AIMC Topic: Amino Acid Substitution

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Can mutation abundance assess the biological behavior of BRAF-positive papillary thyroid carcinoma?

Journal of translational medicine Jul 1, 2025
BACKGROUND: BRAF mutation is the most common genetic change in papillary thyroid carcinoma (PTC). Nevertheless, the association between BRAF mutation status and abundance and the biological behavior of PTC is unclear. Thus, this study investigated wh...
Adult Male Middle Aged Retrospective Studies Female Aged Biopsy, Fine-Needle Amino Acid Substitution Thyroid Cancer, Papillary Proto-Oncogene Proteins B-raf Thyroid Neoplasms ROC Curve Humans Mutation
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Variant Effect Prediction in the Age of Machine Learning.

Cold Spring Harbor perspectives in biology Jul 1, 2024
Over the years, many computational methods have been created for the analysis of the impact of single amino acid substitutions resulting from single-nucleotide variants in genome coding regions. Historically, all methods have been supervised and thus...
Deep Learning Polymorphism, Single Nucleotide Computational Biology Proteins Humans Amino Acid Substitution Machine Learning
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Respiratory Syncytial Virus Vaccine Design Using Structure-Based Machine-Learning Models.

Viruses May 22, 2024
When designing live-attenuated respiratory syncytial virus (RSV) vaccine candidates, attenuating mutations can be developed through biologic selection or reverse-genetic manipulation and may include point mutations, codon and gene deletions, and geno...
Mutation Respiratory Syncytial Virus Infections Respiratory Syncytial Virus, Human Viral Nonstructural Proteins Humans Machine Learning Cell Line Respiratory Syncytial Virus Vaccines Virus Replication Amino Acid Substitution Vaccines, Attenuated
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EvoRator2: Predicting Site-specific Amino Acid Substitutions Based on Protein Structural Information Using Deep Learning.

Journal of molecular biology May 23, 2023
Multiple sequence alignments (MSAs) are the workhorse of molecular evolution and structural biology research. From MSAs, the amino acids that are tolerated at each site during protein evolution can be inferred. However, little is known regarding the ...
Amino Acids Protein Conformation Amino Acid Substitution Deep Learning Computational Biology Proteins Algorithms
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The structure-based cancer-related single amino acid variation prediction.

Scientific reports Jun 30, 2021
Single amino acid variation (SAV) is an amino acid substitution of the protein sequence that can potentially influence the entire protein structure or function, as well as its binding affinity. Protein destabilization is related to diseases, includin...
Neoplasms Support Vector Machine Neoplasm Proteins Models, Biological Amino Acid Substitution Humans
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A Deep-Learning Sequence-Based Method to Predict Protein Stability Changes Upon Genetic Variations.

Genes Jun 12, 2021
Several studies have linked disruptions of protein stability and its normal functions to disease. Therefore, during the last few decades, many tools have been developed to predict the free energy changes upon protein residue variations. Most of these...
Amino Acid Substitution Sequence Analysis, Protein Molecular Dynamics Simulation Genetic Variation Protein Stability Humans Deep Learning
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Machine Learning Prediction and Experimental Validation of Antigenic Drift in H3 Influenza A Viruses in Swine.

mSphere Mar 17, 2021
The antigenic diversity of influenza A viruses (IAV) circulating in swine challenges the development of effective vaccines, increasing zoonotic threat and pandemic potential. High-throughput sequencing technologies can quantify IAV genetic diversity,...
Antigenic Variation Phenotype Animals Orthomyxoviridae Infections Swine Genotype Influenza A Virus, H3N2 Subtype Swine Diseases Machine Learning Regression Analysis Hemagglutinin Glycoproteins, Influenza Virus Amino Acid Substitution
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Screening of a novel free fatty acid receptor 1 (FFAR1) agonist peptide by phage display and machine learning based-amino acid substitution.

Biochemical and biophysical research communications Mar 9, 2021
Free fatty acid receptor 1 (FFAR1 or GPR40) has attracted attention for the treatment of type 2 diabetes mellitus, and various small-molecule agonists have been developed. However, most FFAR1 agonists as well as endogenous ligands, such as linoleic a...
Humans Machine Learning Peptides Insulin Protein Binding Amino Acid Sequence HEK293 Cells Cloning, Molecular Amino Acid Substitution Transforming Growth Factor alpha Peptide Library Cell Line Regression Analysis Receptors, G-Protein-Coupled Glucose Drug Evaluation, Preclinical
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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...
Amino Acid Sequence Amino Acid Substitution Antibodies, Monoclonal HIV Antibodies HIV Envelope Protein gp120 Humans Peptide Fragments Binding Sites, Antibody Antibodies, Neutralizing 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 Polymorphism, Single Nucleotide Humans Receptors, Leptin Protein Domains Neural Networks, Computer Infertility Amino Acid Substitution Molecular Docking Simulation
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