AIMC Topic: Proteins

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MDD-SOH: exploiting maximal dependence decomposition to identify S-sulfenylation sites with substrate motifs.

Bioinformatics (Oxford, England) Sep 26, 2015
UNLABELLED: S-sulfenylation (S-sulphenylation, or sulfenic acid), the covalent attachment of S-hydroxyl (-SOH) to cysteine thiol, plays a significant role in redox regulation of protein functions. Although sulfenic acid is transient and labile, most ...
Cysteine Amino Acid Motifs Sequence Analysis, Protein Protein Processing, Post-Translational Proteins Humans Amino Acids Software Support Vector Machine Sulfur Acids
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IAS: Interaction Specific GO Term Associations for Predicting Protein-Protein Interaction Networks.

IEEE/ACM transactions on computational biology and bioinformatics Sep 25, 2015
Proteins carry out their function in a cell through interactions with other proteins. A large scale protein-protein interaction (PPI) network of an organism provides static yet an essential structure of interactions, which is valuable clue for unders...
Humans Systems Biology Proteins Fungi Plants Animals Gene Ontology Protein Interaction Maps Protein Interaction Mapping
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Sparse Markov chain-based semi-supervised multi-instance multi-label method for protein function prediction.

Journal of bioinformatics and computational biology Sep 16, 2015
Automated assignment of protein function has received considerable attention in recent years for genome-wide study. With the rapid accumulation of genome sequencing data produced by high-throughput experimental techniques, the process of manually pre...
Algorithms Animals Genome-Wide Association Study Supervised Machine Learning Markov Chains Computational Biology Proteins Databases, Protein
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Connecting proteins with drug-like compounds: Open source drug discovery workflows with BindingDB and KNIME.

Database : the journal of biological databases and curation Sep 16, 2015
Today's large, public databases of protein-small molecule interaction data are creating important new opportunities for data mining and integration. At the same time, new graphical user interface-based workflow tools offer facile alternatives to cust...
Pharmaceutical Preparations Drug Interactions Knowledge Bases Pharmacokinetics Drug Discovery Protein Binding Proteins Humans Animals
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APL: An angle probability list to improve knowledge-based metaheuristics for the three-dimensional protein structure prediction.

Computational biology and chemistry Sep 5, 2015
Tertiary protein structure prediction is one of the most challenging problems in structural bioinformatics. Despite the advances in algorithm development and computational strategies, predicting the folded structure of a protein only from its amino a...
Protein Conformation Protein Structure, Tertiary Algorithms Computational Biology Proteins Knowledge Bases
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Predicting protein function and other biomedical characteristics with heterogeneous ensembles.

Methods (San Diego, Calif.) Sep 2, 2015
Prediction problems in biomedical sciences, including protein function prediction (PFP), are generally quite difficult. This is due in part to incomplete knowledge of the cellular phenomenon of interest, the appropriateness and data quality of the va...
Forecasting Proteins Databases, Protein Machine Learning Algorithms
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Enhancing protein function prediction with taxonomic constraints--The Argot2.5 web server.

Methods (San Diego, Calif.) Aug 28, 2015
Argot2.5 (Annotation Retrieval of Gene Ontology Terms) is a web server designed to predict protein function. It is an updated version of the previous Argot2 enriched with new features in order to enhance its usability and its overall performance. The...
Internet Gene Ontology Web Browser Proteins Databases, Protein Algorithms Forecasting
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LncRNA-ID: Long non-coding RNA IDentification using balanced random forests.

Bioinformatics (Oxford, England) Aug 26, 2015
MOTIVATION: Long non-coding RNAs (lncRNAs), which are non-coding RNAs of length above 200 nucleotides, play important biological functions such as gene expression regulation. To fully reveal the functions of lncRNAs, a fundamental step is to annotate...
Ribosomes Animals Humans Proteins Mice Machine Learning Open Reading Frames RNA, Long Noncoding Software
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Accurate contact predictions using covariation techniques and machine learning.

Proteins Aug 14, 2015
Here we present the results of residue-residue contact predictions achieved in CASP11 by the CONSIP2 server, which is based around our MetaPSICOV contact prediction method. On a set of 40 target domains with a median family size of around 40 effectiv...
Sequence Alignment Protein Interaction Domains and Motifs Viruses Protein Structure, Secondary Protein Folding Internet Amino Acid Sequence Bacteria Computational Biology Models, Statistical Proteins Databases, Protein Machine Learning Models, Molecular Humans Neural Networks, Computer Software Computer Simulation
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Protein contact prediction by integrating joint evolutionary coupling analysis and supervised learning.

Bioinformatics (Oxford, England) Aug 14, 2015
MOTIVATION: Protein contact prediction is important for protein structure and functional study. Both evolutionary coupling (EC) analysis and supervised machine learning methods have been developed, making use of different information sources. However...
Algorithms Models, Statistical Evolution, Molecular Machine Learning Proteins Sequence Analysis, Protein Software Protein Conformation Sequence Alignment
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