wCReF – a web server for the cref protein structure predictor

Abstract

The prediction of protein tertiary structure is a problem of Structural Bioinformatics still unsolved by science. The challenge is to understand the relationship between the amino acid sequence of a protein and its three-dimensional structure, which is related to the function of these macromolecules. Among the methods related to protein structure prediction is CReF (Central Residue Fragment-based Method) proposed by Dorn & Norberto Souza. Here we present wCReF, the Web interface for the CReF method developed with a focus on usability. With this tool, users can enter the amino acid sequence of their target protein, and get as a result the approximate 3D structure of a protein without the need to install all the multitude of necessary tools for their use. In order to create an interface that take usability in consideration, we have conducted a study to analyze usability of similar servers (I-TASSER, QUARK and Robetta), guided by experts on both Human-Computer Interaction and Bioinformatics domain areas, using the Nielsens’ Heuristic Evaluation method. Evaluation results have served as guiding orientation to design the key features that wCReF must have and then, develop the first version of the interface. As a final product we present the wCReF protein structure prediction server. Furthermore, this study can contribute to improve the usability of existing bioinformatics applications, the prediction servers analyzed and the development of new scientific tools.