-Tiered Validation Framework for Artificial Intelligence in Drug Discovery: From Reproducibility to Clinical Translation.International journal of molecular sciences · 2026Review
- How to Use Quantum Computers for Biomolecular Free Energies.Journal of chemical theory and computation · 2026Article
- Exploring the mechanism of Dieda Qili Tablet on fracture healing based on network pharmacology combined with machine learning models.Scientific reports · 2026Article
- Electronic Descriptors Governing Binding Energies of Bidentate Aromatic Ligands with Metal Cations: Insights from DFT and Statistical Analysis.The journal of physical chemistry. A · 2026Article
- Prediction of Protein-Ligand Binding Affinities Using Atomic Surface Site Interaction Points.Journal of chemical information and modeling · 2026Article
- RNP interfaces as regulatory "active sites": a repurposing strategy for small molecules targeting viral 5'-untranslated regions.Frontiers in molecular biosciences · 2026Article
- Machine Learning-Driven Bioprospecting of Cholinergic Medicinal Plants for Putative Leads Against Butyrylcholinesterase Towards Alzheimer's Care.Biochemistry research international · 2026Article
- AI-Driven De Novo Binder Design: From Structure Prediction to Closed-Loop Optimization.Computational and structural biotechnology journal · 2026Review
- Assessing Computational Strategies for the Evaluation of Antibody Binding Affinities.Journal of chemical theory and computation · 2025Article
115 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Binding free energy calculations based on molecular simulations provide predicted affinities for biomolecular complexes. These calculations begin with a detailed description of a system, including its chemical composition and the interactions among its components. Simulations of the system are then used to compute thermodynamic information, such as binding affinities. Because of their promise for guiding molecular design, these calculations have recently begun to see widespread applications in early-stage drug discovery. However, many hurdles remain in making them a robust and reliable tool. In this review, we highlight key challenges of these calculations, discuss some examples of these challenges, and call for the designation of standard community benchmark test systems that will help the research community generate and evaluate progress. In our view, progress will require careful assessment and evaluation of new methods, force fields, and modeling innovations on well-characterized benchmark systems, and we lay out our vision for how this can be achieved.
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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.