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Point Mutation

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modeling of the cryptic E2∼ubiquitin-binding site of E6-associated protein (E6AP)/UBE3A reveals the mechanism of polyubiquitin chain assembly.

The Journal of biological chemistry 28924046
To understand the mechanism for assembly of Lys-linked polyubiquitin degradation signals, we previously demonstrated that the E6AP/UBE3A ligase harbors two functionally distinct E2∼ubiquitin-binding sites: a high-affinity Site 1 required for E6AP Cys...
Amino Acid Substitution Animals Binding Sites Biocatalysis Cattle Computational Biology Cysteine Expert Systems Humans Iodine Radioisotopes Isoenzymes Models, Molecular Molecular Docking Simulation Mutagenesis, Site-Directed Point Mutation Protein Conformation Protein Multimerization Recombinant Fusion Proteins Ubiquitin Ubiquitin-Conjugating Enzymes Ubiquitin-Protein Ligases Ubiquitination
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Computational design of thermostabilizing point mutations for G protein-coupled receptors.

eLife 29927385
Engineering of GPCR constructs with improved thermostability is a key for successful structural and biochemical studies of this transmembrane protein family, targeted by 40% of all therapeutic drugs. Here we introduce a comprehensive computational ap...
Amino Acid Sequence Animals Binding Sites Crystallography, X-Ray Gene Expression Humans Kinetics Machine Learning Models, Molecular Point Mutation Protein Binding Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Protein Engineering Protein Interaction Domains and Motifs Protein Stability Receptor, Serotonin, 5-HT2C Sequence Alignment Sequence Homology, Amino Acid Serotonin 5-HT2 Receptor Agonists Serotonin 5-HT2 Receptor Antagonists Thermodynamics
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A Machine Learning Approach for Predicting HIV Reverse Transcriptase Mutation Susceptibility of Biologically Active Compounds.

Journal of chemical information and modeling 29953819
HIV resistance emerging against antiretroviral drugs represents a great threat to the continued prolongation of the lifespans of HIV-infected patients. Therefore, methods capable of predicting resistance susceptibility in the development of compounds...
Bayes Theorem Drug Discovery Drug Resistance, Viral HIV Infections HIV Reverse Transcriptase HIV-1 Humans Machine Learning Models, Biological Point Mutation Reverse Transcriptase Inhibitors
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Identifying mouse developmental essential genes using machine learning.

Disease models & mechanisms 30563825
The genes that are required for organismal survival are annotated as 'essential genes'. Identifying all the essential genes of an animal species can reveal critical functions that are needed during the development of the organism. To inform studies o...
Algorithms Animals Chromosomes, Mammalian Conserved Sequence Databases, Genetic Gene Ontology Genes, Developmental Genes, Essential Humans Machine Learning Mice Molecular Sequence Annotation Mutagenesis Phenotype Point Mutation Protein Interaction Maps Reproducibility of Results Software
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DeepDDG: Predicting the Stability Change of Protein Point Mutations Using Neural Networks.

Journal of chemical information and modeling 30759982
Accurately predicting changes in protein stability due to mutations is important for protein engineering and for understanding the functional consequences of missense mutations in proteins. We have developed DeepDDG, a neural network-based method, fo...
Computational Biology Neural Networks, Computer Point Mutation Protein Stability Proteins Transition Temperature
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Seq2seq Fingerprint with Byte-Pair Encoding for Predicting Changes in Protein Stability upon Single Point Mutation.

IEEE/ACM transactions on computational biology and bioinformatics 30946675
The engineering of stable proteins is crucial for various industrial purposes. Several machine learning methods have been developed to predict changes in the stability of proteins corresponding to single point mutations. To improve the prediction acc...
Amino Acid Sequence Computational Biology Databases, Genetic Humans Neural Networks, Computer Point Mutation Protein Stability Proteins Sequence Analysis, Protein Unsupervised Machine Learning
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Robust Prediction of Single and Multiple Point Protein Mutations Stability Changes.

Biomolecules 31906171
Accurate prediction of protein stability changes resulting from amino acid substitutions is of utmost importance in medicine to better understand which mutations are deleterious, leading to diseases, and which are neutral. Since conducting wet lab ex...
Amino Acids Databases, Protein Machine Learning Neural Networks, Computer Point Mutation Protein Stability Proteins Thermodynamics
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Ensemble-Based Somatic Mutation Calling in Cancer Genomes.

Methods in molecular biology (Clifton, N.J.) 32124310
Identification of somatic mutations in tumor tissue is challenged by both technical artifacts, diverse somatic mutational processes, and genetic heterogeneity in the tumors. Indeed, recent independent benchmark studies have revealed low concordance b...
Genome, Human Genomics Humans INDEL Mutation Mutation Neoplasms Point Mutation Polymorphism, Single Nucleotide Software Supervised Machine Learning
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Machine Learning Techniques for Classifying the Mutagenic Origins of Point Mutations.

Genetics 32193188
There is increasing interest in developing diagnostics that discriminate individual mutagenic mechanisms in a range of applications that include identifying population-specific mutagenesis and resolving distinct mutation signatures in cancer samples....
Animals Ethylnitrosourea Machine Learning Mice Mutagens Nucleotide Motifs Point Mutation Sequence Analysis, DNA
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Decoding whole-genome mutational signatures in 37 human pan-cancers by denoising sparse autoencoder neural network.

Oncogene 32528130
Millions of somatic mutations have recently been discovered in cancer genomes. These mutations in cancer genomes occur due to internal and external mutagenesis forces. Decoding the mutational processes by examining their unique patterns has successfu...
Deep Learning DNA Genome, Human Humans INDEL Mutation Neoplasms Point Mutation
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