MOTIVATION: The identification of protein-protein interaction (PPI) sites is an important step towards the characterization of protein functional integration in the cell complexity. Experimental methods are costly and time-consuming and computational...
SUMMARY: Protein quality assessment is a long-standing problem in bioinformatics. For more than a decade we have developed state-of-art predictors by carefully selecting and optimising inputs to a machine learning method. The correlation has increase...
MOTIVATION: Loops are often vital for protein function, however, their irregular structures make them difficult to model accurately. Current loop modelling algorithms can mostly be divided into two categories: knowledge-based, where databases of frag...
Conformationally heterogenous or "fuzzy" proteins have often been described as lacking specificity in binding and in function. The activation domains, for example, of transcriptional activators were labeled as negative noodles, with little structure ...
MOTIVATION: Capturing long-range interactions between structural but not sequence neighbors of proteins is a long-standing challenging problem in bioinformatics. Recently, long short-term memory (LSTM) networks have significantly improved the accurac...
MOTIVATION: Protein model quality assessment (QA) plays a very important role in protein structure prediction. It can be divided into two groups of methods: single model and consensus QA method. The consensus QA methods may fail when there is a large...
International journal of bioinformatics research and applications
Jan 1, 2015
Structure prediction of proteins is considered a limiting step and determining factor in drug development and in the introduction of new therapies. Since the 3D structures of proteins determine their functionalities, prediction of dihedral angles rem...
Medicinal chemistry (Shariqah (United Arab Emirates))
Jan 1, 2015
A protein contact map is a simplified, two-dimensional version of the three-dimensional protein structure. Protein contact map is proved to be crucial in forming the three-dimensional structure. Contact map prediction has now become an indispensable ...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2015
Advancement of science and technology has prompted researchers to develop new intelligent systems that can solve a variety of problems such as pattern recognition, prediction, and optimization. The ability of the human brain to learn in a fashion tha...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2015
We present a GEneral Neural Network (GENN) for learning trends from existing data and making predictions of unknown information. The main novelty of GENN is in its generality, simplicity of use, and its specific handling of windowed input/output. Its...