AIMC Topic: Protein Domains

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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 ...
Deep Learning Mutation Reproducibility of Results Transcription, Genetic Epistasis, Genetic Lac Repressors Protein Domains Escherichia coli Proteins
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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...
Protein Conformation, beta-Strand Protein Domains Bacterial Outer Membrane Proteins Machine Learning
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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 Protein Domains Algorithms Neural Networks, Computer Deep Learning Software
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DNN-Dom: predicting protein domain boundary from sequence alone by deep neural network.

Bioinformatics (Oxford, England) Dec 15, 2019
MOTIVATION: Accurate delineation of protein domain boundary plays an important role for protein engineering and structure prediction. Although machine-learning methods are widely used to predict domain boundary, these approaches often ignore long-ran...
Neural Networks, Computer Deep Learning Proteins Protein Domains Machine Learning Software
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ConDo: protein domain boundary prediction using coevolutionary information.

Bioinformatics (Oxford, England) Jul 15, 2019
MOTIVATION: Domain boundary prediction is one of the most important problems in the study of protein structure and function. Many sequence-based domain boundary prediction methods are either template-based or machine learning (ML) based. ML-based met...
Sequence Alignment Protein Domains Protein Structure, Secondary Machine Learning Proteins
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BIPSPI: a method for the prediction of partner-specific protein-protein interfaces.

Bioinformatics (Oxford, England) Feb 1, 2019
MOTIVATION: Protein-Protein Interactions (PPI) are essentials for most cellular processes and thus, unveiling how proteins interact is a crucial question that can be better understood by identifying which residues are responsible for the interaction....
Protein Domains Binding Sites Sequence Analysis, Protein Protein Interaction Maps Proteins Machine Learning
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DeepDom: Predicting protein domain boundary from sequence alone using stacked bidirectional LSTM.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing Jan 1, 2019
Protein domain boundary prediction is usually an early step to understand protein function and structure. Most of the current computational domain boundary prediction methods suffer from low accuracy and limitation in handling multi-domain types, or ...
Amino Acid Sequence Algorithms Deep Learning Databases, Protein Protein Domains Computational Biology Neural Networks, Computer
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Structure-based prediction of protein- peptide binding regions using Random Forest.

Bioinformatics (Oxford, England) Feb 1, 2018
MOTIVATION: Protein-peptide interactions are one of the most important biological interactions and play crucial role in many diseases including cancer. Therefore, knowledge of these interactions provides invaluable insights into all cellular processe...
Machine Learning Peptides Computational Biology Proteins Protein Binding Humans Protein Tyrosine Phosphatase, Non-Receptor Type 4 Protein Domains Sequence Analysis, Protein
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First steps in automatic summarization of transcription factor properties for RegulonDB: classification of sentences about structural domains and regulated processes.

Database : the journal of biological databases and curation Jan 1, 2017
RegulonDB, http://regulondb.ccg.unam.mx.
Escherichia coli K12 Protein Domains Transcription Factors Regulon Support Vector Machine Serine Endopeptidases Databases, Bibliographic
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Complementary Sources of Protein Functional Information: The Far Side of GO.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2017
The GO captures many aspects of functional annotations, but there are other alternative complementary sources of protein function information. For example, enzyme functional annotations are described in a range of resources from the Enzyme Commission...
Computational Biology Enzymes Signal Transduction Gene Ontology Humans Genome Animals Protein Domains Software Databases, Genetic Internet Protein Interaction Maps Proteins Molecular Sequence Annotation
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