AIMC Topic: Models, Molecular

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T Cell Epitope Prediction and Its Application to Immunotherapy.

Frontiers in immunology Sep 15, 2021
T cells play a crucial role in controlling and driving the immune response with their ability to discriminate peptides derived from healthy as well as pathogenic proteins. In this review, we focus on the currently available computational tools for ep...
Histocompatibility Antigens Class I Base Sequence Antigen Presentation Mass Spectrometry Models, Molecular Receptors, Antigen, T-Cell T-Cell Antigen Receptor Specificity Computational Biology Immunotherapy Humans Antigens, Neoplasm Neural Networks, Computer Sequence Analysis, DNA Neoplasms Epitopes, T-Lymphocyte Peptides
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Improved 3-D Protein Structure Predictions using Deep ResNet Model.

The protein journal Sep 12, 2021
Protein Structure Prediction (PSP) is considered to be a complicated problem in computational biology. In spite of, the remarkable progress made by the co-evolution-based method in PSP, it is still a challenging and unresolved problem. Recently, alon...
Neural Networks, Computer Software Models, Molecular Protein Conformation Protein Folding Computational Biology Proteins Databases, Protein
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CYPlebrity: Machine learning models for the prediction of inhibitors of cytochrome P450 enzymes.

Bioorganic & medicinal chemistry Aug 28, 2021
The vast majority of approved drugs are metabolized by the five major cytochrome P450 (CYP) isozymes, 1A2, 2C9, 2C19, 2D6 and 3A4. Inhibition of CYP isozymes can cause drug-drug interactions with severe pharmacological and toxicological consequences....
Humans Machine Learning Dose-Response Relationship, Drug Structure-Activity Relationship Models, Molecular Cytochrome P-450 Enzyme Inhibitors Molecular Structure Cytochrome P-450 Enzyme System
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Protein inter-residue contact and distance prediction by coupling complementary coevolution features with deep residual networks in CASP14.

Proteins Aug 19, 2021
This article reports and analyzes the results of protein contact and distance prediction by our methods in the 14th Critical Assessment of techniques for protein Structure Prediction (CASP14). A new deep learning-based contact/distance predictor was ...
Software Deep Learning Computational Biology Sequence Alignment Sequence Analysis, Protein Proteins Models, Molecular Protein Conformation
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Machine Learning Directed Optimization of Classical Molecular Modeling Force Fields.

Journal of chemical information and modeling Aug 17, 2021
Accurate force fields are necessary for predictive molecular simulations. However, developing force fields that accurately reproduce experimental properties is challenging. Here, we present a machine learning directed, multiobjective optimization wor...
Gases Thermodynamics Machine Learning Prospective Studies Models, Molecular
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PYTHIA: Deep Learning Approach for Local Protein Conformation Prediction.

International journal of molecular sciences Aug 17, 2021
Protein Blocks (PBs) are a widely used structural alphabet describing local protein backbone conformation in terms of 16 possible conformational states, adopted by five consecutive amino acids. The representation of complex protein 3D structures as 1...
Protein Conformation Sequence Analysis, Protein Proteins Humans Software Neural Networks, Computer Databases, Protein Algorithms Models, Molecular Deep Learning
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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...
Models, Molecular Protein Structure, Secondary Software Deep Learning Proteins
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A Machine Learning Study on the Thermostability Prediction of (R)--Selective Amine Transaminase from Aspergillus terreus.

BioMed research international Aug 16, 2021
Artificial intelligence technologies such as machine learning have been applied to protein engineering, with unique advantages in protein structure, function prediction, catalytic activity, and other issues in recent years. Screening better mutants i...
Protein Engineering Models, Molecular Protein Stability Transaminases Hot Temperature Protein Structural Elements Machine Learning Amines Aspergillus Substrate Specificity
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Deep learning to design nuclear-targeting abiotic miniproteins.

Nature chemistry Aug 9, 2021
There are more amino acid permutations within a 40-residue sequence than atoms on Earth. This vast chemical search space hinders the use of human learning to design functional polymers. Here we show how machine learning enables the de novo design of ...
Deep Learning Molecular Weight Protein Conformation Datasets as Topic Protein Transport Cytosol Cell Nucleus Proteins Models, Molecular
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Comparison of UV- and Raman-based monitoring of the Protein A load phase and evaluation of data fusion by PLS models and CNNs.

Biotechnology and bioengineering Aug 8, 2021
A promising application of Process Analytical Technology to the downstream process of monoclonal antibodies (mAbs) is the monitoring of the Protein A load phase as its control promises economic benefits. Different spectroscopic techniques have been e...
Neural Networks, Computer Staphylococcal Protein A Spectrum Analysis, Raman Models, Molecular Spectrophotometry, Ultraviolet
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