AIMC Topic: Protein Domains

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Morinda officinalis polysaccharides inhibit the expression and activity of NOD-like receptor thermal protein domain associated protein 3 in inflammatory periodontal ligament cells by upregulating silent information regulator sirtuin 1.

Hua xi kou qiang yi xue za zhi = Huaxi kouqiang yixue zazhi = West China journal of stomatology Dec 1, 2023
OBJECTIVES: This study aims to investigate the effect of morinda officinalis polysaccharides (MOP) in inflammatory microenvironment on the expression of silent information regulator sirtuin 1 (SIRT1) and NOD-like receptor thermal protein domain assoc...
Protein Domains NLR Family, Pyrin Domain-Containing 3 Protein NLR Proteins Sirtuin 1 Periodontal Ligament Inflammation Interleukin-18 Lipopolysaccharides Morinda Animals Rats
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ProteinMAE: masked autoencoder for protein surface self-supervised learning.

Bioinformatics (Oxford, England) Dec 1, 2023
SUMMARY: The biological functions of proteins are determined by the chemical and geometric properties of their surfaces. Recently, with the booming progress of deep learning, a series of learning-based surface descriptors have been proposed and achie...
Protein Domains Supervised Machine Learning Binding Sites Membrane Proteins Natural Language Processing
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CoCoNat: a novel method based on deep learning for coiled-coil prediction.

Bioinformatics (Oxford, England) Aug 1, 2023
MOTIVATION: Coiled-coil domains (CCD) are widespread in all organisms and perform several crucial functions. Given their relevance, the computational detection of CCD is very important for protein functional annotation. State-of-the-art prediction me...
Protein Domains Molecular Sequence Annotation Deep Learning Proteins Neural Networks, Computer
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PPICT: an integrated deep neural network for predicting inter-protein PTM cross-talk.

Briefings in bioinformatics Mar 19, 2023
Post-translational modifications (PTMs) fine-tune various signaling pathways not only by the modification of a single residue, but also by the interplay of different modifications on residue pairs within or between proteins, defined as PTM cross-talk...
Proteome Signal Transduction Protein Processing, Post-Translational Neural Networks, Computer Protein Domains
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High-accuracy protein model quality assessment using attention graph neural networks.

Briefings in bioinformatics Mar 19, 2023
Great improvement has been brought to protein tertiary structure prediction through deep learning. It is important but very challenging to accurately rank and score decoy structures predicted by different models. CASP14 results show that existing qua...
Proteins Protein Domains Algorithms Protein Conformation Amino Acids Computational Biology Neural Networks, Computer
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Structural analogue-based protein structure domain assembly assisted by deep learning.

Bioinformatics (Oxford, England) Sep 30, 2022
MOTIVATION: With the breakthrough of AlphaFold2, the protein structure prediction problem has made remarkable progress through deep learning end-to-end techniques, in which correct folds could be built for nearly all single-domain proteins. However, ...
Proteins Databases, Protein Software Deep Learning Protein Domains Humans
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GRaSP-web: a machine learning strategy to predict binding sites based on residue neighborhood graphs.

Nucleic acids research Jul 5, 2022
Proteins are essential macromolecules for the maintenance of living systems. Many of them perform their function by interacting with other molecules in regions called binding sites. The identification and characterization of these regions are of fund...
Protein Domains Ligands Binding Sites Protein Binding Proteins Machine Learning
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CoCoPRED: coiled-coil protein structural feature prediction from amino acid sequence using deep neural networks.

Bioinformatics (Oxford, England) Jan 12, 2022
MOTIVATION: Coiled-coil is composed of two or more helices that are wound around each other. It widely exists in proteins and has been discovered to play a variety of critical roles in biology processes. Generally, there are three types of structural...
Protein Structure, Secondary Neural Networks, Computer Protein Domains Amino Acid Sequence Proteins
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Evotuning protocols for Transformer-based variant effect prediction on multi-domain proteins.

Briefings in bioinformatics Nov 5, 2021
Accurate variant effect prediction has broad impacts on protein engineering. Recent machine learning approaches toward this end are based on representation learning, by which feature vectors are learned and generated from unlabeled sequences. However...
Algorithms Reproducibility of Results Deep Learning Protein Binding Neural Networks, Computer Protein Interaction Domains and Motifs Protein Domains Computational Biology Amino Acid Sequence Proteins
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dSPRINT: predicting DNA, RNA, ion, peptide and small molecule interaction sites within protein domains.

Nucleic acids research Jul 21, 2021
Domains are instrumental in facilitating protein interactions with DNA, RNA, small molecules, ions and peptides. Identifying ligand-binding domains within sequences is a critical step in protein function annotation, and the ligand-binding properties ...
Binding Sites Ions Ligands Humans DNA Protein Domains Machine Learning Peptides RNA
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