ArticleGenomics, proteomics & bioinformatics2024
Q-BioLiP: A Comprehensive Resource for Quaternary Structure-based Protein-ligand Interactions.
Article in Genomics, proteomics & bioinformatics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- A Site-Aware Representation Learning Framework For Unified Molecular Interaction Modeling and Generative Design.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- ProRB: a structure-free unified framework for joint prediction and design of protein-RNA interactions.Nucleic acids research · 2026Article
- DNAreader: accurate prediction of DNA-binding residues in structured and disordered proteins using transformers and contrastive learning.Nucleic acids research · 2026Article
- Protein-nucleic acid binding site prediction using interpretable Kolmogorov-Arnold networks with hypergraph representation learning.Bioinformatics (Oxford, England) · 2026Article
- MotifLeadDB: A Hierarchical Structural Data Set for Congeneric Ligand Binding Activity Change.Journal of chemical information and modeling · 2026Article
- Artificial Intelligence Powers Protein Functional Annotation.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Generative design and validation of therapeutic peptides for glioblastoma based on a potential target ATP5A.Briefings in bioinformatics · 2026Article
- ViralBindPredict: empowering viral protein-ligand binding sites through deep learning and protein sequence-derived insights.GigaScience · 2026Article
- β-Carotene liposome-based responsive hydrogel inhibits palmitoylation to restore intracellular calcium homeostasis for effective periodontitis treatment.Journal of nanobiotechnology · 2025Article
- Leveraging large language models for literature-driven prioritization of protein binding pockets.Bioinformatics (Oxford, England) · 2025Article
- Learning Universal Representations of Intermolecular Interactions with ATOMICA.bioRxiv : the preprint server for biology · 2025Article
- Natural Language Processing Methods for the Study of Protein-Ligand Interactions.Journal of chemical information and modeling · 2025Review
- Databases of ligand-binding pockets and protein-ligand interactions.Computational and structural biotechnology journal · 2024Review
- Article
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Authors and funding
4 authors.
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Abstract
Since its establishment in 2013, BioLiP has become one of the widely used resources for protein-ligand interactions. Nevertheless, several known issues occurred with it over the past decade. For example, the protein-ligand interactions are represented in the form of single chain-based tertiary structures, which may be inappropriate as many interactions involve multiple protein chains (known as quaternary structures). We sought to address these issues, resulting in Q-BioLiP, a comprehensive resource for quaternary structure-based protein-ligand interactions. The major features of Q-BioLiP include: (1) representing protein structures in the form of quaternary structures rather than single chain-based tertiary structures; (2) pairing DNA/RNA chains properly rather than separation; (3) providing both experimental and predicted binding affinities; (4) retaining both biologically relevant and irrelevant interactions to alleviate the wrong justification of ligands' biological relevance; and (5) developing a new quaternary structure-based algorithm for the modelling of protein-ligand complex structure. With these new features, Q-BioLiP is expected to be a valuable resource for studying biomolecule interactions, including protein-small molecule interaction, protein-metal ion interaction, protein-peptide interaction, protein-protein interaction, protein-DNA/RNA interaction, and RNA-small molecule interaction. Q-BioLiP is freely available at https://yanglab.qd.sdu.edu.cn/Q-BioLiP/.
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