Banca de QUALIFICAÇÃO: LAURA SHIMOHARA BRADASCHIA

Uma banca de QUALIFICAÇÃO de MESTRADO foi cadastrada pelo programa.
STUDENT : LAURA SHIMOHARA BRADASCHIA
DATE: 16/02/2026
TIME: 08:30
LOCAL: Google Meet
TITLE:

Graph Theory and its Applications in the Analysis and Visualization of Protein Conformational Ensembles

KEY WORDS:

protein-folding; conformational ensembles; graph theory; residue Interactive network (RIN); molecular dynamics (MD); Bioinformatics Webtools

PAGES: 32
BIG AREA: Ciências Biológicas
AREA: Biologia Geral
SUMMARY:

The intricate relationship of protein structure and its folding dynamics remains elusive, despite the optimal growth structural biology has experienced over the past years. This is due to the growing understanding of the non-static nature of proteins, whose functions often depend on conformational changes and complex interactions occurring over a conformational ensemble. Among the computational approaches seeking to understand these dynamic properties, Residue interaction network (RIN) analysis emerged as a powerful tool. By representing proteins as networks - where residues become nodes, and its chemical and physical interactions with elements of their structures become edges - one can rapidly deduce key residues influencing structure and function using network parameters such as degree, betweenness and clustering coefficient. These analyses provide relevant insights into its dynamics comprehension. However, conventional RIN analysis is usually limited by its reliance on single, static protein structures, failing to capture the inherent flexibility of dynamic transitions proteins undergo through its folding. To address such matters - and explore the applicability graph theory in the protein ensemble analysis - we present SlytheRINs: an interactive webtool built for comparative analysis of protein conformations via RINs. The webtool enables dynamic ensembles analysis through the breakdown of interaction network data from multiple conformations of a single protein, as well as detailed mapping using comparative plots of residue interactions across conformational changes

COMMITTEE MEMBERS:
Interno - ***.610.027-** - DIEGO MARQUES COELHO - UFRN
Presidente - 1513597 - JOAO PAULO MATOS SANTOS LIMA
Interno - 3063244 - TETSU SAKAMOTO