ArticleNucleic acids research2024
BioLiP2: an updated structure database for biologically relevant ligand-protein interactions.
Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 papers, 1 of them a synthesis that pooled it.
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Who cites it
69 citing papers in PubMed, 1 synthesis or guideline pooled it, 126 citations in OpenAlex.
- Protein Sequence Analysis landscape: A Systematic Review of Task Types, Databases, Datasets, Word Embeddings Methods, and Language Models.Database : the journal of biological databases and curation · 2025Pooled it
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- DNAreader: accurate prediction of DNA-binding residues in structured and disordered proteins using transformers and contrastive learning.Nucleic acids research · 2026Article
- CB-Dock3: an enhanced web server for protein-ligand blind docking.Nucleic acids research · 2026Article
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- SPPIDER-seq: sequence-based partner-aware predictor of protein-protein interaction sites.Bioinformatics (Oxford, England) · 2026Article
- Functional analysis of LIPID TRANSFER PROTEIN 6 (LTP6) in pennycress and Arabidopsis reveals divergent roles in oil storage and seed coat development.The Plant journal : for cell and molecular biology · 2026Article
- Probe-based identification of metal-binding sites using deep learning representations.Nature communications · 2026Article
- Direct Detection and Atomic Modeling of Ligands in Cryo-EM Maps Using Deep Learning.bioRxiv : the preprint server for biology · 2026Article
- A protein surface-aware multimodal framework for residue-level metal-binding site recognition.Cell reports methods · 2026Article
- SPPIDER-seq: Sequence-based partner-aware predictor of protein-protein interaction sites.bioRxiv : the preprint server for biology · 2026Article
- Automatically Defining Protein Words for Diverse Functional Predictions Based on Attention Analysis of a Protein Language Model.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
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- Deconvolving mutation effects on protein stability and function with disentangled protein language models.bioRxiv : the preprint server for biology · 2026Article
- More Accurate Binding Affinity Prediction Using Protein Homology and Ligand-Based Transfer Learning.Journal of chemical information and modeling · 2026Article
- Drug-Target Interaction Prediction with PIGLET.bioRxiv : the preprint server for biology · 2026Article
- Deciphering DEL pocket patterns through contrastive learning.Nature communications · 2026Article
- A fully automated benchmarking suite to compare macromolecular complexes.Nature methods · 2026Review
9 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
With the progress of structural biology, the Protein Data Bank (PDB) has witnessed rapid accumulation of experimentally solved protein structures. Since many structures are determined with purification and crystallization additives that are unrelated to a protein's in vivo function, it is nontrivial to identify the subset of protein-ligand interactions that are biologically relevant. We developed the BioLiP2 database (https://zhanggroup.org/BioLiP) to extract biologically relevant protein-ligand interactions from the PDB database. BioLiP2 assesses the functional relevance of the ligands by geometric rules and experimental literature validations. The ligand binding information is further enriched with other function annotations, including Enzyme Commission numbers, Gene Ontology terms, catalytic sites, and binding affinities collected from other databases and a manual literature survey. Compared to its predecessor BioLiP, BioLiP2 offers significantly greater coverage of nucleic acid-protein interactions, and interactions involving large complexes that are unavailable in PDB format. BioLiP2 also integrates cutting-edge structural alignment algorithms with state-of-the-art structure prediction techniques, which for the first time enables composite protein structure and sequence-based searching and significantly enhances the usefulness of the database in structure-based function annotations. With these new developments, BioLiP2 will continue to be an important and comprehensive database for docking, virtual screening, and structure-based protein function analyses.
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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.