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Information 2018, 9(1), 20; https://doi.org/10.3390/info9010020

Usability as the Key Factor to the Design of a Web Server for the CReF Protein Structure Predictor: The wCReF

Graduate Program in Computer Science—PPGCC, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Ipiranga Avenue, 6681 Partenon, Porto Alegre 90619-900, Rio Grande do Sul, Brazil
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Received: 20 December 2017 / Revised: 11 January 2018 / Accepted: 13 January 2018 / Published: 17 January 2018
(This article belongs to the Special Issue Information Technology: New Generations (ITNG 2017))
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Abstract

Protein structure prediction servers use various computational methods to predict the three-dimensional structure of proteins from their amino acid sequence. Predicted models are used to infer protein function and guide experimental efforts. This can contribute to solving the problem of predicting tertiary protein structures, one of the main unsolved problems in bioinformatics. 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. This article is an extended version of the article wCReF: The Web Server for the Central Residue Fragment-based Method (CReF) Protein Structure Predictor, published in the 14th International Conference on Information Technology: New Generations. In the first version, we presented the wCReF, a protein structure prediction server for the central residue fragment-based method. The wCReF interface was developed with a focus on usability and user interaction. With this tool, users can enter the amino acid sequence of their target protein and obtain its approximate 3D structure without the need to install all the multitude of necessary tools. In this extended version, we present the design process of the prediction server in detail, which includes: (A) identification of user needs: aiming at understanding the features of a protein structure prediction server, the end user profiles and the commonly-performed tasks; (B) server usability inspection: in order to define wCReF’s requirements and features, we have used heuristic evaluation guided by experts in both the human-computer interaction and bioinformatics domain areas, applied to the protein structure prediction servers I-TASSER, QUARK and Robetta; as a result, changes were found in all heuristics resulting in 89 usability problems; (C) software requirements document and prototype: assessment results guiding the key features that wCReF must have compiled in a software requirements document; from this step, prototyping was carried out; (D) wCReF usability analysis: a glimpse at the detection of new usability problems with end users by adapting the Ssemugabi satisfaction questionnaire; users’ evaluation had 80% positive feedback; (E) finally, some specific guidelines for interface design are presented, which may contribute to the design of interactive computational resources for the field of bioinformatics. In addition to the results of the original article, we present the methodology used in wCReF’s design and evaluation process (sample, procedures, evaluation tools) and the results obtained. View Full-Text
Keywords: bioinformatics; prediction servers of tertiary structures of proteins; usability; web interface; heuristic evaluation; human-computer interaction bioinformatics; prediction servers of tertiary structures of proteins; usability; web interface; heuristic evaluation; human-computer interaction
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).
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Machado Paixão-Cortes, V.S.; dos Santos da Silva Tanus, M.; Paixão-Cortes, W.R.; de Souza, O.N.; de Borba Campos, M.; Silveira, M.S. Usability as the Key Factor to the Design of a Web Server for the CReF Protein Structure Predictor: The wCReF. Information 2018, 9, 20.

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