ArticleBioinformatics (Oxford, England)2015
Structure-PPi: a module for the annotation of cancer-related single-nucleotide variants at protein-protein interfaces.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed, 41 citations in OpenAlex.
- DL-PPI: a method on prediction of sequenced protein-protein interaction based on deep learning.BMC bioinformatics · 2023Article
- Disruptor: Computational identification of oncogenic mutants disrupting protein-protein and protein-DNA interactions.Communications biology · 2023Article
- Brain radiotoxicity-related 15CAcBRT gene expression signature predicts survival prognosis of glioblastoma patients.Neuro-oncology · 2023Article
- A computational and structural analysis of germline and somatic variants affecting the DDR mechanism, and their impact on human diseases.Scientific reports · 2021Article
- Leveraging biochemical reactions to unravel functional impacts of cancer somatic variants affecting protein interaction interfaces.F1000Research · 2021Article
- Multi-layered proteomic analyses decode compositional and functional effects of cancer mutations on kinase complexes.Nature communications · 2020Article
- Geleophysic dysplasia: novel missense variants and insights into ADAMTSL2 intracellular trafficking.Molecular genetics and metabolism reports · 2019Article
- Gain-of-Function Mutations: An Emerging Advantage for Cancer Biology.Trends in biochemical sciences · 2019Review
- Integrating molecular networks with genetic variant interpretation for precision medicine.Wiley interdisciplinary reviews. Systems biology and medicine · 2019Review
- Role of MDH2 pathogenic variant in pheochromocytoma and paraganglioma patients.Genetics in medicine : official journal of the American College of Medical Genetics · 2018Article
- Mutational signatures and mutable motifs in cancer genomes.Briefings in bioinformatics · 2018Review
- The Emerging Potential for Network Analysis to Inform Precision Cancer Medicine.Journal of molecular biology · 2018Review
- Comparison of algorithms for the detection of cancer drivers at subgene resolution.Nature methods · 2017Article
- Functional variomics and network perturbation: connecting genotype to phenotype in cancer.Nature reviews. Genetics · 2017Review
- Multiscale mutation clustering algorithm identifies pan-cancer mutational clusters associated with pathway-level changes in gene expression.PLoS computational biology · 2017Article
- The recurrent architecture of tumour initiation, progression and drug sensitivity.Nature reviews. Cancer · 2017Review
- PinSnps: structural and functional analysis of SNPs in the context of protein interaction networks.Bioinformatics (Oxford, England) · 2016Article
- KinMutRF: a random forest classifier of sequence variants in the human protein kinase superfamily.BMC genomics · 2016Article
- Computational analysis of prolyl hydroxylase domain-containing protein 2 (PHD2) mutations promoting polycythemia insurgence in humans.Scientific reports · 2016Article
- Structure-Based Analysis Reveals Cancer Missense Mutations Target Protein Interaction Interfaces.PloS one · 2016Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationThe interpretation of cancer-related single-nucleotide variants (SNVs) considering the protein features they affect, such as known functional sites, protein-protein interfaces, or relation with already annotated mutations, might complement the annotation of genetic variants in the analysis of NGS data. Current tools that annotate mutations fall short on several aspects, including the ability to use protein structure information or the interpretation of mutations in protein complexes.
resultsWe present the Structure-PPi system for the comprehensive analysis of coding SNVs based on 3D protein structures of protein complexes. The 3D repository used, Interactome3D, includes experimental and modeled structures for proteins and protein-protein complexes. Structure-PPi annotates SNVs with features extracted from UniProt, InterPro, APPRIS, dbNSFP and COSMIC databases. We illustrate the usefulness of Structure-PPi with the interpretation of 1 027 122 non-synonymous SNVs from COSMIC and the 1000G Project that provides a collection of ∼172 700 SNVs mapped onto the protein 3D structure of 8726 human proteins (43.2% of the 20 214 SwissProt-curated proteins in UniProtKB release 2014_06) and protein-protein interfaces with potential functional implications. AVAILABILITY AND IMPLEMENTATION: Structure-PPi, along with a user manual and examples, isavailable at http://structureppi.bioinfo.cnio.es/Structure, the code for local installations at https://github.com/Rbbt-Workflows
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