eprintid: 29498
rev_number: 26
userid: 5901
dir: disk0/00/02/94/98
datestamp: 2016-09-19 15:52:43
lastmod: 2021-04-11 02:55:26
status_changed: 2016-09-19 15:52:43
type: article
metadata_visibility: show
eprint_status: archive
creators_name: Luciani, T
creators_name: Wenskovitch, J
creators_name: Chen, K
creators_name: Koes, D
creators_name: Travers, T
creators_name: Elisabeta Marai, G
creators_email: 
creators_email: 
creators_email: 
creators_email: dkoes@pitt.edu
creators_email: tst7@pitt.edu
creators_email: 
creators_id: 
creators_id: 
creators_id: 
creators_id: DKOES
creators_id: TST7
creators_id: 
creators_orcid: 
creators_orcid: 
creators_orcid: 
creators_orcid: 0000-0002-6892-6614
creators_orcid: 
creators_orcid: 
title: FixingTIM: Interactive exploration of sequence and structural data to identify functional mutations in protein families
ispublished: pub
divisions: sch_as_compsci
divisions: sch_is_informationscience
divisions: sch_med_Computational_Systems_Biology
full_text_status: public
abstract: 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.
date: 2014-08-28
date_type: published
publication: BMC Proceedings
volume: 8
refereed: TRUE
id_number: 10.1186/1753-6561-8-S2-S3
citation:   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.       
document_url: http://d-scholarship-dev.library.pitt.edu/29498/1/art%253A10.1186%252F1753-6561-8-S2-S3.pdf
document_url: http://d-scholarship-dev.library.pitt.edu/29498/7/licence.txt