Affiliations: Department of Bioinformatics and Telemedicine,
Collegium Medicum – Jagiellonian University, Kopernika 17, 31-501 Cracow,
Poland. Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060
Cracow, Poland. E-mail: [email protected] | Institute of Biochemistry, Collegium Medicum –
Jagiellonian University, Kopernika 7, 31-034 Cracow, Poland. E-mail:
[email protected] | Department of Bioinformatics and Telemedicine,
Collegium Medicum – Jagiellonian University Kopernika 17, 31-501 Cracow,
Poland. E-mail: [email protected]
Note: [] Corresponding author
Abstract: Estimation of structure predictability for a particular protein is
difficult. Many methods estimate it in an a posteriori system evaluating the
final, native protein structure. The SPI scale is intended to estimate the
structure predictability of a {particular} amino acid sequence in an a priori
system. A sequence-to-structure library was created based on the complete
Protein Data Bank. The tetrapeptide was selected as a unit representing a
well-defined structural motif. The early-stage folding structure (a model of
which was presented elsewhere) was taken as the object for protein structure
classification. Seven structural forms were distinguished for structure
classification. The degree of determinability was estimated for the
sequence-to-structure and structure-to-sequence relations particularly
interesting for threading methods. A comparative analysis of the SPI and Q7
scales with the commonly used SOV and Q3 scales is presented. The complete
contingency table, supplementary materials and all the programs used are
available on request.
Keywords: protein structure prediction, predictability scale, early-stage of folding
