AIMC Topic: Protein Structure, Secondary

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Improved protein relative solvent accessibility prediction using deep multi-view feature learning framework.

Analytical biochemistry Aug 31, 2021
The accurate prediction of the relative solvent accessibility of a protein is critical to understanding its 3D structure and biological function. In this study, a novel deep multi-view feature learning (DMVFL) framework that integrates three differen...
Neural Networks, Computer Databases, Protein Feedback Internet Deep Learning Solvents Computational Biology Proteins Protein Structure, Secondary
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Assigning secondary structure in proteins using AI.

Journal of molecular modeling Aug 17, 2021
Knowledge about protein structure assignment enriches the structural and functional understanding of proteins. Accurate and reliable structure assignment data is crucial for secondary structure prediction systems. Since the 1980s, various methods bas...
Proteins Models, Molecular Protein Structure, Secondary Software Deep Learning
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A Multitask Deep-Learning Method for Predicting Membrane Associations and Secondary Structures of Proteins.

Journal of proteome research Jul 8, 2021
Prediction of residue-level structural attributes and protein-level structural classes helps model protein tertiary structures and understand protein functions. Existing methods are either specialized on only one class of proteins or developed to pre...
Deep Learning Databases, Protein Computational Biology Protein Structure, Secondary Proteome
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Protein-Protein Interface Topology as a Predictor of Secondary Structure and Molecular Function Using Convolutional Deep Learning.

Journal of chemical information and modeling Jul 6, 2021
To power the specific recognition and binding of protein partners into functional complexes, a wealth of information about the structure and function of the partners is necessarily encoded into the global shape of protein-protein interfaces and their...
Deep Learning Proteins Protein Structure, Secondary Neural Networks, Computer
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RNA Backbone Torsion and Pseudotorsion Angle Prediction Using Dilated Convolutional Neural Networks.

Journal of chemical information and modeling May 26, 2021
RNA three-dimensional structure prediction has been relied on using a predicted or experimentally determined secondary structure as a restraint to reduce the conformational sampling space. However, the secondary-structure restraints are limited to pa...
RNA Protein Structure, Secondary Neural Networks, Computer Proteins
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Active Learning and the Potential of Neural Networks Accelerate Molecular Screening for the Design of a New Molecule Effective against SARS-CoV-2.

BioMed research international May 25, 2021
A global pandemic has emerged following the appearance of the new severe acute respiratory virus whose official name is the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), strongly affecting the health sector as well as the world econom...
Substrate Specificity Antiviral Agents Thermodynamics SARS-CoV-2 Protein Binding Coronavirus 3C Proteases Biological Products Protease Inhibitors Molecular Docking Simulation COVID-19 Drug Treatment Humans Drug Design Gene Expression Small Molecule Libraries Catalytic Domain Neural Networks, Computer Kinetics Protein Structure, Secondary Protein Interaction Domains and Motifs
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Detecting protein and DNA/RNA structures in cryo-EM maps of intermediate resolution using deep learning.

Nature communications Apr 16, 2021
An increasing number of density maps of macromolecular structures, including proteins and DNA/RNA complexes, have been determined by cryo-electron microscopy (cryo-EM). Although lately maps at a near-atomic resolution are routinely reported, there ar...
RNA Nucleic Acid Conformation Cryoelectron Microscopy DNA Models, Molecular Protein Structure, Secondary Software Deep Learning Computational Biology
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A novel end-to-end method to predict RNA secondary structure profile based on bidirectional LSTM and residual neural network.

BMC bioinformatics Mar 31, 2021
BACKGROUND: Studies have shown that RNA secondary structure, a planar structure formed by paired bases, plays diverse vital roles in fundamental life activities and complex diseases. RNA secondary structure profile can record whether each base is pai...
Binding Sites Protein Structure, Secondary Neural Networks, Computer Research Design RNA
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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 Disulfides Protein Processing, Post-Translational Sulfonic Acids Amino Acid Sequence Cations, Divalent Structure-Activity Relationship Cysteine Sulfides Protein Structure, Secondary Glutathione Electron Transport Complex IV Models, Molecular Protein Domains
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Comprehensive Study on Enhancing Low-Quality Position-Specific Scoring Matrix with Deep Learning for Accurate Protein Structure Property Prediction: Using Bagging Multiple Sequence Alignment Learning.

Journal of computational biology : a journal of computational molecular cell biology Feb 22, 2021
Sequence Alignment Position-Specific Scoring Matrices Proteins Protein Conformation Protein Structure, Secondary Neural Networks, Computer Deep Learning Algorithms Computational Biology
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