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Contingency Table Browser prediction of early stage protein structure



Barbara Kalinowska1,2, Artur Krzykalski2, Irena Roterman1*




1Department of Bioinformatics and Telemedicine, Collegium Medium, Jagiellonian University, Lazarza 16, 31-530 Krakow, Poland; 2Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, 30-348, Łojasiewicza 11, Krakow, Poland


Email;   *Corresponding author


Article Type




Received October 02, 2015; Revised October 05, 2015; Accepted October 19, 2015; Published October 31, 2015



The Early Stage (ES) intermediate represents the starting structure in protein folding simulations based on the Fuzzy Oil Drop (FOD) model. The accuracy of FOD predictions is greatly dependent on the accuracy of the chosen intermediate. A suitable intermediate can be constructed using the sequence-structure relationship information contained in the so-called contingency table this table expresses the likelihood of encountering various structural motifs for each tetrapeptide fragment in the amino acid sequence. The limited accuracy with which such structures could previously be predicted provided the motivation for a more in-depth study of the contingency table itself. The Contingency Table Browser is a tool which can visualize, search and analyze the table. Our work presents possible applications of Contingency Table Browser, among them analysis of specific protein sequences from the point of view of their structural ambiguity.



Kalinowska et al. Bioinformation 11(10):486-488 (2015)

Edited by

P Kangueane






Biomedical Informatics



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.