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Databases, Protein

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ResPRE: high-accuracy protein contact prediction by coupling precision matrix with deep residual neural networks.

Bioinformatics (Oxford, England) Nov 1, 2019
MOTIVATION: Contact-map of a protein sequence dictates the global topology of structural fold. Accurate prediction of the contact-map is thus essential to protein 3D structure prediction, which is particularly useful for the protein sequences that do...
Computational Biology Proteins Databases, Protein Sequence Alignment Neural Networks, Computer
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Graph kernels combined with the neural network on protein classification.

Journal of bioinformatics and computational biology Oct 1, 2019
At present, most of the researches on protein classification are based on graph kernels. The essence of graph kernels is to extract the substructure and use the similarity of substructures as the kernel values. In this paper, we propose a novel graph...
Reproducibility of Results Computational Biology Proteins Neural Networks, Computer Databases, Protein Protein Conformation Algorithms Computer Graphics
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BioSeq-Analysis: a platform for DNA, RNA and protein sequence analysis based on machine learning approaches.

Briefings in bioinformatics Jul 19, 2019
With the avalanche of biological sequences generated in the post-genomic age, one of the most challenging problems is how to computationally analyze their structures and functions. Machine learning techniques are playing key roles in this field. Typi...
Computational Biology Sequence Analysis Sequence Analysis, RNA Machine Learning Humans Sequence Analysis, DNA Databases, Nucleic Acid Software Databases, Protein Sequence Analysis, Protein Algorithms Internet
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NetGO: improving large-scale protein function prediction with massive network information.

Nucleic acids research Jul 2, 2019
Automated function prediction (AFP) of proteins is of great significance in biology. AFP can be regarded as a problem of the large-scale multi-label classification where a protein can be associated with multiple gene ontology terms as its labels. Bas...
Models, Molecular Internet Benchmarking Proteins Databases, Protein Structure-Activity Relationship Gene Ontology Protein Interaction Mapping Sequence Alignment Sequence Homology, Amino Acid Plants Amino Acid Sequence Molecular Sequence Annotation Humans Animals Computational Biology Machine Learning Software Sequence Analysis, Protein Prokaryotic Cells
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Development of a protein-ligand extended connectivity (PLEC) fingerprint and its application for binding affinity predictions.

Bioinformatics (Oxford, England) Apr 15, 2019
MOTIVATION: Fingerprints (FPs) are the most common small molecule representation in cheminformatics. There are a wide variety of FPs, and the Extended Connectivity Fingerprint (ECFP) is one of the best-suited for general applications. Despite the ove...
Databases, Protein Ligands Machine Learning Protein Binding Proteins
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Identification of hormone binding proteins based on machine learning methods.

Mathematical biosciences and engineering : MBE Mar 22, 2019
The soluble carrier hormone binding protein (HBP) plays an important role in the growth of human and other animals. HBP can also selectively and non-covalently interact with hormone. Therefore, accurate identification of HBP is an important prerequis...
Amino Acids Reproducibility of Results Hormones Animals Analysis of Variance Software Peptides Carrier Proteins Algorithms Humans Databases, Protein Computer Simulation Computational Biology Machine Learning Support Vector Machine
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Identifying short disorder-to-order binding regions in disordered proteins with a deep convolutional neural network method.

Journal of bioinformatics and computational biology Feb 1, 2019
Molecular recognition features (MoRFs) are key functional regions of intrinsically disordered proteins (IDPs), which play important roles in the molecular interaction network of cells and are implicated in many serious human diseases. Identifying MoR...
Binding Sites Databases, Protein Amino Acid Sequence Intrinsically Disordered Proteins Deep Learning Humans Protein Binding Computational Biology Neural Networks, Computer Membrane Proteins
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Using two-dimensional convolutional neural networks for identifying GTP binding sites in Rab proteins.

Journal of bioinformatics and computational biology Feb 1, 2019
Deep learning has been increasingly and widely used to solve numerous problems in various fields with state-of-the-art performance. It can also be applied in bioinformatics to reduce the requirement for feature extraction and reach high performance. ...
Deep Learning Computational Biology Databases, Protein Binding Sites rab GTP-Binding Proteins Amino Acids Amino Acid Sequence Humans Neural Networks, Computer Guanosine Triphosphate
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UniProt: a worldwide hub of protein knowledge.

Nucleic acids research Jan 8, 2019
The UniProt Knowledgebase is a collection of sequences and annotations for over 120 million proteins across all branches of life. Detailed annotations extracted from the literature by expert curators have been collected for over half a million of the...
Knowledge Bases Molecular Sequence Annotation Data Curation Proteome Sequence Analysis, Protein Databases, Protein
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Machine Learning to Predict Binding Affinity.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2019
Recent progress in the development of scientific libraries with machine-learning techniques paved the way for the implementation of integrated computational tools to predict ligand-binding affinity. The prediction of binding affinity uses the atomic ...
Cyclin-Dependent Kinase 2 Proteins Databases, Protein Molecular Dynamics Simulation Humans Supervised Machine Learning HIV Protease Algorithms Machine Learning Ligands Web Browser Molecular Docking Simulation Software Models, Statistical
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