title: Contingency Table Browser - prediction of early stage protein structure.
abstract: 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 indepth 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.
authors.affiliation: Department of Bioinformatics and Telemedicine, Collegium Medium, Jagiellonian University, Lazarza 16, 31-530 Krakow, Poland ; Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, 30-348, Łojasiewicza 11, Krakow, Poland.
authors.forename: Barbara
authors.initials: B
authors.lastname: Kalinowska
authors.affiliation: Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, 30-348, Łojasiewicza 11, Krakow, Poland.
authors.forename: Artur
authors.initials: A
authors.lastname: Krzykalski
authors.affiliation: Department of Bioinformatics and Telemedicine, Collegium Medium, Jagiellonian University, Lazarza 16, 31-530 Krakow, Poland.
authors.forename: Irena
authors.initials: I
authors.lastname: Roterman