AIMC Topic: Amino Acid Substitution

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Prediction of Contact Residues in Anti-HIV Neutralizing Antibody by Deep Learning.

Japanese journal of infectious diseases Jan 31, 2020
The monoclonal antibody 1C10 targets the V3 loop of HIV-1 and neutralizes a broad range of clade B viruses. However, the mode of interaction between 1C10 and the V3 loop remains unclear because crystallization of 1C10 and the V3 peptide was unsuccess...
Binding Sites, Antibody Antibodies, Monoclonal Peptide Fragments Antibodies, Neutralizing HIV Antibodies HIV Envelope Protein gp120 Amino Acid Sequence Amino Acid Substitution Humans Molecular Docking Simulation Deep Learning
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Computational and artificial neural network based study of functional SNPs of human LEPR protein associated with reproductive function.

Journal of cellular biochemistry Jun 25, 2019
Genetic polymorphisms are mostly associated with inherited diseases, detecting and analyzing the biological significance of functional single-nucleotide polymorphisms (SNPs) using wet laboratory experiments is an arduous task hence the computational ...
Mutation, Missense Receptors, Leptin Infertility Polymorphism, Single Nucleotide Protein Domains Amino Acid Substitution Neural Networks, Computer Molecular Docking Simulation Humans
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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...
Colorectal Neoplasms Spectroscopy, Near-Infrared Mutation Alleles Humans Neural Networks, Computer Reproducibility of Results DNA Mutational Analysis Amino Acid Substitution Proto-Oncogene Proteins B-raf
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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...
Proteins Amino Acid Substitution Mutation, Missense Protein Structure, Secondary Algorithms Support Vector Machine
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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...
Middle Aged Adult Adolescent Cross-Sectional Studies Polymorphism, Single Nucleotide Amino Acid Substitution PPAR gamma Humans Genotype Male Nutrigenomics Vitamin E Female Adiponectin Young Adult
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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 Neural Networks, Computer Computer Simulation Proteins Mutation Support Vector Machine Decision Trees
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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...
Expert Systems Biocatalysis Protein Conformation Amino Acid Substitution Recombinant Fusion Proteins Ubiquitin-Conjugating Enzymes Cysteine Ubiquitin-Protein Ligases Computational Biology Models, Molecular Iodine Radioisotopes Ubiquitination Binding Sites Animals Protein Multimerization Mutagenesis, Site-Directed Molecular Docking Simulation Ubiquitin Cattle Isoenzymes Humans Point Mutation
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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...
Neural Networks, Computer Female Male Severity of Illness Index Amino Acid Substitution Humans Amyloid Neuropathies, Familial Models, Biological Prealbumin Mutation, Missense
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Relationship between immunogenicity and protein structure at amino acid substitution sites of blood group antigens.

Blood Jul 24, 2025
Polypeptide blood group antigens, many of which are created by single exofacial amino acid substitutions, have varying immunogenicities. Why some amino acid substitutions are more immunogenic than others is little understood. Using AlphaFold2, an art...
Models, Molecular Protein Conformation Amino Acid Substitution Blood Group Antigens Humans
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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...
Deep Learning Models, Genetic Evolution, Molecular Amino Acid Substitution Computer Simulation Phylogeny Likelihood Functions Sequence Alignment
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