AIMC Topic: Amino Acid Sequence

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MSA-Regularized Protein Sequence Transformer toward Predicting Genome-Wide Chemical-Protein Interactions: Application to GPCRome Deorphanization.

Journal of chemical information and modeling Mar 23, 2021
Small molecules play a critical role in modulating biological systems. Knowledge of chemical-protein interactions helps address fundamental and practical questions in biology and medicine. However, with the rapid emergence of newly sequenced genes, t...
Amino Acid Sequence Humans Ligands Machine Learning Sequence Alignment Phylogeny Computational Biology
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Deep Learning for Novel Antimicrobial Peptide Design.

Biomolecules Mar 22, 2021
Antimicrobial resistance is an increasing issue in healthcare as the overuse of antibacterial agents rises during the COVID-19 pandemic. The need for new antibiotics is high, while the arsenal of available agents is decreasing, especially for the tre...
ROC Curve Escherichia coli Area Under Curve Bayes Theorem Amino Acid Sequence Molecular Conformation Protein Conformation, alpha-Helical Pore Forming Cytotoxic Proteins Machine Learning Deep Learning
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Integrating structure-based machine learning and co-evolution to investigate specificity in plant sesquiterpene synthases.

PLoS computational biology Mar 22, 2021
Sesquiterpene synthases (STSs) catalyze the formation of a large class of plant volatiles called sesquiterpenes. While thousands of putative STS sequences from diverse plant species are available, only a small number of them have been functionally ch...
Alkyl and Aryl Transferases Evolution, Molecular Protein Conformation Machine Learning Plants Amino Acid Sequence Sesquiterpenes Cations Substrate Specificity Sequence Homology, Amino Acid
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Exploration of natural red-shifted rhodopsins using a machine learning-based Bayesian experimental design.

Communications biology Mar 19, 2021
Microbial rhodopsins are photoreceptive membrane proteins, which are used as molecular tools in optogenetics. Here, a machine learning (ML)-based experimental design method is introduced for screening rhodopsins that are likely to be red-shifted from...
Light Amino Acid Sequence Proof of Concept Study Sequence Analysis, Protein Ion Channels Optogenetics Protein Conformation, alpha-Helical Rhodopsins, Microbial Databases, Protein Bayes Theorem Color Hydrogen-Ion Concentration Machine Learning Escherichia coli
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Accelerated antimicrobial discovery via deep generative models and molecular dynamics simulations.

Nature biomedical engineering Mar 11, 2021
The de novo design of antimicrobial therapeutics involves the exploration of a vast chemical repertoire to find compounds with broad-spectrum potency and low toxicity. Here, we report an efficient computational method for the generation of antimicrob...
Drug Design Drug Discovery Deep Learning Microbial Sensitivity Tests Anti-Bacterial Agents Drug Resistance, Bacterial Female Animals Staphylococcus aureus Mice, Inbred BALB C Antimicrobial Cationic Peptides Structure-Activity Relationship Mice Klebsiella pneumoniae Klebsiella Infections Escherichia coli Molecular Dynamics Simulation Amino Acid Sequence Pseudomonas aeruginosa Acinetobacter baumannii
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DeepTCR is a deep learning framework for revealing sequence concepts within T-cell repertoires.

Nature communications Mar 11, 2021
Deep learning algorithms have been utilized to achieve enhanced performance in pattern-recognition tasks. The ability to learn complex patterns in data has tremendous implications in immunogenomics. T-cell receptor (TCR) sequencing assesses the diver...
T-Lymphocytes Deep Learning RNA-Seq Receptors, Antigen, T-Cell Mice Databases, Genetic Humans Amino Acid Sequence Neural Networks, Computer High-Throughput Nucleotide Sequencing Algorithms Animals
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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...
Protein Binding Peptide Library Cell Line Regression Analysis Humans Machine Learning Peptides Insulin HEK293 Cells Cloning, Molecular Amino Acid Substitution Transforming Growth Factor alpha Receptors, G-Protein-Coupled Glucose Drug Evaluation, Preclinical Amino Acid Sequence
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Advances in machine learning for directed evolution.

Current opinion in structural biology Feb 26, 2021
Machine learning (ML) can expedite directed evolution by allowing researchers to move expensive experimental screens in silico. Gathering sequence-function data for training ML models, however, can still be costly. In contrast, raw protein sequence d...
Amino Acid Sequence Machine Learning Computer Simulation Proteins
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DeepCys: Structure-based multiple cysteine function prediction method trained on deep neural network: Case study on domains of unknown functions belonging to COX2 domains.

Proteins Feb 22, 2021
Cysteine (Cys) is the most reactive amino acid participating in a wide range of biological functions. In-silico predictions complement the experiments to meet the need of functional characterization. Multiple Cys function prediction algorithm is scar...
Nitroso Compounds Software Sulfinic Acids Deep Learning Cysteine Protein Processing, Post-Translational Cations, Divalent Protein Structure, Secondary Sulfides Electron Transport Complex IV Structure-Activity Relationship Glutathione Models, Molecular Disulfides Protein Domains Sulfonic Acids Amino Acid Sequence
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Deep learning the collisional cross sections of the peptide universe from a million experimental values.

Nature communications Feb 19, 2021
The size and shape of peptide ions in the gas phase are an under-explored dimension for mass spectrometry-based proteomics. To investigate the nature and utility of the peptide collisional cross section (CCS) space, we measure more than a million dat...
Caenorhabditis elegans Ions HeLa Cells Saccharomyces cerevisiae Drosophila melanogaster Peptides Humans Deep Learning Neural Networks, Computer Proteomics Escherichia coli Animals Proteome Workflow Amino Acid Sequence Tandem Mass Spectrometry
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