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Databases, Protein

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Protein secondary structure prediction improved by recurrent neural networks integrated with two-dimensional convolutional neural networks.

Journal of bioinformatics and computational biology Oct 1, 2018
Protein secondary structure prediction (PSSP) is an important research field in bioinformatics. The representation of protein sequence features could be treated as a matrix, which includes the amino-acid residue (time-step) dimension and the feature ...
Proteins Databases, Protein Protein Structure, Secondary Neural Networks, Computer Deep Learning Computational Biology
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PANNZER2: a rapid functional annotation web server.

Nucleic acids research Jul 2, 2018
The unprecedented growth of high-throughput sequencing has led to an ever-widening annotation gap in protein databases. While computational prediction methods are available to make up the shortfall, a majority of public web servers are hindered by pr...
High-Throughput Nucleotide Sequencing Molecular Sequence Annotation Gene Ontology Software Databases, Protein Algorithms Internet Computational Biology
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Computational identification of binding energy hot spots in protein-RNA complexes using an ensemble approach.

Bioinformatics (Oxford, England) May 1, 2018
MOTIVATION: Identifying RNA-binding residues, especially energetically favored hot spots, can provide valuable clues for understanding the mechanisms and functional importance of protein-RNA interactions. Yet, limited availability of experimentally r...
Machine Learning Protein Binding Models, Molecular RNA Binding Sites Computational Biology Proteins Databases, Protein
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Sixty-five years of the long march in protein secondary structure prediction: the final stretch?

Briefings in bioinformatics May 1, 2018
Protein secondary structure prediction began in 1951 when Pauling and Corey predicted helical and sheet conformations for protein polypeptide backbone even before the first protein structure was determined. Sixty-five years later, powerful new method...
Proteins Databases, Protein Protein Structure, Secondary Algorithms Computational Biology Models, Theoretical Humans Neural Networks, Computer
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The Reactome Pathway Knowledgebase.

Nucleic acids research Jan 4, 2018
The Reactome Knowledgebase (https://reactome.org) provides molecular details of signal transduction, transport, DNA replication, metabolism, and other cellular processes as an ordered network of molecular transformations-an extended version of a clas...
Databases, Protein Computer Graphics Metabolic Networks and Pathways Humans Internet User-Computer Interface Knowledge Bases Signal Transduction Databases, Chemical Molecular Sequence Annotation
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iPTMnet: an integrated resource for protein post-translational modification network discovery.

Nucleic acids research Jan 4, 2018
Protein post-translational modifications (PTMs) play a pivotal role in numerous biological processes by modulating regulation of protein function. We have developed iPTMnet (http://proteininformationresource.org/iPTMnet) for PTM knowledge discovery, ...
Enzymes Data Mining Sequence Alignment Protein Processing, Post-Translational Databases, Protein Phosphorylation Internet Knowledge Bases Animals Protein Interaction Maps Computational Biology Humans
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Extracting chemical-protein relations with ensembles of SVM and deep learning models.

Database : the journal of biological databases and curation Jan 1, 2018
Mining relations between chemicals and proteins from the biomedical literature is an increasingly important task. The CHEMPROT track at BioCreative VI aims to promote the development and evaluation of systems that can automatically detect the chemica...
Proteins Reproducibility of Results Databases, Protein Models, Theoretical Neural Networks, Computer Support Vector Machine Databases, Chemical Machine Learning Data Curation
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Leveraging prior knowledge for protein-protein interaction extraction with memory network.

Database : the journal of biological databases and curation Jan 1, 2018
Automatically extracting protein-protein interactions (PPIs) from biomedical literature provides additional support for precision medicine efforts. This paper proposes a novel memory network-based model (MNM) for PPI extraction, which leverages prior...
Statistics as Topic Knowledge Protein Interaction Mapping Algorithms Databases, Protein Neural Networks, Computer
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Prediction of Nitrated Tyrosine Residues in Protein Sequences by Extreme Learning Machine and Feature Selection Methods.

Combinatorial chemistry & high throughput screening Jan 1, 2018
BACKGROUND: Accurately recognizing nitrated tyrosine residues from protein sequences would pave a way for understanding the mechanism of nitration and the screening of the tyrosine residues in sequences.
Databases, Protein Tyrosine Amino Acid Sequence Nitrates Machine Learning Computational Biology Protein Processing, Post-Translational
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Survey of Computational Approaches for Prediction of DNA-Binding Residues on Protein Surfaces.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2018
The increasing number of protein structures with uncharacterized function necessitates the development of in silico prediction methods for functional annotations on proteins. In this chapter, different kinds of computational approaches are briefly in...
Databases, Protein DNA DNA-Binding Proteins Amino Acid Sequence Protein Conformation Molecular Docking Simulation Protein Binding Computational Biology Machine Learning Binding Sites Sequence Analysis, Protein
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