ArticleBMC bioinformatics2011
Comprehensive, atomic-level characterization of structurally characterized protein-protein interactions: the PICCOLO database.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- COCFrontiers in bioinformatics · 2025Article
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- Statistical analysis of sequential motifs at biologically relevant protein-protein interfaces.Computational and structural biotechnology journal · 2024Article
- Inhibition of FOXP3 by stapled alpha-helical peptides dampens regulatory T cell function.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Structural landscapes of PPI interfaces.Briefings in bioinformatics · 2022Review
- mPPI: a database extension to visualize structural interactome in a one-to-many manner.Database : the journal of biological databases and curation · 2021Article
- Structural motifs in protein cores and at protein-protein interfaces are different.Protein science : a publication of the Protein Society · 2021Article
- Propedia: a database for protein-peptide identification based on a hybrid clustering algorithm.BMC bioinformatics · 2021Article
- VTR: A Web Tool for Identifying Analogous Contacts on Protein Structures and Their Complexes.Frontiers in bioinformatics · 2021Article
- Proteus: An algorithm for proposing stabilizing mutation pairs based on interactions observed in known protein 3D structures.BMC bioinformatics · 2020Article
- The Early Phase of β2m Aggregation: An Integrative Computational Study Framed on the D76N Mutant and the ΔN6 Variant.Biomolecules · 2019Article
- Proteome-wide, Structure-Based Prediction of Protein-Protein Interactions/New Molecular Interactions Viewer.Plant physiology · 2019Article
- Protein-protein interactions leave evolutionary footprints: High molecular coevolution at the core of interfaces.Protein science : a publication of the Protein Society · 2017Article
- Arpeggio: A Web Server for Calculating and Visualising Interatomic Interactions in Protein Structures.Journal of molecular biology · 2017Article
- Article
- Small molecules, big targets: drug discovery faces the protein-protein interaction challenge.Nature reviews. Drug discovery · 2016Review
- Distinctive Behaviors of Druggable Proteins in Cellular Networks.PLoS computational biology · 2015Article
- Matched Peptides: Tuning Matched Molecular Pair Analysis for Biopharmaceutical Applications.Journal of chemical information and modeling · 2015Article
- Flexibility and small pockets at protein-protein interfaces: New insights into druggability.Progress in biophysics and molecular biology · 2015Review
- Algorithmic approaches to protein-protein interaction site prediction.Algorithms for molecular biology : AMB · 2015Article
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3 authors.
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Abstract
backgroundStructural studies are increasingly providing huge amounts of information on multi-protein assemblies. Although a complete understanding of cellular processes will be dependent on an explicit characterization of the intermolecular interactions that underlie these assemblies and mediate molecular recognition, these are not well described by standard representations.
resultsHere we present PICCOLO, a comprehensive relational database capturing the details of structurally characterized protein-protein interactions. Interactions are described at the level of interacting pairs of atoms, residues and polypeptide chains, with the physico-chemical nature of the interactions being characterized. Distance and angle terms are used to distinguish 12 different interaction types, including van der Waals contacts, hydrogen bonds and hydrophobic contacts. The explicit aim of PICCOLO is to underpin large-scale analyses of the properties of protein-protein interfaces. This is exemplified by an analysis of residue propensity and interface contact preferences derived from a much larger data set than previously reported. However, PICCOLO also supports detailed inspection of particular systems of interest.
conclusionsThe current PICCOLO database comprises more than 260 million interacting atom pairs from 38,202 protein complexes. A web interface for the database is available at http://www-cryst.bioc.cam.ac.uk/piccolo.
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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.