ArticleBioinformatics (Oxford, England)2022
AHoJ: rapid, tailored search and retrieval of apo and holo protein structures for user-defined ligands.
Article in Bioinformatics (Oxford, England), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- EmmaEmb: A quantitative framework for analyzing embedding spaces in molecular biology.Patterns (New York, N.Y.) · 2026Article
- PrankWeb 4: a modular web server for protein-ligand binding site prediction and downstream analysis.Nucleic acids research · 2025Article
- CryptoBench: cryptic protein-ligand binding sites dataset and benchmark.Bioinformatics (Oxford, England) · 2024Article
- AlphaFold2-Based Characterization of Apo and Holo Protein Structures and Conformational Ensembles Using Randomized Alanine Sequence Scanning Adaptation: Capturing Shared Signature Dynamics and Ligand-Induced Conformational Changes.International journal of molecular sciences · 2024Article
- DiffBindFR: an SE(3) equivariant network for flexible protein-ligand docking.Chemical science · 2024Article
- Article
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Authors and funding
4 authors.
Funding
Abstract
summaryUnderstanding the mechanism of action of a protein or designing better ligands for it, often requires access to a bound (holo) and an unbound (apo) state of the protein. Resources for the quick and easy retrieval of such conformations are severely limited. Apo-Holo Juxtaposition (AHoJ), is a web application for retrieving apo-holo structure pairs for user-defined ligands. Given a query structure and one or more user-specified ligands, it retrieves all other structures of the same protein that feature the same binding site(s), aligns them, and examines the superimposed binding sites to determine whether each structure is apo or holo, in reference to the query. The resulting superimposed datasets of apo-holo pairs can be visualized and downloaded for further analysis. AHoJ accepts multiple input queries, allowing the creation of customized apo-holo datasets. AVAILABILITY AND IMPLEMENTATION: Freely available for non-commercial use at http://apoholo.cz. Source code available at https://github.com/cusbg/AHoJ-project. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.