ArticleCurrent opinion in structural biology2009
Computational evaluation of protein-small molecule binding.
Article in Current opinion in structural biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 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.
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.
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Who cites it
38 citing papers in PubMed.
- Article
- The impact of curation errors in the PDBBind Database on machine learning predictions of protein-protein binding affinity.Database : the journal of biological databases and curation · 2025Article
- Protein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning.Journal of cheminformatics · 2024Article
- A Hybrid Structure-Based Machine Learning Approach for Predicting Kinase Inhibition by Small Molecules.Journal of chemical information and modeling · 2023Article
- A New Hybrid Neural Network Deep Learning Method for Protein-Ligand Binding Affinity Prediction and De Novo Drug Design.International journal of molecular sciences · 2022Article
- OnionNet-2: A Convolutional Neural Network Model for Predicting Protein-Ligand Binding Affinity Based on Residue-Atom Contacting Shells.Frontiers in chemistry · 2021Article
- Second harmonic generation detection of Ras conformational changes and discovery of a small molecule binder.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Revealing the Mechanisms of Protein Disorder and N-Glycosylation in CD44-Hyaluronan Binding Using Molecular Simulation.Frontiers in immunology · 2015Review
- Site Identification by Ligand Competitive Saturation (SILCS) simulations for fragment-based drug design.Methods in molecular biology (Clifton, N.J.) · 2015Article
- Role of Desolvation in Thermodynamics and Kinetics of Ligand Binding to a Kinase.Journal of chemical theory and computation · 2014Article
- Supramolecular assemblies of a conjugate of nucleobase, amino acids, and saccharide act as agonists for proliferation of embryonic stem cells and development of zygotes.Bioconjugate chemistry · 2014Article
- Does a more precise chemical description of protein-ligand complexes lead to more accurate prediction of binding affinity?Journal of chemical information and modeling · 2014Article
- Large scale affinity calculations of cyclodextrin host-guest complexes: Understanding the role of reorganization in the molecular recognition process.Journal of chemical theory and computation · 2013Article
- Article
- Balancing target flexibility and target denaturation in computational fragment-based inhibitor discovery.Journal of computational chemistry · 2012Article
- Role of Ligand Reorganization and Conformational Restraints on the Binding Free Energies of DAPY Non-Nucleoside Inhibitors to HIV Reverse Transcriptase.Computational molecular bioscience · 2012Article
- Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition.Quarterly reviews of biophysics · 2012Review
- Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations.Journal of chemical theory and computation · 2012Article
- Flexibility and binding affinity in protein-ligand, protein-protein and multi-component protein interactions: limitations of current computational approaches.Journal of the Royal Society, Interface · 2012Review
- Quantitative predictions of binding free energy changes in drug-resistant influenza neuraminidase.PLoS computational biology · 2012Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Determining protein-small molecule binding affinity is a key component of present-day rational drug discovery. To circumvent the time, labor, and materials costs associated with experimental protein-small molecule binding assays, a variety of structure-based computational methods have been developed for determining protein-small molecule binding affinities. These methods can be placed in one of two classes: accurate but slow (Class 1), and fast but approximate (Class 2). Class 1 methods, which explicitly take into account protein flexibility and include an atomic-level description of solvation, are capable of quantitatively reproducing experimental protein-small molecule absolute binding free energies. However, Class 1 computational requirements make screening thousands to millions of small molecules against a protein, as required for rational drug design, infeasible for the foreseeable future. Class 2 methods, on the contrary, are sufficiently fast to perform such inhibitor screening, yet they suffer from limited descriptions of protein flexibility and solvation, which in turn limit their ability to select and rank-order small molecules by computed binding affinities. This review presents an overview of Class 1 and Class 2 methods, and avenues of research in Class 2 methods aimed at bringing them closer to Class 1 accuracy.
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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.