WONKA is a tool for the systematic analysis of an ensemble of protein-ligand structures. It makes the identification of conserved and unusual features within such an ensemble straightforward. WONKA uses an intuitive workflow to process structural co-ordinates. Ligand and protein features are summarised and then presented within an interactive web application. WONKA's power in consolidating and ...

Molecular recognition is often mediated by flexible loops that have widely fluctuating structures and are sometimes disordered, but that form particular complex structures following ligand binding. In fact, many loop structures found in the PDB database are too flexible to be determined precisely. A new loop modeling method was therefore developed using force-biased multicanonical molecular dyn...

Pattern recognition systems are widely used in a host of different fields. Due to some reasons such as lack of knowledge about a method based on which the best classifier is detected for any arbitrary problem, and thanks to significant improvement in accuracy, researchers turn to ensemble methods in almost every task of pattern recognition. Classification as a major task in pattern recognition,...

Capability of the Proper Orthogonal Decomposition (POD) method in extraction of the coherent structures from a spatio-temporal chaotic field is assessed in this paper. As the chaotic field, an ensemble of 40 snapshots, obtained from Direct Numerical Simulation (DNS) of the Kuramoto-Sivashinsky (KS) equation, has been used. Contrary to the usual methods, where the ergodicity of the field is need...

The long development process of novel pharmaceutical compounds begins with the identification of a lead inhibitor compound. Computational screening to identify those ligands, or small molecules, most likely to inhibit a target protein may benefit the pharmaceutical development process by reducing the time required to identify a lead compound. Typically, computational ligand screening utilizes h...