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Databases, Protein

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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...
Proteins Databases, Protein Ligands Machine Learning Protein Binding
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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...
Databases, Protein Amino Acids Hormones Computational Biology Support Vector Machine Software Carrier Proteins Algorithms Computer Simulation Reproducibility of Results Animals Peptides Analysis of Variance Humans Machine Learning
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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...
Intrinsically Disordered Proteins Binding Sites Databases, Protein Amino Acid Sequence Humans Neural Networks, Computer Deep Learning Protein Binding Computational Biology 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. ...
Humans Databases, Protein Amino Acids Amino Acid Sequence Neural Networks, Computer Deep Learning Computational Biology Guanosine Triphosphate Binding Sites rab GTP-Binding Proteins
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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...
Proteome Databases, Protein Knowledge Bases Molecular Sequence Annotation Data Curation Sequence Analysis, 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 ...
Algorithms Web Browser Humans Molecular Docking Simulation Machine Learning Supervised Machine Learning Cyclin-Dependent Kinase 2 Proteins Models, Statistical Software Ligands Databases, Protein HIV Protease Molecular Dynamics Simulation
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An enhanced workflow for variant interpretation in UniProtKB/Swiss-Prot improves consistency and reuse in ClinVar.

Database : the journal of biological databases and curation Jan 1, 2019
Personalized genomic medicine depends on integrated analyses that combine genetic and phenotypic data from individual patients with reference knowledge of the functional and clinical significance of sequence variants. Sources of this reference knowle...
Knowledge Bases Genetic Variation Copper-Transporting ATPases Zinc Finger Protein Gli3 Databases, Protein Nerve Tissue Proteins Workflow
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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 ...
Neural Networks, Computer Algorithms Databases, Protein Deep Learning Protein Domains Computational Biology Amino Acid Sequence
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Recent Advances in Machine Learning Methods for Predicting Heat Shock Proteins.

Current drug metabolism Jan 1, 2019
BACKGROUND: As molecular chaperones, Heat Shock Proteins (HSPs) not only play key roles in protein folding and maintaining protein stabilities, but are also linked with multiple kinds of diseases. Therefore, HSPs have been regarded as the focus of dr...
Databases, Protein Amino Acid Sequence Heat-Shock Proteins Machine Learning Computational Biology
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Blind prediction of protein B-factor and flexibility.

The Journal of chemical physics Oct 7, 2018
The Debye-Waller factor, a measure of X-ray attenuation, can be experimentally observed in protein X-ray crystallography. Previous theoretical models have made strong inroads in the analysis of beta (B)-factors by linearly fitting protein B-factors f...
Computer Graphics Algorithms Humans Elasticity Receptors, Fc Machine Learning Crystallography, X-Ray Animals Protein Conformation Databases, Protein
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