AIMC Topic: Dipeptides

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Predicting antifreeze proteins with weighted generalized dipeptide composition and multi-regression feature selection ensemble.

BMC bioinformatics Jun 23, 2021
BACKGROUND: Antifreeze proteins (AFPs) are a group of proteins that inhibit body fluids from growing to ice crystals and thus improve biological antifreeze ability. It is vital to the survival of living organisms in extremely cold environments. Howev...
Reproducibility of Results Support Vector Machine Dipeptides Antifreeze Proteins Algorithms
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Discovering Collective Variables of Molecular Transitions via Genetic Algorithms and Neural Networks.

Journal of chemical theory and computation Mar 4, 2021
With the continual improvement of computing hardware and algorithms, simulations have become a powerful tool for understanding all sorts of (bio)molecular processes. To handle the large simulation data sets and to accelerate slow, activated transitio...
Neural Networks, Computer Algorithms Dipeptides Alanine
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Classifying the superfamily of small heat shock proteins by using g-gap dipeptide compositions.

International journal of biological macromolecules Nov 17, 2020
Small heat shock protein (sHSP) is a superfamily of molecular chaperone and is found from archaea to human. Recent researches have demonstrated that sHSPs participate in a series of biological processes and are even closely associated with serious di...
Sequence Alignment Heat-Shock Proteins, Small Databases, Protein Humans Amino Acid Sequence Computational Biology Dipeptides Proteomics Machine Learning Animals
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Learning molecular dynamics with simple language model built upon long short-term memory neural network.

Nature communications Oct 9, 2020
Recurrent neural networks have led to breakthroughs in natural language processing and speech recognition. Here we show that recurrent networks, specifically long short-term memory networks can also capture the temporal evolution of chemical/biophysi...
Neural Networks, Computer Artificial Intelligence Memory Single Molecule Imaging Language Molecular Dynamics Simulation Models, Statistical Markov Chains Kinetics Dipeptides
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Identifying Heat Shock Protein Families from Imbalanced Data by Using Combined Features.

Computational and mathematical methods in medicine Sep 23, 2020
Heat shock proteins (HSPs) are ubiquitous in living organisms. HSPs are an essential component for cell growth and survival; the main function of HSPs is controlling the folding and unfolding process of proteins. According to molecular function and m...
Dipeptides Mathematical Concepts Amino Acids Amino Acid Sequence Heat-Shock Proteins Humans Algorithms Support Vector Machine Databases, Protein Animals Computational Biology
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Robosample: A rigid-body molecular simulation program based on robot mechanics.

Biochimica et biophysica acta. General subjects Apr 13, 2020
BACKGROUND: Compared with all-atom molecular dynamics (MD), constrained MD methods allow for larger time steps, potentially reducing computational cost. For this reason, there has been continued interest in improving constrained MD algorithms to incr...
Software Monte Carlo Method Alanine Robotics Molecular Dynamics Simulation Dipeptides
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Toward Building Protein Force Fields by Residue-Based Systematic Molecular Fragmentation and Neural Network.

Journal of chemical theory and computation Jan 7, 2019
Accurate force fields are crucial for molecular dynamics investigation of complex biological systems. Building accurate protein force fields from quantum mechanical (QM) calculations is challenging due to the complexity of proteins and high computati...
Thermodynamics Quantum Theory Dipeptides Static Electricity Models, Chemical Amino Acids Molecular Dynamics Simulation Peptides Proteins Neural Networks, Computer
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Accurate prediction of Gram-negative bacterial secreted protein types by fusing multiple statistical features from PSI-BLAST profile.

SAR and QSAR in environmental research Apr 24, 2018
Gram-negative bacterial secreted proteins play different roles in invaded eukaryotic cells and cause various diseases. Prediction of Gram-negative bacterial secreted protein types is a meaningful and challenging task. In this paper, we develop a mult...
Structure-Activity Relationship Bacterial Proteins Dipeptides Support Vector Machine Gram-Negative Bacteria Models, Statistical
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Specific chemiluminescent protocol for dual-site recognition of Streptococcus mutans utilizing strong affinity between teicoplanin and Gram-positive bacteria.

Talanta Nov 6, 2017
A novel dual-site recognition protocol was developed for chemiluminescent (CL) detection of Streptococcus mutans (S. mutans) based on a designed antibiotic-affinity strategy. Teicoplanin, a broad-spectrum antibiotic against Gram-positive bacteria, wa...
Milk Rats Cell Wall Fresh Water Horseradish Peroxidase Teicoplanin Limit of Detection Streptococcus mutans Iodobenzenes Luminescent Measurements Animals Saliva Humans Luminol Hydrogen Peroxide Magnetite Nanoparticles Dipeptides Anti-Bacterial Agents Protein Binding Immunoglobulin G Bacterial Proteins
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In silico identification of milk antihypertensive di- and tripeptides involved in angiotensin I-converting enzyme inhibitory activity.

Nutrition research (New York, N.Y.) Jul 28, 2017
Identification of bioactive milk peptides could improve food technology through improved selection of food supplements with a focus on antihypertensive properties. We hypothesized that angiotensin I-converting enzyme (ACE) inhibitory activities of mi...
Expert Systems Catalytic Domain Oligopeptides Protein Conformation Hydrogen Bonding Angiotensin-Converting Enzyme Inhibitors Quantitative Structure-Activity Relationship Dietary Supplements Animals Peptide Fragments Antihypertensive Agents Molecular Docking Simulation Dipeptides Models, Molecular Humans Cattle Hydrophobic and Hydrophilic Interactions Computational Biology Milk Proteins Peptidyl-Dipeptidase A Proteolysis Binding Sites
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