AIMC Topic: Protein Domains

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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...
Protein Processing, Post-Translational Protein Domains Neural Networks, Computer Proteome Signal Transduction
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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...
Neural Networks, Computer Algorithms Protein Domains Amino Acids Protein Conformation Computational Biology Proteins
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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, ...
Humans Protein Domains Proteins Databases, Protein Software Deep Learning
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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 Binding Proteins Machine Learning Binding Sites Protein Domains Ligands
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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 Proteins Protein Domains Amino Acid Sequence
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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...
Amino Acid Sequence Protein Interaction Domains and Motifs Proteins Protein Domains Algorithms Neural Networks, Computer Reproducibility of Results Protein Binding Deep Learning Computational Biology
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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 ...
Peptides DNA Protein Domains RNA Humans Machine Learning Binding Sites Ions Ligands
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Deep representation learning improves prediction of LacI-mediated transcriptional repression.

Proceedings of the National Academy of Sciences of the United States of America Jul 6, 2021
Recent progress in DNA synthesis and sequencing technology has enabled systematic studies of protein function at a massive scale. We explore a deep mutational scanning study that measured the transcriptional repression function of 43,669 variants of ...
Reproducibility of Results Epistasis, Genetic Deep Learning Lac Repressors Escherichia coli Proteins Mutation Transcription, Genetic Protein Domains
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Structures of the β-barrel assembly machine recognizing outer membrane protein substrates.

FASEB journal : official publication of the Federation of American Societies for Experimental Biology Jan 1, 2021
β-barrel outer membrane proteins (β-OMPs) play critical roles in nutrition acquisition, protein import/export, and other fundamental biological processes. The assembly of β-OMPs in Gram-negative bacteria is mediated by the β-barrel assembly machinery...
Bacterial Outer Membrane Proteins Protein Conformation, beta-Strand Machine Learning Protein Domains
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FUpred: detecting protein domains through deep-learning-based contact map prediction.

Bioinformatics (Oxford, England) Jun 1, 2020
MOTIVATION: Protein domains are subunits that can fold and function independently. Correct domain boundary assignment is thus a critical step toward accurate protein structure and function analyses. There is, however, no efficient algorithm available...
Computational Biology Algorithms Neural Networks, Computer Protein Domains Software Deep Learning
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