ReviewCurrent opinion in structural biology2011
Advances in all atom sampling methods for modeling protein-ligand binding affinities.
Review in Current opinion in structural biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
59 citing papers in PubMed.
- An Automated Workflow for Diagnosing Sampling Issues Caused by Slow Torsional Motions in Molecular Simulations.Journal of chemical information and modeling · 2026Article
- Dual-LAO for calculating fast and robust relative binding free energies of simple and complex transformations.Communications chemistry · 2026Article
- AutoPocket2CREST: Automating Binding Pocket Extraction for the CREST Conformer Generation Pipeline.Journal of chemical information and modeling · 2026Article
- Alchemical Enhanced Sampling with Optimized Phase Space Overlap.Journal of chemical theory and computation · 2024Article
- Modern Alchemical Free Energy Methods for Drug Discovery Explained.ACS physical chemistry Au · 2023Review
- Scaffold Hopping and Optimization of Small Molecule Soluble Adenyl Cyclase Inhibitors Led by Free Energy Perturbation.Journal of chemical information and modeling · 2023Article
- Identification of and Mechanistic Insights into SARS-CoV-2 Main Protease Non-Covalent Inhibitors: An In-Silico Study.International journal of molecular sciences · 2023Article
- ACES: Optimized Alchemically Enhanced Sampling.Journal of chemical theory and computation · 2023Article
- Assessing the effect of forcefield parameter sets on the accuracy of relative binding free energy calculations.Frontiers in molecular biosciences · 2022Article
- Free Energy-Based Computational Methods for the Study of Protein-Peptide Binding Equilibria.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Binding thermodynamics and interaction patterns of human purine nucleoside phosphorylase-inhibitor complexes from extensive free energy calculations.Journal of computer-aided molecular design · 2021Article
- Variational Method for Networkwide Analysis of Relative Ligand Binding Free Energies with Loop Closure and Experimental Constraints.Journal of chemical theory and computation · 2021Article
- Thermodynamics and Kinetics of Drug-Target Binding by Molecular Simulation.Chemical reviews · 2020Review
- MovableType Software for Fast Free Energy-Based Virtual Screening: Protocol Development, Deployment, Validation, and Assessment.Journal of chemical information and modeling · 2020Article
- A fast and high-quality charge model for the next generation general AMBER force field.The Journal of chemical physics · 2020Article
- Improved Alchemical Free Energy Calculations with Optimized Smoothstep Softcore Potentials.Journal of chemical theory and computation · 2020Article
- Combining Machine Learning and Enhanced Sampling Techniques for Efficient and Accurate Calculation of Absolute Binding Free Energies.Journal of chemical theory and computation · 2020Article
- SAMPL6 host-guest binding affinities and binding poses from spherical-coordinates-biased simulations.Journal of computer-aided molecular design · 2020Article
- Article
- Absolute Protein Binding Free Energy Simulations for Ligands with Multiple Poses, a Thermodynamic Path That Avoids Exhaustive Enumeration of the Poses.Journal of computational chemistry · 2020Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Conformational dynamics plays a fundamental role in the regulation of molecular recognition processes. Conformational heterogeneity and entropy variations upon binding, although not always evident from the analysis of structural data, can substantially affect affinity and specificity. Computer modeling is able to provide some of the most direct insights into these aspects of molecular recognition. We review recent physics-based computational studies that employ advanced conformational sampling algorithms and effective potentials to model the three main classes of degrees of freedom relevant to the binding process: ligand positioning relative to the receptor, ligand and receptor internal reorganization, and hydration. Collectively these studies show that all of these elements are important for proper modeling of protein-ligand interactions.
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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.