AIMC Topic: Amino Acid Substitution

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Detection of the BRAF V600E Mutation in Colorectal Cancer by NIR Spectroscopy in Conjunction with Counter Propagation Artificial Neural Network.

Molecules (Basel, Switzerland) Jun 15, 2019
This paper proposes a sensitive, sample preparation-free, rapid, and low-cost method for the detection of the B-rapidly accelerated fibrosarcoma (BRAF) gene mutation involving a substitution of valine to glutamic acid at codon 600 (V600E) in colorect...
Humans Neural Networks, Computer Amino Acid Substitution Proto-Oncogene Proteins B-raf Mutation Alleles DNA Mutational Analysis Reproducibility of Results Colorectal Neoplasms Spectroscopy, Near-Infrared
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An in-silico method for identifying aggregation rate enhancer and mitigator mutations in proteins.

International journal of biological macromolecules Jun 24, 2018
Newly synthesized polypeptides must pass stringent quality controls in cells to ensure appropriate folding and function. However, mutations, environmental stresses and aging can reduce efficiencies of these controls, leading to accumulation of protei...
Protein Structure, Secondary Algorithms Support Vector Machine Proteins Amino Acid Substitution Mutation, Missense
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Interaction of Vitamin E Intake and Pro12Ala Polymorphism of PPARG with Adiponectin Levels.

Journal of nutrigenetics and nutrigenomics Feb 2, 2018
BACKGROUND/AIM: One of the beneficial effects associated with vitamin E intake is the enhancement of peroxisome proliferator-activated receptor gamma (PPARγ) activity and the consequent upregulation of adiponectin expression. The aim of this study wa...
Nutrigenomics PPAR gamma Vitamin E Genotype Middle Aged Humans Adult Adiponectin Female Adolescent Cross-Sectional Studies Amino Acid Substitution Young Adult Polymorphism, Single Nucleotide Male
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Predicting the Effect of Single and Multiple Mutations on Protein Structural Stability.

Molecules (Basel, Switzerland) Jan 27, 2018
Predicting how a point mutation alters a protein's stability can guide pharmaceutical drug design initiatives which aim to counter the effects of serious diseases. Conducting mutagenesis studies in physical proteins can give insights about the effect...
Thermodynamics Protein Stability Protein Conformation Amino Acid Substitution Decision Trees Proteins Mutation Computer Simulation Neural Networks, Computer Support Vector Machine
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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 Sep 18, 2017
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...
Iodine Radioisotopes Expert Systems Biocatalysis Protein Conformation Protein Multimerization Cattle Humans Mutagenesis, Site-Directed Cysteine Isoenzymes Computational Biology Ubiquitin-Conjugating Enzymes Ubiquitin Ubiquitin-Protein Ligases Animals Point Mutation Models, Molecular Ubiquitination Amino Acid Substitution Molecular Docking Simulation Recombinant Fusion Proteins Binding Sites
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Applying an artificial neural network model for developing a severity score for patients with hereditary amyloid polyneuropathy.

Amyloid : the international journal of experimental and clinical investigation : the official journal of the International Society of Amyloidosis Jul 18, 2017
Hereditary (familial) amyloid polyneuropathy (FAP) is a systemic disease that includes a sensorimotor polyneuropathy related to transthyretin (TTR) mutations. So far, a scale designed to classify the severity of this disease has not yet been validate...
Humans Neural Networks, Computer Female Prealbumin Male Mutation, Missense Severity of Illness Index Amyloid Neuropathies, Familial Models, Biological Amino Acid Substitution
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An efficient deep learning method for amino acid substitution model selection.

Journal of evolutionary biology Jan 3, 2025
Amino acid substitution models play an important role in studying the evolutionary relationships among species from protein sequences. The amino acid substitution model consists of a large number of parameters; therefore, it is estimated from hundred...
Computer Simulation Evolution, Molecular Amino Acid Substitution Likelihood Functions Sequence Alignment Phylogeny Deep Learning Models, Genetic
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Computational prediction of the effect of amino acid changes on the binding affinity between SARS-CoV-2 spike RBD and human ACE2.

Proceedings of the National Academy of Sciences of the United States of America Oct 19, 2021
The association of the receptor binding domain (RBD) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein with human angiotensin-converting enzyme 2 (hACE2) represents the first required step for cellular entry. SARS-CoV-2 ha...
Amino Acid Substitution Binding Sites Molecular Dynamics Simulation Host-Pathogen Interactions Angiotensin-Converting Enzyme 2 Humans Neural Networks, Computer SARS-CoV-2 Spike Glycoprotein, Coronavirus
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A systematic exploration of [Formula: see text] cutoff ranges in machine learning models for protein mutation stability prediction.

Journal of bioinformatics and computational biology Oct 1, 2018
Discerning how a mutation affects the stability of a protein is central to the study of a wide range of diseases. Mutagenesis experiments on physical proteins provide precise insights about the effects of amino acid substitutions, but such studies ar...
Algorithms Computational Biology Support Vector Machine Neural Networks, Computer Machine Learning Random Allocation Amino Acid Substitution Proteins Mutation Protein Stability
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