Pregled bibliografske jedinice broj: 1111506
Reduced representation of protein structure for fast comparison and database search
Reduced representation of protein structure for fast comparison and database search // Bioinformatics Institute Singapore Annual Meeting
Singapur, 2008. 155, 12 (predavanje, međunarodna recenzija, sažetak, znanstveni)
CROSBI ID: 1111506 Za ispravke kontaktirajte CROSBI podršku putem web obrasca
Naslov
Reduced representation of protein structure for fast comparison and database search
Autori
Zhang, Zong Hong ; Lee, Hwee Kuan ; Mihalek, Ivana
Vrsta, podvrsta i kategorija rada
Sažeci sa skupova, sažetak, znanstveni
Skup
Bioinformatics Institute Singapore Annual Meeting
Mjesto i datum
Singapur, 07.11.2008. - 08.11.2008
Vrsta sudjelovanja
Predavanje
Vrsta recenzije
Međunarodna recenzija
Ključne riječi
protein structure ; databse 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, Biotehnologija, Biotehnologija u biomedicini (prirodno područje, biomedicina i zdravstvo, biotehničko područje)
