ArticleProteins2010
A comprehensive examination of the contributions to the binding entropy of protein-ligand complexes.
Article in Proteins, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 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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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.
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Who cites it
30 citing papers in PubMed.
- In Silico Isomerization Produces Apt Negative Data for VHTS Validation.Journal of chemical information and modeling · 2026Article
- BindPred: a framework for predicting protein-protein binding affinity from language model embeddings.Bioinformatics (Oxford, England) · 2026Article
- Entropy estimation in acetylcholinesterase-donepezil interaction through topological indices: a graph theoretical perspective.Frontiers in chemistry · 2026Article
- l-DOPA-Containing Protein Autoxidation: An Empirical Valence Bond Simulation of the Rate-Limiting Step.The journal of physical chemistry. B · 2025Article
- Integrated Network Pharmacology, Molecular Modeling, LC-MS Profiling, and Semisynthetic Approach for the Roots ofACS omega · 2025Article
- Ligand Reorganization for End-Point Binding Free Energy Calculations: Identifying Preferred Poses of Fentanyls in the μ Opioid Receptor.Journal of chemical theory and computation · 2025Article
- Expression, Purification and Biophysical Characterisation of Klebsiella Pneumoniae Protein Adenylyltransferase: A Systematic Integration of Empirical and Computational Modelling Approaches.The protein journal · 2024Article
- Full-Length NADBiochemistry · 2023Article
- Delineating the activity of the potent nicotinic acetylcholine receptor agonists (+)-anatoxin-a and (-)-hosieine-A.Acta crystallographica. Section F, Structural biology communications · 2022Article
- Enthalpy-Entropy Compensation in Biomolecular Recognition: A Computational Perspective.ACS omega · 2021Review
- The Energetic Origin of Different Catalytic Activities in Temperature-Adapted Trypsins.ACS omega · 2020Article
- On Restraints in End-Point Protein-Ligand Binding Free Energy Calculations.Journal of computational chemistry · 2020Article
- Validating the Water Flooding Approach by Comparing It to Grand Canonical Monte Carlo Simulations.The journal of physical chemistry. B · 2017Article
- Entropy in molecular recognition by proteins.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Structural characterization of metal binding to a cold-adapted frataxin.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2015Article
- The entropic contributions in vitamin B12 enzymes still reflect the electrostatic paradigm.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Methyltransferases do not work by compression, cratic, or desolvation effects, but by electrostatic preorganization.Proteins · 2015Article
- Computer aided enzyme design and catalytic concepts.Current opinion in chemical biology · 2014Review
- Article
- Capturing the energetics of water insertion in biological systems: the water flooding approach.Proteins · 2013Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
One of the most important requirements in computer-aided drug design is the ability to reliably evaluate the binding free energies. However, the process of ligand binding is very complex because of the intricacy of the interrelated processes that are difficult to predict and quantify. In fact, the deeper understanding of the origin of the observed binding free energies requires the ability to decompose these free energies to their contributions from different interactions. Furthermore, it is important to evaluate the relative entropic and enthalpic contributions to the overall free energy. Such an evaluation is useful for assessing temperature effects and exploring specialized options in enzyme design. Unfortunately, calculations of binding entropies have been much more challenging than calculations of binding free energies. This work is probably the first to present microscopic evaluation of all of the relevant components to the binding entropy, namely configurational, polar solvation, and hydrophobic entropies. All of these contributions are evaluated by the restraint release approach. The calculated results shed an interesting light on major compensation effects in both the solvation and hydrophobic effect and, despite some overestimate, can provide very useful insight. This study also helps in analyzing some problems with the widely used molecular mechanics/Poisson-Boltzmann surface area approach.
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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.