ArticlePLoS computational biology2015
Local Geometry and Evolutionary Conservation of Protein Surfaces Reveal the Multiple Recognition Patches in Protein-Protein Interactions.
Article in PLoS computational biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- PRESCOTT: a population aware, epistatic, and structural model accurately predicts missense effects.Genome biology · 2025Article
- Impact of phylogeny on the inference of functional sectors from protein sequence data.PLoS computational biology · 2024Article
- Assessing the functional impact of protein binding site definition.Protein science : a publication of the Protein Society · 2024Article
- Article
- Deep Local Analysis deconstructs protein-protein interfaces and accurately estimates binding affinity changes upon mutation.Bioinformatics (Oxford, England) · 2023Article
- Deep Local Analysis evaluates protein docking conformations with locally oriented cubes.Bioinformatics (Oxford, England) · 2022Article
- Deep graph learning of inter-protein contacts.Bioinformatics (Oxford, England) · 2022Article
- From complete cross-docking to partners identification and binding sites predictions.PLoS computational biology · 2022Article
- Protein structure, amino acid composition and sequence determine proteome vulnerability to oxidation-induced damage.The EMBO journal · 2020Article
- Multiple protein-DNA interfaces unravelled by evolutionary information, physico-chemical and geometrical properties.PLoS computational biology · 2020Article
- Article
- Water follows polar and nonpolar protein surface domains.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Interactome of Glyceraldehyde-3-Phosphate Dehydrogenase Points to the Existence of Metabolons inFrontiers in microbiology · 2019Article
- Identification and visualization of protein binding regions with the ArDock server.Nucleic acids research · 2018Article
- Meet-U: Educating through research immersion.PLoS computational biology · 2018Article
- Protein-protein interaction specificity is captured by contact preferences and interface composition.Bioinformatics (Oxford, England) · 2018Article
- JET2 Viewer: a database of predicted multiple, possibly overlapping, protein-protein interaction sites for PDB structures.Nucleic acids research · 2017Article
- Protein social behavior makes a stronger signal for partner identification than surface geometry.Proteins · 2017Article
- Great interactions: How binding incorrect partners can teach us about protein recognition and function.Proteins · 2016Article
- Coevolution analysis of Hepatitis C virus genome to identify the structural and functional dependency network of viral proteins.Scientific reports · 2016Article
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2 authors.
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Abstract
Protein-protein interactions (PPIs) are essential to all biological processes and they represent increasingly important therapeutic targets. Here, we present a new method for accurately predicting protein-protein interfaces, understanding their properties, origins and binding to multiple partners. Contrary to machine learning approaches, our method combines in a rational and very straightforward way three sequence- and structure-based descriptors of protein residues: evolutionary conservation, physico-chemical properties and local geometry. The implemented strategy yields very precise predictions for a wide range of protein-protein interfaces and discriminates them from small-molecule binding sites. Beyond its predictive power, the approach permits to dissect interaction surfaces and unravel their complexity. We show how the analysis of the predicted patches can foster new strategies for PPIs modulation and interaction surface redesign. The approach is implemented in JET2, an automated tool based on the Joint Evolutionary Trees (JET) method for sequence-based protein interface prediction. JET2 is freely available at www.lcqb.upmc.fr/JET2.
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