ArticleBMC bioinformatics2020
GSP4PDB: a web tool to visualize, search and explore protein-ligand structural patterns.
Article in BMC bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Novel metal sites revealed by spectroscopic and structural characterization of the ferric uptake regulator fromComputational and structural biotechnology journal · 2025Article
- User-centric design of a 3D search interface for protein-ligand complexes.Journal of computer-aided molecular design · 2024Article
- An optimized relational database for querying structural patterns in proteins.Database : the journal of biological databases and curation · 2024Article
- Comparative in silico analysis of CNS-active molecules targeting the blood-brain barrier choline transporter for Alzheimer's disease therapy.In silico pharmacology · 2024Article
- Structure-Based Design of Small Imine Reductase Panels for Target Substrates.ACS catalysis · 2023Article
- Databases and Tools to Investigate Protein-Metabolite Interactions.Methods in molecular biology (Clifton, N.J.) · 2023Article
- An Overview of Antiviral Peptides and Rational Biodesign Considerations.Biodesign research · 2022Review
- Computational methods directed towards drug repurposing for COVID-19: advantages and limitations.RSC advances · 2021Review
- Computational Enzyme Engineering Pipelines for Optimized Production of Renewable Chemicals.Frontiers in bioengineering and biotechnology · 2021Review
- Main findings and advances in bioinformatics and biomedical engineering- IWBBIO 2018.BMC bioinformatics · 2020Article
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Authors and funding
5 authors.
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Abstract
backgroundIn the field of protein engineering and biotechnology, the discovery and characterization of structural patterns is highly relevant as these patterns can give fundamental insights into protein-ligand interaction and protein function. This paper presents GSP4PDB, a bioinformatics web tool that enables the user to visualize, search and explore protein-ligand structural patterns within the entire Protein Data Bank.
resultsWe introduce the notion of graph-based structural pattern (GSP) as an abstract model for representing protein-ligand interactions. A GSP is a graph where the nodes represent entities of the protein-ligand complex (amino acids and ligands) and the edges represent structural relationships (e.g. distances ligand - amino acid). The novel feature of GSP4PDB is a simple and intuitive graphical interface where the user can "draw" a GSP and execute its search in a relational database containing the structural data of each PDB entry. The results of the search are displayed using the same graph-based representation of the pattern. The user can further explore and analyse the results using a wide range of filters, or download their related information for external post-processing and analysis.
conclusionsGSP4PDB is a user-friendly and efficient application to search and discover new patterns of protein-ligand interaction.
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