AIMC Topic: Protein Structure, Secondary

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An introduction to deep learning on biological sequence data: examples and solutions.

Bioinformatics (Oxford, England)
MOTIVATION: Deep neural network architectures such as convolutional and long short-term memory networks have become increasingly popular as machine learning tools during the recent years. The availability of greater computational resources, more data...

Capturing non-local interactions by long short-term memory bidirectional recurrent neural networks for improving prediction of protein secondary structure, backbone angles, contact numbers and solvent accessibility.

Bioinformatics (Oxford, England)
MOTIVATION: The accuracy of predicting protein local and global structural properties such as secondary structure and solvent accessible surface area has been stagnant for many years because of the challenge of accounting for non-local interactions b...

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 ...

VH-VL orientation prediction for antibody humanization candidate selection: A case study.

mAbs
Antibody humanization describes the procedure of grafting a non-human antibody's complementarity-determining regions, i.e., the variable loop regions that mediate specific interactions with the antigen, onto a β-sheet framework that is representative...

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...

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...