ArticleNucleic acids research2015
Mechismo: predicting the mechanistic impact of mutations and modifications on molecular interactions.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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Who cites it
50 citing papers in PubMed.
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- Molecular Tweezers Block the Functional Pore of a Protein Machine.Journal of the American Chemical Society · 2025Article
- Identification of coevolving positions by ancestral reconstruction.Communications biology · 2025Article
- Interface-guided phenotyping of coding variants in the transcription factor RUNX1.Cell reports · 2024Article
- Singleton mutations in large-scale cancer genome studies: uncovering the tail of cancer genome.NAR cancer · 2024Article
- Focal structural variants revealed by whole genome sequencing disrupt the histone demethylase KDM4C in B-cell lymphomas.Haematologica · 2023Article
- Experimental analysis of bladder cancer-associated mutations in EP300 identifies EP300-R1627W as a driver mutation.Molecular medicine (Cambridge, Mass.) · 2023Article
- PTMint database of experimentally verified PTM regulation on protein-protein interaction.Bioinformatics (Oxford, England) · 2023Article
- EXPANSION: a webserver to explore the functional consequences of protein-coding alternative splice variants in cancer genomics.Bioinformatics advances · 2023Article
- d-StructMAn: Containerized structural annotation on the scale from genetic variants to whole proteomes.GigaScience · 2022Article
- Never-homozygous genetic variants in healthy populations are potential recessive disease candidates.NPJ genomic medicine · 2022Article
- Evidence for reduced BRCA2 functional activity in Homo sapiens after divergence from the chimpanzee-human last common ancestor.Cell reports · 2022Article
- Comparative Phosphoproteomic Analysis of Sporulated Oocysts and Tachyzoites ofMolecules (Basel, Switzerland) · 2022Article
- Mechnetor: a web server for exploring protein mechanism and the functional context of genetic variants.Nucleic acids research · 2021Article
- Molecular dynamics shows complex interplay and long-range effects of post-translational modifications in yeast protein interactions.PLoS computational biology · 2021Article
- RhoGAP19D inhibits Cdc42 laterally to control epithelial cell shape and prevent invasion.The Journal of cell biology · 2021Article
- LBSL: Case Series and DARS2 Variant Analysis in Early Severe Forms With Unexpected Presentations.Neurology. Genetics · 2021Article
- Leveraging biochemical reactions to unravel functional impacts of cancer somatic variants affecting protein interaction interfaces.F1000Research · 2021Article
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18 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Systematic interrogation of mutation or protein modification data is important to identify sites with functional consequences and to deduce global consequences from large data sets. Mechismo (mechismo.russellab.org) enables simultaneous consideration of thousands of 3D structures and biomolecular interactions to predict rapidly mechanistic consequences for mutations and modifications. As useful functional information often only comes from homologous proteins, we benchmarked the accuracy of predictions as a function of protein/structure sequence similarity, which permits the use of relatively weak sequence similarities with an appropriate confidence measure. For protein-protein, protein-nucleic acid and a subset of protein-chemical interactions, we also developed and benchmarked a measure of whether modifications are likely to enhance or diminish the interactions, which can assist the detection of modifications with specific effects. Analysis of high-throughput sequencing data shows that the approach can identify interesting differences between cancers, and application to proteomics data finds potential mechanistic insights for how post-translational modifications can alter biomolecular interactions.
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