AIMC Topic: Proteins

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Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening.

PLoS computational biology Jan 8, 2018
This work introduces a number of algebraic topology approaches, including multi-component persistent homology, multi-level persistent homology, and electrostatic persistence for the representation, characterization, and description of small molecules...
Computational Biology Models, Neurological Proteins Machine Learning Algorithms Protein Binding Ligands Nucleic Acids Humans Static Electricity Neural Networks, Computer Protein Interaction Mapping Databases, Protein Area Under Curve Molecular Dynamics Simulation
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ProtDet-CCH: Protein Remote Homology Detection by Combining Long Short-Term Memory and Ranking Methods.

IEEE/ACM transactions on computational biology and bioinformatics Jan 5, 2018
As one of the most challenging tasks in sequence analysis, protein remote homology detection has been extensively studied. Methods based on discriminative models and ranking approaches have achieved the state-of-the-art performance, and these two kin...
Humans Neural Networks, Computer Software Computational Biology Support Vector Machine Algorithms Sequence Analysis, Protein Proteins Databases, Protein Databases, Factual Reproducibility of Results Sequence Homology, Amino Acid Amino Acid Motifs
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Potent pairing: ensemble of long short-term memory networks and support vector machine for chemical-protein relation extraction.

Database : the journal of biological databases and curation Jan 1, 2018
Biomedical researchers regularly discover new interactions between chemical compounds/drugs and genes/proteins, and report them in research literature. Having knowledge about these interactions is crucially important in many research areas such as pr...
Data Mining Databases, Chemical Proteins Databases, Protein Pharmaceutical Preparations Neural Networks, Computer Drug Discovery Deep Learning Protein Binding Support Vector Machine
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Extracting chemical-protein relations using attention-based neural networks.

Database : the journal of biological databases and curation Jan 1, 2018
Relation extraction is an important task in the field of natural language processing. In this paper, we describe our approach for the BioCreative VI Task 5: text mining chemical-protein interactions. We investigate multiple deep neural network (DNN) ...
Neural Networks, Computer Databases, Chemical Algorithms Proteins Databases, Protein
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A sparse autoencoder-based deep neural network for protein solvent accessibility and contact number prediction.

BMC bioinformatics Dec 28, 2017
BACKGROUND: Direct prediction of the three-dimensional (3D) structures of proteins from one-dimensional (1D) sequences is a challenging problem. Significant structural characteristics such as solvent accessibility and contact number are essential for...
Machine Learning Algorithms Models, Molecular Proteins Neural Networks, Computer Solvents
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Enhancing Evolutionary Couplings with Deep Convolutional Neural Networks.

Cell systems Dec 20, 2017
While genes are defined by sequence, in biological systems a protein's function is largely determined by its three-dimensional structure. Evolutionary information embedded within multiple sequence alignments provides a rich source of data for inferri...
Probability Protein Conformation Neural Networks, Computer Protein Folding Proteins Forecasting Sequence Alignment Machine Learning Humans Animals Databases, Protein Algorithms Computational Biology Models, Molecular
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New Deep Learning Methods for Protein Loop Modeling.

IEEE/ACM transactions on computational biology and bioinformatics Dec 18, 2017
Computational protein structure prediction is a long-standing challenge in bioinformatics. In the process of predicting protein 3D structures, it is common that parts of an experimental structure are missing or parts of a predicted structure need to ...
Proteins Algorithms Deep Learning Computational Biology
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Utilizing knowledge base of amino acids structural neighborhoods to predict protein-protein interaction sites.

BMC bioinformatics Dec 6, 2017
BACKGROUND: Protein-protein interactions (PPI) play a key role in an investigation of various biochemical processes, and their identification is thus of great importance. Although computational prediction of which amino acids take part in a PPI has b...
Software Computational Biology Amino Acids Models, Statistical Knowledge Bases Proteins Protein Interaction Mapping Databases, Protein
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Protein structure modeling and refinement by global optimization in CASP12.

Proteins Dec 5, 2017
For protein structure modeling in the CASP12 experiment, we have developed a new protocol based on our previous CASP11 approach. The global optimization method of conformational space annealing (CSA) was applied to 3 stages of modeling: multiple sequ...
Protein Interaction Domains and Motifs Protein Conformation Protein Folding Sequence Analysis, Protein Models, Molecular Humans Molecular Dynamics Simulation Crystallography, X-Ray Machine Learning Algorithms Models, Statistical Computational Biology Proteins Support Vector Machine
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Assessment of the model refinement category in CASP12.

Proteins Nov 29, 2017
We here report on the assessment of the model refinement predictions submitted to the 12th Experiment on the Critical Assessment of Protein Structure Prediction (CASP12). This is the fifth refinement experiment since CASP8 (2008) and, as with the pre...
Algorithms Protein Folding Computational Biology Sequence Analysis, Protein Humans Models, Molecular Proteins Machine Learning Crystallography, X-Ray Protein Conformation
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