ReviewComputational and structural biotechnology journal2024
Databases of ligand-binding pockets and protein-ligand interactions.
Review in Computational and structural biotechnology journal, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 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
14 citing papers in PubMed.
- Integrated Framework for Probing Multimodal Protein Foundation Models with Structure-Functional Interpretability Analysis in Detection of Allosteric Binding Sites.bioRxiv : the preprint server for biology · 2026Article
- Predicting and Decoding Allosteric Binding Sites Using Protein Language Models and Structure-Based Machine Learning: An Energy Landscape-Guided Explainable AI Framework.Journal of chemical theory and computation · 2026Article
- Integrated computational and experimental analysis explores FOLH1 expression patterns across cancers and nominates melatonin as a potential modulator in prostate cancer models.PLoS computational biology · 2026Article
- Artemis: Harnessing Knowledge Graphs for Next-Generation Drug Target Prioritization.Computational and structural biotechnology journal · 2026Article
- Computational approaches to druggable site identification: Current status and future perspective.Acta pharmaceutica Sinica. B · 2026Review
- In Silico Laboratory: New and Updated Tools for Protein-Centered Drug Discovery.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Artificial intelligence-guided discovery of a lead compound with antifolate-like activity against bacterial and human thymidylate synthases.Frontiers in cellular and infection microbiology · 2026Article
- The Human Omnibus of Targetable Pockets.Journal of cheminformatics · 2025Article
- In Silico Identification of Molecular Interactions of the Emerging Contaminant Octyl Methoxycinnamate (OMC) on HPT Axis: Implications for Humans and Zebrafish.Pharmaceuticals (Basel, Switzerland) · 2025Article
- Computational drug repurposing: approaches, evaluation of in silico resources and case studies.Nature reviews. Drug discovery · 2025Review
- A Computational Approach to Identify Novel Protein Targets Uncovers New Potential Mechanisms of Action of Mirtazapine S(+) and R(-) Enantiomers in Rett Syndrome.Journal of neurochemistry · 2025Article
- ProCV: A 3D similarity grouping method for enhanced protein pocket recognition and ligand interaction analysis.iScience · 2025Article
- Preparation and Characterization of Cumin Essential Oil Nanoemulsion (CEONE) as an Antibacterial Agent and Growth Promoter in Broilers: A Study on Efficacy, Safety, and Health Impact.Animals : an open access journal from MDPI · 2024Article
- Allostery Illuminated: Harnessing AI and Machine Learning for Drug Discovery.ACS medicinal chemistry letters · 2024Review
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Many research groups and institutions have created a variety of databases curating experimental and predicted data related to protein-ligand binding. The landscape of available databases is dynamic, with new databases emerging and established databases becoming defunct. Here, we review the current state of databases that contain binding pockets and protein-ligand binding interactions. We have compiled a list of such databases, fifty-three of which are currently available for use. We discuss variation in how binding pockets are defined and summarize pocket-finding methods. We organize the fifty-three databases into subgroups based on goals and contents, and describe standard use cases. We also illustrate that pockets within the same protein are characterized differently across different databases. Finally, we assess critical issues of sustainability, accessibility and redundancy.
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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.