ArticleNAR genomics and bioinformatics2022
PDBspheres: a method for finding 3D similarities in local regions in proteins.
Article in NAR genomics and bioinformatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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11 citing papers in PubMed, 10 citations in OpenAlex.
- 3D Geometric Equivariant Graph Neural Networks with Contrastive Learning for Protein-Ligand Binding Affinity Prediction.Interdisciplinary sciences, computational life sciences · 2026Article
- Spacio-Linear Screening for Ligand-Docking Cavities in Protein Structures: SLAM Algorithm.Life (Basel, Switzerland) · 2026Article
- Computational Approaches for Discovering Virulence Factors inJournal of fungi (Basel, Switzerland) · 2025Review
- Unsupervised learning reveals landscape of local structural motifs across protein classes.Bioinformatics (Oxford, England) · 2025Article
- Databases of ligand-binding pockets and protein-ligand interactions.Computational and structural biotechnology journal · 2024Review
- Identification and Ranking of Binding Sites from Structural Ensembles: Application to SARS-CoV-2.Viruses · 2024Article
- Transporter annotations are holding up progress in metabolic modeling.Frontiers in systems biology · 2024Article
- Clustering Protein Binding Pockets and Identifying Potential Drug Interactions: A Novel Ligand-Based Featurization Method.Journal of chemical information and modeling · 2023Article
- A Computational Pipeline to Identify and Characterize Binding Sites and Interacting Chemotypes in SARS-CoV-2.ACS omega · 2023Article
- COLLAPSE: A representation learning framework for identification and characterization of protein structural sites.Protein science : a publication of the Protein Society · 2023Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present a structure-based method for finding and evaluating structural similarities in protein regions relevant to ligand binding. PDBspheres comprises an exhaustive library of protein structure regions ('spheres') adjacent to complexed ligands derived from the Protein Data Bank (PDB), along with methods to find and evaluate structural matches between a protein of interest and spheres in the library. PDBspheres uses the LGA (Local-Global Alignment) structure alignment algorithm as the main engine for detecting structural similarities between the protein of interest and template spheres from the library, which currently contains >2 million spheres. To assess confidence in structural matches, an all-atom-based similarity metric takes side chain placement into account. Here, we describe the PDBspheres method, demonstrate its ability to detect and characterize binding sites in protein structures, show how PDBspheres-a strictly structure-based method-performs on a curated dataset of 2528 ligand-bound and ligand-free crystal structures, and use PDBspheres to cluster pockets and assess structural similarities among protein binding sites of 4876 structures in the 'refined set' of the PDBbind 2019 dataset.
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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.