ReviewInternational journal of molecular sciences2022
Estimating the Similarity between Protein Pockets.
Review in International journal of molecular sciences, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 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
16 citing papers in PubMed, 34 citations in OpenAlex.
- Ligand Design Using Unique Conformations to Preferentially Dock a Specific Site on Collagen-Bound MMP1.Biology · 2026Article
- PockFlex: a web server for flexibility-aware binding site identification and prioritisation from structural ensembles.Nucleic acids research · 2026Article
- Drug design using unique conformations to preferentially target a specific site on collagen-bound MMP1.bioRxiv : the preprint server for biology · 2026Article
- Spacio-Linear Screening for Ligand-Docking Cavities in Protein Structures: SLAM Algorithm.Life (Basel, Switzerland) · 2026Article
- Computational approaches to druggable site identification: Current status and future perspective.Acta pharmaceutica Sinica. B · 2026Review
- Eigenvalue Ratios Reveal Shared Binding Pocket Shapes in RNA and Protein Structures.Computational and structural biotechnology journal · 2026Article
- Multi-Component Synthesis of New Fluorinated-Pyrrolo[3,4-International journal of molecular sciences · 2025Article
- From Concepts to Inhibitors: A Blueprint for Targeting Protein-Protein Interactions.Chemical reviews · 2025Review
- Towards a comprehensive view of the pocketome universe-biological implications and algorithmic challenges.PLoS computational biology · 2025Article
- ProCV: A 3D similarity grouping method for enhanced protein pocket recognition and ligand interaction analysis.iScience · 2025Article
- Proteome-Wide Identification and Comparison of Drug Pockets for Discovering New Drug Indications and Side Effects.Molecules (Basel, Switzerland) · 2025Article
- Databases of ligand-binding pockets and protein-ligand interactions.Computational and structural biotechnology journal · 2024Review
- Comprehensive detection and characterization of human druggable pockets through binding site descriptors.Nature communications · 2024Article
- VirtuousPocketome: a computational tool for screening protein-ligand complexes to identify similar binding sites.Scientific reports · 2024Article
- Integrated Molecular Modeling and Machine Learning for Drug Design.Journal of chemical theory and computation · 2023Review
- AlphaFold, allosteric, and orthosteric drug discovery: Ways forward.Drug discovery today · 2023Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
With the exponential increase in publicly available protein structures, the comparison of protein binding sites naturally emerged as a scientific topic to explain observations or generate hypotheses for ligand design, notably to predict ligand selectivity for on- and off-targets, explain polypharmacology, and design target-focused libraries. The current review summarizes the state-of-the-art computational methods applied to pocket detection and comparison as well as structural druggability estimates. The major strengths and weaknesses of current pocket descriptors, alignment methods, and similarity search algorithms are presented. Lastly, an exhaustive survey of both retrospective and prospective applications in diverse medicinal chemistry scenarios illustrates the capability of the existing methods and the hurdle that still needs to be overcome for more accurate predictions.
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What OpenQuestion holds
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.