A short survey on protein blocks

0352274 - BTÚ 2011 RIV DE eng J - Článek v odborném periodiku
Joseph, A.P. - Agarwal, G. - Mahajan, S. - Gelly, J.Ch. - Swapna, L.S. - Offmann, B. - Cadet, F. - Bornot, A. - Tyagi, M. - Valadié, H. - Schneider, Bohdan - Etchebest, C. - Srinivasan, N. - de Brevern, A.G.
A short survey on protein blocks.
Biophysical reviews. Roč. 2, č. 3 (2010), s. 137-147. ISSN 1867-2450
Výzkumný záměr: CEZ:AV0Z50520701
Klíčová slova: Protein * bioinformatics * structure
Kód oboru RIV: BO - Biofyzika

Protein structures are classically described in terms of secondary structures. The regular secondary structures have relevant physical meaning but their recognition based on atomic coordinates has a number of limitations, such as uncertainties in the assignment of the boundaries of the helical and strand regions. Moreover, an average of about 50% of all residues are assigned to an irregular state, i.e., the coil. These limitations have led different research teams to focus on abstracting the conformation of the protein backbone in the localized short stretches and different geometric measures are being used to cluster local stretches in protein structures. These libraries of local structure prototypes are named structural alphabets. We have developed a structural alphabet, denoted protein blocks, not only to approximate the protein structures but also to predict them from the sequence. Here, we review some of the most interesting applications of this structural alphabet.
Trvalý link: http://hdl.handle.net/11104/0191815