AIMC Topic: Proteins

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Protein structure prediction using deep learning distance and hydrogen-bonding restraints in CASP14.

Proteins Aug 7, 2021
In this article, we report 3D structure prediction results by two of our best server groups ("Zhang-Server" and "QUARK") in CASP14. These two servers were built based on the D-I-TASSER and D-QUARK algorithms, which integrated four newly developed com...
Software Deep Learning Computational Biology Hydrogen Bonding Protein Folding Sequence Alignment Sequence Analysis, Protein Proteins Models, Molecular Protein Conformation
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Accurate Identification of Antioxidant Proteins Based on a Combination of Machine Learning Techniques and Hidden Markov Model Profiles.

Computational and mathematical methods in medicine Aug 7, 2021
Antioxidant proteins (AOPs) play important roles in the management and prevention of several human diseases due to their ability to neutralize excess free radicals. However, the identification of AOPs by using wet-lab experimental techniques is often...
Proteins Computational Biology Markov Chains Humans Databases, Protein Antioxidants Peroxiredoxins Amino Acids Evolution, Molecular Machine Learning Algorithms
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KenDTI: An Ensemble Model for Predicting Drug-Target Interaction by Integrating Multi-Source Information.

IEEE/ACM transactions on computational biology and bioinformatics Aug 6, 2021
The identification of drug-target interactions (DTIs) is an essential step in the process of drug discovery. As experimental validation suffers from high cost and low success rate, various computational models have been exploited to infer potential D...
Humans Neural Networks, Computer Software Natural Language Processing Pharmaceutical Preparations Databases, Pharmaceutical Drug Development Proteins Algorithms Databases, Protein Computer Simulation Computational Biology
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A Convolutional Neural Network System to Discriminate Drug-Target Interactions.

IEEE/ACM transactions on computational biology and bioinformatics Aug 6, 2021
Biological targets are most commonly proteins such as enzymes, ion channels, and receptors. They are anything within a living organism to bind with some other entities (like an endogenous ligand or a drug), resulting in change in their behaviors or f...
Pharmaceutical Preparations Computational Biology Drug Development Proteins Drug Discovery Deep Learning Neural Networks, Computer Algorithms
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Predicting mutant outcome by combining deep mutational scanning and machine learning.

Proteins Jul 31, 2021
Deep mutational scanning provides unprecedented wealth of quantitative data regarding the functional outcome of mutations in proteins. A single experiment may measure properties (eg, structural stability) of numerous protein variants. Leveraging the ...
High-Throughput Nucleotide Sequencing DNA Mutational Analysis Models, Statistical Proteins Mutation Algorithms Protein Interaction Maps Computational Biology Machine Learning
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MCN-CPI: Multiscale Convolutional Network for Compound-Protein Interaction Prediction.

Biomolecules Jul 29, 2021
In the process of drug discovery, identifying the interaction between the protein and the novel compound plays an important role. With the development of technology, deep learning methods have shown excellent performance in various situations. Howeve...
Proteins Humans Kinetics Datasets as Topic High-Throughput Screening Assays Protein Conformation, alpha-Helical Molecular Docking Simulation Binding Sites Protein Conformation, beta-Strand Drugs, Investigational Protein Interaction Domains and Motifs Drug Discovery Deep Learning Protein Binding
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Improving protein tertiary structure prediction by deep learning and distance prediction in CASP14.

Proteins Jul 27, 2021
Substantial progresses in protein structure prediction have been made by utilizing deep-learning and residue-residue distance prediction since CASP13. Inspired by the advances, we improve our CASP14 MULTICOM protein structure prediction system by inc...
Protein Structure, Tertiary Deep Learning Sequence Analysis, Protein Proteins Models, Molecular Humans Sequence Alignment Software Algorithms
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Protein-Peptide Binding Site Detection Using 3D Convolutional Neural Networks.

Journal of chemical information and modeling Jul 22, 2021
Peptides and peptide-based molecules represent a promising therapeutic modality targeting intracellular protein-protein interactions, potentially combining the beneficial properties of biologics and small-molecule drugs. Protein-peptide complexes occ...
Neural Networks, Computer Proteins Binding Sites Peptides Protein Binding
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Accurate prediction of protein structures and interactions using a three-track neural network.

Science (New York, N.Y.) Jul 15, 2021
DeepMind presented notably accurate predictions at the recent 14th Critical Assessment of Structure Prediction (CASP14) conference. We explored network architectures that incorporate related ideas and obtained the best performance with a three-track ...
Protein Conformation Cryoelectron Microscopy Protein Folding Sphingosine N-Acyltransferase Multiprotein Complexes Protein Subunits Amino Acid Sequence ADAM Proteins Crystallography, X-Ray Databases, Protein Receptors, G-Protein-Coupled Models, Molecular Neural Networks, Computer Membrane Proteins Proteins Computer Simulation Deep Learning
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Highly accurate protein structure prediction with AlphaFold.

Nature Jul 15, 2021
Proteins are essential to life, and understanding their structure can facilitate a mechanistic understanding of their function. Through an enormous experimental effort, the structures of around 100,000 unique proteins have been determined, but this r...
Proteins Databases, Protein Models, Molecular Reproducibility of Results Deep Learning Computational Biology Sequence Alignment Amino Acid Sequence Protein Conformation Protein Folding Neural Networks, Computer
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