AIMC Topic: Protein Conformation

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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...
Machine Learning Cations Substrate Specificity Evolution, Molecular Sequence Homology, Amino Acid Alkyl and Aryl Transferases Plants Amino Acid Sequence Sesquiterpenes Protein Conformation
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Improved protein structure refinement guided by deep learning based accuracy estimation.

Nature communications Feb 26, 2021
We develop a deep learning framework (DeepAccNet) that estimates per-residue accuracy and residue-residue distance signed error in protein models and uses these predictions to guide Rosetta protein structure refinement. The network uses 3D convolutio...
Proteins Models, Molecular Models, Biological Caspases Protein Conformation Software Algorithms Deep Learning Computational Biology
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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
Neural Networks, Computer Algorithms Deep Learning Protein Structure, Secondary Computational Biology Sequence Alignment Proteins Position-Specific Scoring Matrices Protein Conformation
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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 Analysis, Protein Protein Interaction Domains and Motifs Protein Conformation Software Binding Sites Research Design Sequence Alignment Deep Learning Protein Binding Humans Computational Biology Proteins Databases, Protein Benchmarking
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CASSPER is a semantic segmentation-based particle picking algorithm for single-particle cryo-electron microscopy.

Communications biology Feb 15, 2021
Particle identification and selection, which is a prerequisite for high-resolution structure determination of biological macromolecules via single-particle cryo-electron microscopy poses a major bottleneck for automating the steps of structure determ...
Proteins Models, Molecular Semantics Protein Conformation Single Molecule Imaging Cryoelectron Microscopy Humans Animals Deep Learning Image Processing, Computer-Assisted
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Computational approach for identification, characterization, three-dimensional structure modelling and machine learning-based thermostability prediction of xylanases from the genome of Aspergillus fumigatus.

Computational biology and chemistry Feb 6, 2021
Identification of thermostable and alkaline xylanases from different fungal and bacterial species have gained an interest for the researchers because of its biotechnological relevance in many industries, such as pulp, paper, and bioethanol. In this s...
Endo-1,4-beta Xylanases Sequence Homology, Amino Acid Genome, Fungal Temperature Molecular Docking Simulation Computational Biology Amino Acid Sequence Data Mining Aspergillus fumigatus Machine Learning Enzyme Stability Protein Conformation
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An in silico deep learning approach to multi-epitope vaccine design: a SARS-CoV-2 case study.

Scientific reports Feb 5, 2021
The rampant spread of COVID-19, an infectious disease caused by SARS-CoV-2, all over the world has led to over millions of deaths, and devastated the social, financial and political entities around the world. Without an existing effective medical the...
Drug Design Deep Learning COVID-19 Vaccines Spike Glycoprotein, Coronavirus SARS-CoV-2 Epitopes, T-Lymphocyte Molecular Docking Simulation Molecular Dynamics Simulation Allergens Solubility Immunogenicity, Vaccine Computational Biology Models, Molecular Mutation RNA, Viral Humans COVID-19 Vaccines, Subunit T-Lymphocytes, Helper-Inducer T-Lymphocytes, Cytotoxic Protein Conformation Codon Usage Epitopes, B-Lymphocyte
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diSBPred: A machine learning based approach for disulfide bond prediction.

Computational biology and chemistry Jan 27, 2021
The protein disulfide bond is a covalent bond that forms during post-translational modification by the oxidation of a pair of cysteines. In protein, the disulfide bond is the most frequent covalent link between amino acids after the peptide bond. It ...
Amino Acid Sequence Algorithms Disulfides Support Vector Machine Protein Conformation Proteins
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TopSuite Web Server: A Meta-Suite for Deep-Learning-Based Protein Structure and Quality Prediction.

Journal of chemical information and modeling Jan 19, 2021
Proteins carry out the most fundamental processes of life such as cellular metabolism, regulation, and communication. Understanding these processes at a molecular level requires knowledge of their three-dimensional structures. Experimental techniques...
Proteins Crystallography, X-Ray Protein Conformation Neural Networks, Computer Software Deep Learning
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Application of Machine-Learning Methods to Recognize mitoBK Channels from Different Cell Types Based on the Experimental Patch-Clamp Results.

International journal of molecular sciences Jan 15, 2021
(1) Background: In this work, we focus on the activity of large-conductance voltage- and Ca2+-activated potassium channels (BK) from the inner mitochondrial membrane (mitoBK). The characteristic electrophysiological features of the mitoBK channels ar...
Mitochondria Artificial Intelligence Pregnancy Hippocampus Neural Networks, Computer Potassium Channels Pregnancy, Animal Machine Learning Rats Protein Conformation Fibroblasts Ion Channel Gating Endothelium Kinetics Patch-Clamp Techniques Large-Conductance Calcium-Activated Potassium Channels Female Animals Rats, Wistar Algorithms
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