AIMC Topic: Amino Acid Sequence

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Accurate in silico identification of protein succinylation sites using an iterative semi-supervised learning technique.

Journal of theoretical biology Apr 2, 2015
As a widespread type of protein post-translational modifications (PTMs), succinylation plays an important role in regulating protein conformation, function and physicochemical properties. Compared with the labor-intensive and time-consuming experimen...
Amino Acid Sequence Lysine Binding Sites Amino Acids Internet Supervised Machine Learning Succinates Molecular Sequence Data Algorithms Computer Simulation Reproducibility of Results Protein Processing, Post-Translational Proteins Computational Biology Support Vector Machine Artificial Intelligence
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Improved feature-based prediction of SNPs in human cytochrome P450 enzymes.

Interdisciplinary sciences, computational life sciences Mar 21, 2015
Single nucleotide polymorphisms (SNPs) make up the most common form of mutations in human cytochrome P450 enzymes family, and have the potential to bring with different drug responses or specific diseases in individual patients. Here, based on machin...
Artificial Intelligence Phylogeny Polymorphism, Single Nucleotide Fuzzy Logic Area Under Curve Codon Computational Biology Humans Support Vector Machine Amino Acid Sequence Cytochrome P-450 Enzyme System Base Sequence Models, Molecular Mutation Amino Acids
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Identifying DNA-binding proteins by combining support vector machine and PSSM distance transformation.

BMC systems biology Feb 6, 2015
BACKGROUND: DNA-binding proteins play a pivotal role in various intra- and extra-cellular activities ranging from DNA replication to gene expression control. Identification of DNA-binding proteins is one of the major challenges in the field of genome...
Protein Conformation Nucleic Acid Conformation Molecular Sequence Data Internet Computational Biology Sequence Analysis, Protein DNA-Binding Proteins Support Vector Machine Amino Acid Sequence Models, Molecular
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Types and effects of protein variations.

Human genetics Jan 24, 2015
Variations in proteins have very large number of diverse effects affecting sequence, structure, stability, interactions, activity, abundance and other properties. Although protein-coding exons cover just over 1 % of the human genome they harbor an di...
Models, Molecular Animals Protein Folding Protein Processing, Post-Translational Molecular Dynamics Simulation Protein Structure, Quaternary Humans Amino Acid Sequence Proteins Genetic Variation Databases, Protein Gene Ontology Structure-Activity Relationship Protein Structure, Secondary
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Using support vector machines to identify protein phosphorylation sites in viruses.

Journal of molecular graphics & modelling Dec 24, 2014
Phosphorylation of viral proteins plays important roles in enhancing replication and inhibition of normal host-cell functions. Given its importance in biology, a unique opportunity has arisen to identify viral protein phosphorylation sites. However, ...
Protein Structure, Tertiary Threonine Viral Proteins Serine Support Vector Machine Molecular Sequence Data Databases, Protein Amino Acid Sequence Phosphorylation Tyrosine Phosphoproteins
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Prediction of β-lactamase and its class by Chou's pseudo-amino acid composition and support vector machine.

Journal of theoretical biology Oct 22, 2014
β-Lactam class of antibiotics is used as major therapeutic agent against a number of pathogenic microbes. The widespread and indiscriminate use of antibiotics to treat bacterial infection has prompted evolution of several evading mechanisms from the ...
Sequence Analysis, Protein beta-Lactams Amino Acid Sequence beta-Lactamases Protein Structure, Secondary Anti-Infective Agents Support Vector Machine
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Virtual screening of umami peptides during sufu ripening based on machine learning and molecular docking to umami receptor T1R1/T1R3.

Food chemistry Sep 15, 2025
Umami peptides might significantly contribute to the taste of sufu. However, the inefficiencies of traditional identification methods had great limitations. This study explored a new approach for umami peptides characterization in sufu. Combining pep...
Machine Learning Peptides Molecular Docking Simulation Receptors, G-Protein-Coupled Humans Glycine max Soy Foods Amino Acid Sequence Taste Flavoring Agents
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Virtual Hydrolysis-Based Screening of Wheat-Derived DPP-IV Inhibitory Peptides: A Mechanistic Analysis Integrating Cell Experiments and Molecular Dynamics Simulations.

Journal of agricultural and food chemistry Aug 6, 2025
Dipeptidyl peptidase-IV (DPP-IV) inhibitors play a critical role in the treatment of diabetes and metabolic diseases. This study combines computational simulations with experimental validation to identify peptides with potential DPP-IV inhibitory act...
Hydrolysis Plant Proteins Dipeptidyl Peptidase 4 Triticum Molecular Dynamics Simulation Humans Amino Acid Sequence Peptides Dipeptidyl-Peptidase IV Inhibitors
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PEGASUS: Prediction of MD-derived protein flexibility from sequence.

Protein science : a publication of the Protein Society Aug 1, 2025
Protein flexibility is essential to its biological function. However, experimental methods for its assessment, such as X-ray crystallography and nuclear magnetic resonance spectroscopy, are often limited by experimental variability and high cost, lea...
Databases, Protein Software Amino Acid Sequence Molecular Dynamics Simulation Proteins Protein Conformation
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Screening and preliminary analysis of antimicrobial peptide genes in Octopussinensis.

Fish & shellfish immunology Aug 1, 2025
Antimicrobial peptides (AMPs) are small molecular peptides that widely exist in organisms to resist external microbial invasion and play a crucial role in the host's immune defense system. Owing to their functions of efficient broad-spectrum killing ...
Gene Expression Profiling Animals Immunity, Innate Amino Acid Sequence Gene Expression Regulation Antimicrobial Peptides
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