ArticleBioinformatics (Oxford, England)2018
Protein-protein interaction specificity is captured by contact preferences and interface composition.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Article
- A common network of residue-residue contacts underlies interactions between peptides and HLA class II complex.PloS one · 2026Article
- Article
- Increasing the fraction of correct solutions in ensembles of protein-protein docking models by an iterative consensus algorithm.Protein science : a publication of the Protein Society · 2025Article
- Assessing the functional impact of protein binding site definition.Protein science : a publication of the Protein Society · 2024Article
- DG-Affinity: predicting antigen-antibody affinity with language models from sequences.BMC bioinformatics · 2023Article
- MetaScore: A Novel Machine-Learning-Based Approach to Improve Traditional Scoring Functions for Scoring Protein-Protein Docking Conformations.Biomolecules · 2023Article
- Improving classification of correct and incorrect protein-protein docking models by augmenting the training set.Bioinformatics advances · 2023Article
- Deep Local Analysis evaluates protein docking conformations with locally oriented cubes.Bioinformatics (Oxford, England) · 2022Article
- A unified statistical potential reveals that amino acid stickiness governs nonspecific recruitment of client proteins into condensates.Protein science : a publication of the Protein Society · 2022Article
- Identifying vaccine escape sites via statistical comparisons of short-term molecular dynamics.Biophysical reports · 2022Article
- Engineered protein-small molecule conjugates empower selective enzyme inhibition.Cell chemical biology · 2022Article
- From complete cross-docking to partners identification and binding sites predictions.PLoS computational biology · 2022Article
- A random forest classifier for protein-protein docking models.Bioinformatics advances · 2022Article
- Classification and prediction of protein-protein interaction interface using machine learning algorithm.Scientific reports · 2021Article
- Classification and prediction of protein-protein interaction interface using machine learning algorithm.Scientific reports · 2021Article
- Mutation Edgotype Drives Fitness Effect in Human.Frontiers in bioinformatics · 2021Article
- Docking approaches for modeling multi-molecular assemblies.Current opinion in structural biology · 2020Review
- A knowledge-based scoring function to assess quaternary associations of proteins.Bioinformatics (Oxford, England) · 2020Article
- The mechanism of Single strand binding protein-RecG binding: Implications for SSB interactome function.Protein science : a publication of the Protein Society · 2020Article
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2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Motivation: Large-scale computational docking will be increasingly used in future years to discriminate protein-protein interactions at the residue resolution. Complete cross-docking experiments make in silico reconstruction of protein-protein interaction networks a feasible goal. They ask for efficient and accurate screening of the millions structural conformations issued by the calculations. Results: We propose CIPS (Combined Interface Propensity for decoy Scoring), a new pair potential combining interface composition with residue-residue contact preference. CIPS outperforms several other methods on screening docking solutions obtained either with all-atom or with coarse-grain rigid docking. Further testing on 28 CAPRI targets corroborates CIPS predictive power over existing methods. By combining CIPS with atomic potentials, discrimination of correct conformations in all-atom structures reaches optimal accuracy. The drastic reduction of candidate solutions produced by thousands of proteins docked against each other makes large-scale docking accessible to analysis. Availability and implementation: CIPS source code is freely available at http://www.lcqb.upmc.fr/CIPS. Contact: alessandra.carbone@lip6.fr. Supplementary information: Supplementary data are available at Bioinformatics online.
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