Naslov
Reduced representation of protein structure: implications on efficiency and scope of detection of structural similarity

Autori
Zhang, Zong ; Lee, Hwee ; Mihalek, Ivana

Izvornik
BMC Bioinformatics (1471-2105) 11 (2010), 1; 20338066, 12

Vrsta, podvrsta i kategorija rada
Radovi u časopisima, članak, znanstveni

Ključne riječi
reduced representation of protein structure ; database search

Sažetak
Background: Computational comparison of two protein structures is the starting point of many methods that build on existing knowledge, such as structure modeling (including modeling of protein complexes and conformational changes), molecular replacement, or annotation by structural similarity. In a commonly used strategy, significant effort is invested in matching two sets of atoms. In a complementary approach, a global descriptor is assigned to the overall structure, thus losing track of the substructures within. Results: Using a small set of geometric features, we define a reduced representation of protein structure, together with an optimizing function for matching two representations, to provide a pre-filtering stage in a database search. We show that, in a straightforward implementation, the representation performs well in terms of resolution in the space of protein structures, and its ability to make new predictions. Conclusions: Perhaps unexpectedly, a substantial discriminating power already exists at the level of main features of protein structure, such as directions of secondary structural elements, possibly constrained by their sequential order. This can be used toward efficient comparison of protein (sub)structures, allowing for various degrees of conformational flexibility within the compared pair, which in turn can be used for modeling by homology of protein structure and dynamics.

Izvorni jezik
Engleski

Znanstvena područja
Biologija, Računarstvo, Interdisciplinarne biotehničke znanosti, Integrativna bioetika (prirodne, tehničke, biomedicina i zdravstvo, biotehničke, društvene, humanističke znanosti), Biotehnologija u biomedicini (prirodno područje, biomedicina i zdravstvo, biotehničko područje)

POVEZANOST RADA