AIMC Topic: Protein Domains

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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 Machine Learning Proteins Protein Domains Deep 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 Proteins Machine Learning Protein Structure, Secondary Protein Domains
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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 Interaction Maps Proteins Machine Learning Binding Sites Sequence Analysis, Protein Protein Domains
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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 ...
Databases, Protein Protein Domains Computational Biology Amino Acid Sequence Neural Networks, Computer Deep Learning Algorithms
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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...
Sequence Analysis, Protein Protein Tyrosine Phosphatase, Non-Receptor Type 4 Protein Domains Protein Binding Peptides Proteins Computational Biology Humans Machine Learning
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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.
Regulon Serine Endopeptidases Databases, Bibliographic Escherichia coli K12 Support Vector Machine Transcription Factors Protein Domains
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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...
Molecular Sequence Annotation Internet Genome Gene Ontology Humans Proteins Software Protein Domains Computational Biology Databases, Genetic Signal Transduction Protein Interaction Maps Enzymes Animals
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