ReviewJournal of structural and functional genomics2011
Beyond structural genomics: computational approaches for the identification of ligand binding sites in protein structures.
Review in Journal of structural and functional genomics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 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
20 citing papers in PubMed.
- xBind: an integrated webserver for large language model-enabled cross-molecular protein binding site prediction.Nucleic acids research · 2026Article
- Structural engineering, BSA binding and computational analysis of isonipacotate based enzyme inhibitors containing 1,2,4-triazole.PloS one · 2026Article
- Nanosponge-Encapsulated Polyoxometalates: Unveiling the Multi-Faceted Potential Against Cancers and Metastases Through Comprehensive Preparation, Characterization, and Computational Exploration.Pharmaceuticals (Basel, Switzerland) · 2025Article
- Beyond Chemistry: Investigating the Physical, Pharmacological, and Computational Aspects of Polyoxometalate Integrated Solid Lipid Nanoparticles for Cancer Treatment.International journal of nanomedicine · 2025Article
- Systematic computational strategies for identifying protein targets and lead discovery.RSC medicinal chemistry · 2024Review
- Comprehensive Survey of Consensus Docking for High-Throughput Virtual Screening.Molecules (Basel, Switzerland) · 2022Review
- Identification of Cryptic Binding Sites Using MixMD with Standard and Accelerated Molecular Dynamics.Journal of chemical information and modeling · 2021Article
- Geometric Detection Algorithms for Cavities on Protein Surfaces in Molecular Graphics: A Survey.Computer graphics forum : journal of the European Association for Computer Graphics · 2017Article
- AutoSite: an automated approach for pseudo-ligands prediction-from ligand-binding sites identification to predicting key ligand atoms.Bioinformatics (Oxford, England) · 2016Article
- Predicting Ligand Binding Sites on Protein Surfaces by 3-Dimensional Probability Density Distributions of Interacting Atoms.PloS one · 2016Article
- Computational methods in drug discovery.Beilstein journal of organic chemistry · 2016Review
- Charting a Path to Success in Virtual Screening.Molecules (Basel, Switzerland) · 2015Review
- Identification of binding sites and favorable ligand binding moieties by virtual screening and self-organizing map analysis.BMC bioinformatics · 2015Article
- POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics.Journal of chemical theory and computation · 2014Article
- Pocket-based drug design: exploring pocket space.The AAPS journal · 2013Review
- Exploring the composition of protein-ligand binding sites on a large scale.PLoS computational biology · 2013Article
- Bioinformatics and variability in drug response: a protein structural perspective.Journal of the Royal Society, Interface · 2012Review
- PepSite: prediction of peptide-binding sites from protein surfaces.Nucleic acids research · 2012Article
- SiteComp: a server for ligand binding site analysis in protein structures.Bioinformatics (Oxford, England) · 2012Article
- Ionic channels as targets for drug design: a review on computational methods.Pharmaceutics · 2011Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Structural genomics projects have revealed structures for a large number of proteins of unknown function. Understanding the interactions between these proteins and their ligands would provide an initial step in their functional characterization. Binding site identification methods are a fast and cost-effective way to facilitate the characterization of functionally important protein regions. In this review we describe our recently developed methods for binding site identification in the context of existing methods. The advantage of energy-based approaches is emphasized, since they provide flexibility in the identification and characterization of different types of binding sites.
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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.