AIMC Topic: Proteins

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Structural classification of protein sequences based on signal processing and support vector machines.

Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference
The function of any protein depends directly on its secondary and tertiary structure. Proteins can fold into a three-dimensional shape, which is primarily depended on the arrangement of amino acids in the primary structure. In recent years, with the ...

Convolutional neural network architectures for predicting DNA-protein binding.

Bioinformatics (Oxford, England)
MOTIVATION: Convolutional neural networks (CNN) have outperformed conventional methods in modeling the sequence specificity of DNA-protein binding. Yet inappropriate CNN architectures can yield poorer performance than simpler models. Thus an in-depth...

What is information?

Philosophical transactions. Series A, Mathematical, physical, and engineering sciences
Molecular biology is based on two great discoveries: the first is that genes carry hereditary information in the form of linear sequences of nucleotides; the second is that in protein synthesis a sequence of nucleotides is translated into a sequence ...

Exploiting ontology graph for predicting sparsely annotated gene function.

Bioinformatics (Oxford, England)
MOTIVATION: Systematically predicting gene (or protein) function based on molecular interaction networks has become an important tool in refining and enhancing the existing annotation catalogs, such as the Gene Ontology (GO) database. However, functi...

Machine learning of single molecule free energy surfaces and the impact of chemistry and environment upon structure and dynamics.

The Journal of chemical physics
The conformational states explored by polymers and proteins can be controlled by environmental conditions (e.g., temperature, pressure, and solvent) and molecular chemistry (e.g., molecular weight and side chain identity). We introduce an approach em...

Assessing protein-protein interactions based on the semantic similarity of interacting proteins.

International journal of data mining and bioinformatics
The Gene Ontology (GO) has been used in estimating the semantic similarity of proteins since it has the largest and reliable vocabulary of gene products and characteristics. We developed a new method which can assess Protein-Protein Interactions (PPI...

Granular support vector machine to identify unknown structural classes of protein.

International journal of data mining and bioinformatics
To date, classification of structural class using local protein structure rather than the whole structure has been gaining widespread attention. It is noted that the structural class lies in local composition or arrangement of secondary structure, wh...

DAPD: A Knowledgebase for Diabetes Associated Proteins.

IEEE/ACM transactions on computational biology and bioinformatics
Recent advancements in genomics and proteomics provide a solid foundation for understanding the pathogenesis of diabetes. Proteomics of diabetes associated pathways help to identify the most potent target for the management of diabetes. The relevant ...

Sequence-based protein superfamily classification using computational intelligence techniques: a review.

International journal of data mining and bioinformatics
Protein superfamily classification deals with the problem of predicting the family membership of newly discovered amino acid sequence. Although many trivial alignment methods are already developed by previous researchers, but the present trend demand...