wCReF – A Web Server for the CReF Protein Structure Predictor

Machado, Vanessa Stangherlin; Tanus, Michele dos Santos da Silva; Paixão-Cortes, Walter Ritzel; Souza, Osmar Norberto de; Campos, Márcia de Borba; Silveira, Milene Selbach

doi:10.1007/978-3-319-54978-1_103

Cited by 1 publication

(2 citation statements)

References 19 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This article is an extended version of the article titled wCReF-The Web Server for the CReF Protein Structure Predictor, accepted at the Information Technology Conference-New Generations-ITNG 2017 [26], where we describe the creation process behind wCReF and discuss usability issues considered in its design and identified during the assessment with Human-Computer Interaction (HCI) and bioinformatics experts and end users. This release also describes the wCReF design process in detail:…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

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

et al. 2018

View full text Add to dashboard Cite

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.

show abstract

Section: Introductionmentioning

confidence: 99%

“…In order to automate the method, facilitate its use and make it available to users, a web server for predicting protein structures has been developed: wCReF [26].…”

Section: Introductionmentioning

confidence: 99%