Title

Never born proteins as a test case for ab initio protein structures prediction

Authors

 Giovanni Minervini¹, Giuseppe Evangelista¹ , Fabricio Polticelli¹, Monika Piwowar²,  Marek Kochanczyk^{2, 3}, Lukasz Flis³, Maciej Malawski⁴, Tomasz Szepieniec⁵, Zdzisław Wiśniowski², Ewa Matczyńska^{2, 6} , Katarzyna Prymula^{2, 7}, Irena Roterman^2, *

Affiliation

¹Department of Biology, University Roma Tre, Viale G. Marconi 446, 00146 Rome, Italy; ²Department of Bioinformatics and Telemedicine, Collegium Medicum - Jagiellonian University, Lazarza 16, 31-530 Krakow, Poland; ³Faculty of Physics, Astronomy and Applied Informatics, Reymonta 4, 30-059 Krakow, Poland; ⁴Institute of Computer Science AGH, Mickiewicza 30, 30-059 Krakow, Poland; ⁵cademic Computer Center CYFRONET, Nawojki 11, 30-950 Krakow, Poland;⁶Faculty of Mathematics and Informatics, Jagiellonian University, Lojasiewicza 6, 30-348 Krakow, Poland; ⁷ Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland;

Email

 myroterm@cyf-kr.edu.pl; * Corresponding author

Article Type

Hypothesis

Date

received Novemeber 20, 2008; accepted November 23, 2008; published December 06, 2008

Abstract

The number of natural proteins although large is significantly smaller than the theoretical number of proteins that can be obtained combining the 20 natural amino acids, the so-called "never born proteins" (NBPs). The study of the structure and properties of these proteins allows to investigate the sources of the natural proteins being of unique characteristics or special properties. However the structural study of NPBs can also been intended as an ideal test for evaluating the efficiency of software packages for the ab initio protein structure prediction. In this research, 10.000 three-dimensional structures of proteins of completely random sequence generated according to ROSETTA and FOD model were compared. The results show the limits of these software packages, but at the same time indicate that in many cases there is a significant agreement between the prediction obtained.

Keywords

 ab initio; never born proteins; structure prediction; software; grid

Citation

 Minervini et al., Bioinformation 3(4): 177-179 (2008)

Edited by

P. Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.