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FixingTIM: Interactive exploration of sequence and structural data to identify functional mutations in protein families

Luciani, T and Wenskovitch, J and Chen, K and Koes, D and Travers, T and Elisabeta Marai, G (2014) FixingTIM: Interactive exploration of sequence and structural data to identify functional mutations in protein families. BMC Proceedings, 8.

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Abstract

© 2014 Luciani et al.; licensee BioMed Central Ltd. Background: Knowledge of the 3D structure and functionality of proteins can lead to insight into the associated cellular processes, speed up the creation of pharmaceutical products, and develop drugs that are more effective in combating disease. Methods: We present the design and implementation of a visual mining and analysis tool to help identify protein mutations across a family of structural models and to help discover the effect of these mutations on protein function. We integrate 3D structure and sequence information in a common visual interface; multiple linked views and a computational backbone allow comparison at the molecular and atomic levels, while a novel trend-image visual abstraction allows for the sorting and mining of large collections of sequences and of their residues. Results: We evaluate our approach on the triosephosphate isomerase (TIM) family structural models and sequence data and show that our tool provides an effective, scalable way to navigate a family of proteins, as well as a means to inspect the structure and sequence of individual proteins. Conclusions: The TIM application shows that our tool can assist in the navigation of families of proteins, as well as in the exploration of individual protein structures. In conjunction with domain expert knowledge, this interactive tool can help provide biophysical insight into why specific mutations affect function and potentially suggest additional modifications to the protein that could be used to rescue functionality.


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Details

Item Type: Article
Status: Published
Creators/Authors:
CreatorsEmailPitt UsernameORCID
Luciani, T
Wenskovitch, J
Chen, K
Koes, Ddkoes@pitt.eduDKOES0000-0002-6892-6614
Travers, Ttst7@pitt.eduTST7
Elisabeta Marai, G
Date: 28 August 2014
Date Type: Publication
Journal or Publication Title: BMC Proceedings
Volume: 8
DOI or Unique Handle: 10.1186/1753-6561-8-s2-s3
Schools and Programs: Dietrich School of Arts and Sciences > Computer Science
School of Information Sciences > Information Science
School of Medicine > Computational and Systems Biology
Refereed: Yes
Date Deposited: 19 Sep 2016 15:52
Last Modified: 02 Feb 2019 14:56
URI: http://d-scholarship.pitt.edu/id/eprint/29498

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