AIMC Topic: Amino Acids

Clear Filters Showing 31 to 40 of 229 articles

Protein design using structure-based residue preferences.

Nature communications Feb 22, 2024
Recent developments in protein design rely on large neural networks with up to 100s of millions of parameters, yet it is unclear which residue dependencies are critical for determining protein function. Here, we show that amino acid preferences at in...
Neural Networks, Computer Amino Acids Proteins Mutation
View on PubMed DOI

Leveraging machine learning to dissect role of combinations of amino acids in modulating the effect of zinc on mammalian cell growth.

Biotechnology progress Feb 15, 2024
Although the contributions of individual components of cell culture media are largely known, their combinatorial effects are far less understood. Experiments varying one component at a time cannot identify combinatorial effects, and analysis of the l...
Amino Acids CHO Cells Cricetulus Animals Zinc Cell Proliferation Culture Media Machine Learning
View on PubMed DOI

Learning the shape of protein microenvironments with a holographic convolutional neural network.

Proceedings of the National Academy of Sciences of the United States of America Feb 1, 2024
Proteins play a central role in biology from immune recognition to brain activity. While major advances in machine learning have improved our ability to predict protein structure from sequence, determining protein function from its sequence or struct...
Neural Networks, Computer Proteins Machine Learning Amino Acids Algorithms
View on PubMed DOI

DRBpred: A sequence-based machine learning method to effectively predict DNA- and RNA-binding residues.

Computers in biology and medicine Jan 29, 2024
DNA-binding and RNA-binding proteins are essential to an organism's normal life cycle. These proteins have diverse functions in various biological processes. DNA-binding proteins are crucial for DNA replication, transcription, repair, packaging, and ...
DNA-Binding Proteins RNA RNA-Binding Proteins Databases, Protein DNA Amino Acids Algorithms Computational Biology Machine Learning
View on PubMed DOI

Mining and rational design of psychrophilic catalases using metagenomics and deep learning models.

Applied microbiology and biotechnology Jan 4, 2024
A complete catalase-encoding gene, designated soiCat1, was obtained from soil samples via metagenomic sequencing, assembly, and gene prediction. soiCat1 showed 73% identity to a catalase-encoding gene of Mucilaginibacter rubeus strain P1, and the ami...
Soil Deep Learning Catalase Amino Acids Amino Acid Sequence
View on PubMed DOI

Unmasking crucial residues in adipose triglyceride lipase for coactivation with comparative gene identification-58.

Journal of lipid research Dec 20, 2023
Lipolysis is an essential metabolic process that releases unesterified fatty acids from neutral lipid stores to maintain energy homeostasis in living organisms. Adipose triglyceride lipase (ATGL) plays a key role in intracellular lipolysis and can be...
Triglycerides Lipolysis 1-Acylglycerol-3-Phosphate O-Acyltransferase Artificial Intelligence Amino Acids Lipase Animals Mice
View on PubMed DOI

DeepPPThermo: A Deep Learning Framework for Predicting Protein Thermostability Combining Protein-Level and Amino Acid-Level Features.

Journal of computational biology : a journal of computational molecular cell biology Dec 13, 2023
Using wet experimental methods to discover new thermophilic proteins or improve protein thermostability is time-consuming and expensive. Machine learning methods have shown powerful performance in the study of protein thermostability in recent years....
Proteins Amino Acids Algorithms Neural Networks, Computer Deep Learning
View on PubMed DOI

SPIN-CGNN: Improved fixed backbone protein design with contact map-based graph construction and contact graph neural network.

PLoS computational biology Dec 7, 2023
Recent advances in deep learning have significantly improved the ability to infer protein sequences directly from protein structures for the fix-backbone design. The methods have evolved from the early use of multi-layer perceptrons to convolutional ...
Amino Acid Sequence Neural Networks, Computer Cluster Analysis Amino Acids Diffusion
View on PubMed DOI

Effective Local and Secondary Protein Structure Prediction by Combining a Neural Network-Based Approach with Extensive Feature Design and Selection without Reliance on Evolutionary Information.

International journal of molecular sciences Oct 27, 2023
Protein structure prediction continues to pose multiple challenges despite outstanding progress that is largely attributable to the use of novel machine learning techniques. One of the widely used representations of local 3D structure-protein blocks ...
Amino Acids Protein Structure, Secondary Algorithms Neural Networks, Computer Amino Acid Sequence Proteins
View on PubMed DOI

Machine learning-based model for accurate identification of druggable proteins using light extreme gradient boosting.

Journal of biomolecular structure & dynamics Oct 18, 2023
The identification of druggable proteins (DPs) is significant for the development of new drugs, personalized medicine, understanding of disease mechanisms, drug repurposing, and economic benefits. By identifying new druggable targets, researchers can...
Drug Discovery Computational Biology Machine Learning Position-Specific Scoring Matrices Proteins Algorithms Humans Amino Acids
View on PubMed DOI
Popular Topics
Recent Journals