AIMC Topic: Computational Biology

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Structure-based prediction of protein- peptide binding regions using Random Forest.

Bioinformatics (Oxford, England) Feb 1, 2018
MOTIVATION: Protein-peptide interactions are one of the most important biological interactions and play crucial role in many diseases including cancer. Therefore, knowledge of these interactions provides invaluable insights into all cellular processe...
Humans Machine Learning Peptides Protein Domains Sequence Analysis, Protein Protein Tyrosine Phosphatase, Non-Receptor Type 4 Computational Biology Proteins Protein Binding
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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, ...
Sequence Alignment Databases, Protein Protein Interaction Maps Enzymes Humans Phosphorylation Knowledge Bases Animals Computational Biology Data Mining Internet Protein Processing, Post-Translational
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A Network Integration Method for Deciphering the Types of Metabolic Pathway of Chemicals with Heterogeneous Information.

Combinatorial chemistry & high throughput screening Jan 1, 2018
AIM AND OBJECTIVE: A metabolic pathway is an important type of biological pathway, which is composed of a series of chemical reactions. It provides essential molecules and energies for living organisms. To date, several metabolic pathways have been u...
Models, Molecular Support Vector Machine Organic Chemicals Structure-Activity Relationship Molecular Structure Computational Biology Metabolic Networks and Pathways
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Deep Forest-based Prediction of Protein Subcellular Localization.

Current gene therapy Jan 1, 2018
MOTIVATION: Knowledge of the correct protein subcellular localization is necessary for understanding the function of a protein and revealing the mechanism of many human diseases due to protein subcellular mislocalization, which is required before app...
Computational Biology Proteins Protein Transport Neural Networks, Computer Reproducibility of Results Genetic Therapy Algorithms Deep Learning Intracellular Space Humans
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Computing and Visualizing Gene Function Similarity and Coherence with NaviGO.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2018
Gene ontology (GO) is a controlled vocabulary of gene functions across all species, which is widely used for functional analyses of individual genes and large-scale proteomic studies. NaviGO is a webserver for visualizing and quantifying the relation...
Software Gene Ontology Computational Biology Proteins
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Structural Risk Evaluation of a Deep Neural Network and a Markov Model in Extracting Medical Information from Phonocardiography.

Studies in health technology and informatics Jan 1, 2018
This paper presents a method for exploring structural risk of any artificial intelligence-based method in bioinformatics, the A-Test method. This method provides a way to not only quantitate the structural risk associated with a classification method...
Risk Assessment Neural Networks, Computer Humans Computational Biology Phonocardiography Heart Sounds Artificial Intelligence Algorithms
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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.
Machine Learning Databases, Protein Amino Acid Sequence Computational Biology Nitrates Protein Processing, Post-Translational Tyrosine
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YummyData: providing high-quality open life science data.

Database : the journal of biological databases and curation Jan 1, 2018
Many life science datasets are now available via Linked Data technologies, meaning that they are represented in a common format (the Resource Description Framework), and are accessible via standard APIs (SPARQL endpoints). While this is an important ...
Databases, Factual Computational Biology Biological Ontologies Data Curation Metadata
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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 ...
Drug Interactions Supervised Machine Learning Molecular Targeted Therapy Amino Acid Sequence Drug Discovery Computational Biology Drug Repositioning Humans Drug Delivery Systems
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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...
Computational Biology Databases, Protein DNA Molecular Docking Simulation Protein Binding Protein Conformation Binding Sites Sequence Analysis, Protein DNA-Binding Proteins Amino Acid Sequence Machine Learning
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