AIMC Topic: Sequence Analysis, Protein

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Deducing high-accuracy protein contact-maps from a triplet of coevolutionary matrices through deep residual convolutional networks.

PLoS computational biology Mar 26, 2021
The topology of protein folds can be specified by the inter-residue contact-maps and accurate contact-map prediction can help ab initio structure folding. We developed TripletRes to deduce protein contact-maps from discretized distance profiles by en...
Protein Conformation Protein Folding Sequence Analysis, Protein Reproducibility of Results Neural Networks, Computer Computational Biology Proteins
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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...
Machine Learning Escherichia coli Databases, Protein Hydrogen-Ion Concentration Optogenetics Bayes Theorem Proof of Concept Study Light Sequence Analysis, Protein Color Protein Conformation, alpha-Helical Amino Acid Sequence Ion Channels Rhodopsins, Microbial
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PredNTS: Improved and Robust Prediction of Nitrotyrosine Sites by Integrating Multiple Sequence Features.

International journal of molecular sciences Mar 8, 2021
Nitrotyrosine, which is generated by numerous reactive nitrogen species, is a type of protein post-translational modification. Identification of site-specific nitration modification on tyrosine is a prerequisite to understanding the molecular functio...
Protein Processing, Post-Translational Proteins Tyrosine Machine Learning Computational Biology Support Vector Machine Sequence Analysis, Protein
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PFP-WGAN: Protein function prediction by discovering Gene Ontology term correlations with generative adversarial networks.

PloS one Feb 25, 2021
Understanding the functionality of proteins has emerged as a critical problem in recent years due to significant roles of these macro-molecules in biological mechanisms. However, in-laboratory techniques for protein function prediction are not as eff...
Humans Proteins Gene Regulatory Networks Gene Ontology Computational Biology Sequence Analysis, Protein
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Combination of deep neural network with attention mechanism enhances the explainability of protein contact prediction.

Proteins Feb 16, 2021
Deep learning has emerged as a revolutionary technology for protein residue-residue contact prediction since the 2012 CASP10 competition. Considerable advancements in the predictive power of the deep learning-based contact predictions have been achie...
Sequence Alignment Sequence Analysis, Protein Protein Interaction Domains and Motifs Protein Conformation Binding Sites Protein Binding Computational Biology Proteins Databases, Protein Benchmarking Software Research Design Deep Learning Humans
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CrystalM: A Multi-View Fusion Approach for Protein Crystallization Prediction.

IEEE/ACM transactions on computational biology and bioinformatics Feb 3, 2021
Improving the accuracy of predicting protein crystallization is very important for protein crystallization projects, which is a critical step for the determination of protein structure by X-ray crystallography. At present, many machine learning metho...
Position-Specific Scoring Matrices Computational Biology Support Vector Machine Models, Statistical Proteins Crystallization Sequence Analysis, Protein
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Template-based prediction of protein structure with deep learning.

BMC genomics Dec 29, 2020
BACKGROUND: Accurate prediction of protein structure is fundamentally important to understand biological function of proteins. Template-based modeling, including protein threading and homology modeling, is a popular method for protein tertiary struct...
Proteins Databases, Protein Software Protein Conformation Algorithms Sequence Analysis, Protein Deep Learning
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Noninvasive diagnostic of periprosthetic joint infection by urinary peptide markers: A preliminary study.

Journal of orthopaedic research : official publication of the Orthopaedic Research Society Nov 25, 2020
Previous immunohistochemical analyses revealed altered protein expression in the periprosthetic membranes of patients with periprosthetic joint infection (PJI). Proteins are degraded to peptides that may pass the blood-kidney barrier depending on the...
Proteome Humans Support Vector Machine Biomarkers Aged Prosthesis-Related Infections Peptide Hydrolases Peptides Sequence Analysis, Protein
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ReFold-MAP: Protein remote homology detection and fold recognition based on features extracted from profiles.

Analytical biochemistry Nov 6, 2020
Protein remote homology detection and protein fold recognition are two important tasks in protein structure and function prediction. There are three kinds of methods in this field, including the discriminative methods, the alignment methods, and the ...
Proteins Sequence Alignment Databases, Protein Artificial Intelligence Sequence Analysis, Protein Protein Folding
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A novel fusion based on the evolutionary features for protein fold recognition using support vector machines.

Scientific reports Sep 1, 2020
Protein fold recognition plays a crucial role in discovering three-dimensional structure of proteins and protein functions. Several approaches have been employed for the prediction of protein folds. Some of these approaches are based on extracting fe...
Amino Acid Sequence Evolution, Molecular Computational Biology Protein Folding Proteins Sequence Analysis, Protein Support Vector Machine Databases, Protein
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