AIMC Topic: Mutation, Missense

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Discrimination of driver and passenger mutations in epidermal growth factor receptor in cancer.

Mutation research Jul 20, 2015
Cancer is one of the most life-threatening diseases and mutations in several genes are the vital cause in tumorigenesis. Protein kinases play essential roles in cancer progression and specifically, epidermal growth factor receptor (EGFR) is an import...
Humans Support Vector Machine ErbB Receptors Mutation, Missense Neoplasms Polymorphism, Single Nucleotide Models, Genetic
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MIMP: predicting the impact of mutations on kinase-substrate phosphorylation.

Nature methods May 4, 2015
Protein phosphorylation is important in cellular pathways and altered in disease. We developed MIMP (http://mimp.baderlab.org/), a machine learning method to predict the impact of missense single-nucleotide variants (SNVs) on kinase-substrate interac...
Phosphorylation Amino Acid Sequence Substrate Specificity Mutation, Missense Phosphotransferases Artificial Intelligence Software Polymorphism, Single Nucleotide Signal Transduction
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RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease.

Science (New York, N.Y.) Dec 18, 2014
To facilitate precision medicine and whole-genome annotation, we developed a machine-learning technique that scores how strongly genetic variants affect RNA splicing, whose alteration contributes to many diseases. Analysis of more than 650,000 intron...
RNA Splice Sites Mutation, Missense Quantitative Trait Loci RNA Splicing RNA-Binding Proteins Exons Genetic Variation Models, Genetic Computer Simulation Genetic Code Molecular Sequence Annotation Child Development Disorders, Pervasive Adaptor Proteins, Signal Transducing Humans Nuclear Proteins Genome-Wide Association Study MutL Protein Homolog 1 Introns Colorectal Neoplasms, Hereditary Nonpolyposis DNA Artificial Intelligence Polymorphism, Single Nucleotide Genetic Markers Muscular Atrophy, Spinal
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protPheMut: An Interpretable Machine Learning Tool for Classification of Cancer and Neurodevelopmental Disorders in Human Missense Mutations.

Journal of chemical information and modeling Aug 11, 2025
Recent advances in human genomics have revealed that missense mutations in a single protein can lead to distinctly different phenotypes. In particular, some mutations in oncoproteins like MEK1, MEK2, PI3Kα, PTEN, SHAP2, and RAS are linked various can...
Computational Biology Humans Mutation, Missense Neurodevelopmental Disorders Machine Learning Phenotype Neoplasms
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AFFIPred: AlphaFold2 structure-based Functional Impact Prediction of missense variations.

Protein science : a publication of the Protein Society Feb 1, 2025
Protein structure holds immense potential for pathogenicity prediction, albeit structure-based predictors are limited compared to the sequence-based counterparts due to the "structure knowledge gap" between large number of available protein sequences...
Protein Conformation Mutation, Missense Humans Proteins Databases, Protein Machine Learning Models, Molecular Software Computational Biology
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Discovering predisposing genes for hereditary breast cancer using deep learning.

Briefings in bioinformatics May 23, 2024
Breast cancer (BC) is the most common malignancy affecting Western women today. It is estimated that as many as 10% of BC cases can be attributed to germline variants. However, the genetic basis of the majority of familial BC cases has yet to be iden...
Mutation, Missense Germ-Line Mutation Deep Learning Genetic Predisposition to Disease Humans Pedigree Female Breast Neoplasms
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Characterizing and predicting ccRCC-causing missense mutations in Von Hippel-Lindau disease.

Human molecular genetics Jan 20, 2024
BACKGROUND: Mutations within the Von Hippel-Lindau (VHL) tumor suppressor gene are known to cause VHL disease, which is characterized by the formation of cysts and tumors in multiple organs of the body, particularly clear cell renal cell carcinoma (c...
Humans Mutation, Missense von Hippel-Lindau Disease Von Hippel-Lindau Tumor Suppressor Protein Machine Learning Kidney Neoplasms Carcinoma, Renal Cell
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Predicting the pathogenicity of missense variants using features derived from AlphaFold2.

Bioinformatics (Oxford, England) May 4, 2023
MOTIVATION: Missense variants are a frequent class of variation within the coding genome, and some of them cause Mendelian diseases. Despite advances in computational prediction, classifying missense variants into pathogenic or benign remains a major...
Virulence Mutation, Missense Artificial Intelligence Computational Biology Mutation Humans
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mCSM-PPI2: predicting the effects of mutations on protein-protein interactions.

Nucleic acids research Jul 2, 2019
Protein-protein Interactions are involved in most fundamental biological processes, with disease causing mutations enriched at their interfaces. Here we present mCSM-PPI2, a novel machine learning computational tool designed to more accurately predic...
Mutation, Missense Protein Interaction Mapping Protein Interaction Domains and Motifs Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Crystallography, X-Ray Binding Sites Thermodynamics Benchmarking Datasets as Topic Humans Machine Learning Software Protein Binding Proteins Internet
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