ArticleProteins2014
Binding interface prediction by combining protein-protein docking results.
Article in Proteins, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- A Two-Layer SVM Ensemble-Classifier to Predict Interface Residue Pairs of Protein Trimers.Molecules (Basel, Switzerland) · 2020Article
- Article
- SKEMPI 2.0: an updated benchmark of changes in protein-protein binding energy, kinetics and thermodynamics upon mutation.Bioinformatics (Oxford, England) · 2019Article
- Protein-protein binding supersites.PLoS computational biology · 2019Article
- Interactome INSIDER: a structural interactome browser for genomic studies.Nature methods · 2018Article
- Performance of ZDOCK and IRAD in CAPRI rounds 28-34.Proteins · 2017Article
- Identification and characterization of a neutralizing monoclonal antibody that provides complete protection against Yersinia pestis.PloS one · 2017Article
- A novel index of protein-protein interface propensity improves interface residue recognition.BMC systems biology · 2016Article
- Great interactions: How binding incorrect partners can teach us about protein recognition and function.Proteins · 2016Article
- Protein-protein docking by fast generalized Fourier transforms on 5D rotational manifolds.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- A hybrid method for protein-protein interface prediction.Protein science : a publication of the Protein Society · 2016Article
- Progress and challenges in predicting protein interfaces.Briefings in bioinformatics · 2016Review
- Review
- CRF-based models of protein surfaces improve protein-protein interaction site predictions.BMC bioinformatics · 2014Article
- Drug-Like Protein-Protein Interaction Modulators: Challenges and Opportunities for Drug Discovery and Chemical Biology.Molecular informatics · 2014Review
- Performance of ZDOCK in CAPRI rounds 20-26.Proteins · 2013Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
We developed a method called residue contact frequency (RCF), which uses the complex structures generated by the protein-protein docking algorithm ZDOCK to predict interface residues. Unlike interface prediction algorithms that are based on monomers alone, RCF is binding partner specific. We evaluated the performance of RCF using the area under the precision-recall (PR) curve (AUC) on a large protein docking Benchmark. RCF (AUC = 0.44) performed as well as meta-PPISP (AUC = 0.43), which is one of the best monomer-based interface prediction methods. In addition, we test a support vector machine (SVM) to combine RCF with meta-PPISP and another monomer-based interface prediction algorithm Evolutionary Trace to further improve the performance. We found that the SVM that combined RCF and meta-PPISP achieved the best performance (AUC = 0.47). We used RCF to predict the binding interfaces of proteins that can bind to multiple partners and RCF was able to correctly predict interface residues that are unique for the respective binding partners. Furthermore, we found that residues that contributed greatly to binding affinity (hotspot residues) had significantly higher RCF than other residues.
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Registered trials
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