AIMC Topic: Protein Folding

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Energy-dependent protein folding: modeling how a protein folding machine may work.

F1000Research Jan 5, 2021
Proteins fold robustly and reproducibly , but many cannot fold in isolation from cellular components. Despite the remarkable progress that has been achieved by the artificial intelligence approaches in predicting the protein native conformations, t...
Proteins Protein Conformation Protein Folding Artificial Intelligence Peptides
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A protein folding robot driven by a self-taught agent.

Bio Systems Dec 29, 2020
This paper presents a computer simulation of a virtual robot that behaves as a peptide chain of the Hemagglutinin-Esterase protein (HEs) from human coronavirus. The robot can learn efficient protein folding policies by itself and then use them to sol...
Algorithms Computer Simulation Systems Biology Systems Analysis Humans Robotics Coronavirus Neural Networks, Computer Hemagglutinins, Viral Models, Molecular Viral Fusion Proteins Machine Learning Amino Acid Sequence Protein Conformation Viral Proteins Protein Folding
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DeepFrag-k: a fragment-based deep learning approach for protein fold recognition.

BMC bioinformatics Nov 18, 2020
BACKGROUND: One of the most essential problems in structural bioinformatics is protein fold recognition. In this paper, we design a novel deep learning architecture, so-called DeepFrag-k, which identifies fold discriminative features at fragment leve...
Neural Networks, Computer Deep Learning Computational Biology Proteins Protein Folding
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Machine Learning Enables Selection of Epistatic Enzyme Mutants for Stability Against Unfolding and Detrimental Aggregation.

Chembiochem : a European journal of chemical biology Nov 17, 2020
Machine learning (ML) has pervaded most areas of protein engineering, including stability and stereoselectivity. Using limonene epoxide hydrolase as the model enzyme and innov'SAR as the ML platform, comprising a digital signal process, we achieved h...
Rhodococcus Limonene Protein Engineering Machine Learning Mutation Molecular Dynamics Simulation Protein Folding Protein Multimerization Epoxide Hydrolases
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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 ...
Protein Folding Sequence Alignment Sequence Analysis, Protein Artificial Intelligence Proteins Databases, Protein
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A Machine Learning Protocol for Predicting Protein Infrared Spectra.

Journal of the American Chemical Society Oct 30, 2020
Infrared (IR) absorption provides important chemical fingerprints of biomolecules. Protein secondary structure determination from IR spectra is tedious since its theoretical interpretation requires repeated expensive quantum-mechanical calculations i...
Protein Folding Ubiquitin Amides Machine Learning Spectrophotometry, Infrared Quantum Theory Protein Structure, Secondary Temperature Peptides Proteins
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ODiNPred: comprehensive prediction of protein order and disorder.

Scientific reports Sep 8, 2020
Structural disorder is widespread in eukaryotic proteins and is vital for their function in diverse biological processes. It is therefore highly desirable to be able to predict the degree of order and disorder from amino acid sequence. It is, however...
Proteins Databases, Protein Models, Molecular Amino Acids Intrinsically Disordered Proteins Protein Folding Software Algorithms Computational Biology Humans Neural Networks, Computer
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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...
Protein Folding Proteins Sequence Analysis, Protein Computational Biology Databases, Protein Support Vector Machine Amino Acid Sequence Evolution, Molecular
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The proteome landscape of the kingdoms of life.

Nature Jun 17, 2020
Proteins carry out the vast majority of functions in all biological domains, but for technological reasons their large-scale investigation has lagged behind the study of genomes. Since the first essentially complete eukaryotic proteome was reported, ...
Species Specificity Peptides Animals Homeostasis Deep Learning Photosynthesis Proteolysis Glycolysis Oxidation-Reduction Carbohydrate Metabolism Bacteroides Ion Transport Chromatography Proteomics Protein Folding Iron-Sulfur Proteins Classification Proteome Protein Biosynthesis
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Exploring Successful Parameter Region for Coarse-Grained Simulation of Biomolecules by Bayesian Optimization and Active Learning.

Biomolecules Mar 21, 2020
Accompanied with an increase of revealed biomolecular structures owing to advancements in structural biology, the molecular dynamics (MD) approach, especially coarse-grained (CG) MD suitable for macromolecules, is becoming increasingly important for ...
Protein Folding Proton-Translocating ATPases Machine Learning Molecular Dynamics Simulation
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