AIMC Topic: Amino Acid Sequence

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Accurate prediction of protein contact maps by coupling residual two-dimensional bidirectional long short-term memory with convolutional neural networks.

Bioinformatics (Oxford, England) Dec 1, 2018
MOTIVATION: Accurate prediction of a protein contact map depends greatly on capturing as much contextual information as possible from surrounding residues for a target residue pair. Recently, ultra-deep residual convolutional networks were found to b...
Proteins Amino Acid Sequence Protein Interaction Mapping Neural Networks, Computer Computational Biology
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High precision in protein contact prediction using fully convolutional neural networks and minimal sequence features.

Bioinformatics (Oxford, England) Oct 1, 2018
MOTIVATION: In addition to substitution frequency data from protein sequence alignments, many state-of-the-art methods for contact prediction rely on additional sources of information, or features, of protein sequences in order to predict residue-res...
Proteins Amino Acid Sequence Sequence Alignment Neural Networks, Computer Algorithms Protein Interaction Domains and Motifs Computational Biology
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Learned protein embeddings for machine learning.

Bioinformatics (Oxford, England) Aug 1, 2018
MOTIVATION: Machine-learning models trained on protein sequences and their measured functions can infer biological properties of unseen sequences without requiring an understanding of the underlying physical or biological mechanisms. Such models enab...
Machine Learning Software Bacteria Humans Amino Acid Sequence Eukaryota Sequence Analysis, Protein Computational Biology Proteins Models, Biological
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DeepSol: a deep learning framework for sequence-based protein solubility prediction.

Bioinformatics (Oxford, England) Aug 1, 2018
MOTIVATION: Protein solubility plays a vital role in pharmaceutical research and production yield. For a given protein, the extent of its solubility can represent the quality of its function, and is ultimately defined by its sequence. Thus, it is imp...
Computer Simulation Deep Learning Computational Biology Proteins Amino Acid Sequence Solubility
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ComplexContact: a web server for inter-protein contact prediction using deep learning.

Nucleic acids research Jul 2, 2018
ComplexContact (http://raptorx2.uchicago.edu/ComplexContact/) is a web server for sequence-based interfacial residue-residue contact prediction of a putative protein complex. Interfacial residue-residue contacts are critical for understanding how pro...
Protein Structure, Secondary Sequence Alignment Sequence Homology, Amino Acid Proteins Internet Amino Acid Sequence Protein Interaction Domains and Motifs Structural Homology, Protein Humans Software Databases, Factual Deep Learning Computational Biology Escherichia coli
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Complex Network Study of the Immune Epitope Database for Parasitic Organisms.

Current topics in medicinal chemistry Feb 9, 2018
BACKGROUND: Complex network approach allows the representation and analysis of complex systems of interacting agents in an ordered and effective manner, thus increasing the probability of discovering significant properties of them. In the present stu...
Amino Acid Sequence Data Mining Parasites Databases, Factual Animals Epitopes 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.
Amino Acid Sequence Nitrates Tyrosine Computational Biology Protein Processing, Post-Translational Machine Learning Databases, Protein
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Prediction of Human Drug Targets and Their Interactions Using Machine Learning Methods: Current and Future Perspectives.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2018
Identification of drug targets and drug target interactions are important steps in the drug-discovery pipeline. Successful computational prediction methods can reduce the cost and time demanded by the experimental methods. Knowledge of putative drug ...
Computational Biology Drug Repositioning Drug Interactions Supervised Machine Learning Humans Amino Acid Sequence Drug Delivery Systems Molecular Targeted Therapy Drug Discovery
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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...
DNA-Binding Proteins Amino Acid Sequence Protein Conformation Binding Sites Computational Biology Machine Learning Sequence Analysis, Protein Databases, Protein Molecular Docking Simulation DNA Protein Binding
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NNAlign: a platform to construct and evaluate artificial neural network models of receptor-ligand interactions.

Nucleic acids research Jul 3, 2017
Peptides are extensively used to characterize functional or (linear) structural aspects of receptor-ligand interactions in biological systems, e.g. SH2, SH3, PDZ peptide-recognition domains, the MHC membrane receptors and enzymes such as kinases and ...
Sequence Alignment Databases, Protein HLA-A1 Antigen Basic Helix-Loop-Helix Leucine Zipper Transcription Factors Algorithms HLA-B8 Antigen HLA-B7 Antigen Cell Cycle Proteins Forkhead Transcription Factors Internet Peptides Humans HLA-DRB1 Chains Binding Sites Amino Acid Sequence Protein Binding Neural Networks, Computer Trans-Activators Ligands Software
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