SPI - structure predictability index for protein sequences

TitleSPI - structure predictability index for protein sequences
Publication TypeJournal Article
Year of Publication2005
AuthorsBrylinski M, Konieczny L, Roterman I
JournalIn Silico Biol
Volume5
Issue3
Pagination227-37
Date Published2005
ISSN1386-6338
KeywordsAmino Acid Sequence, Molecular Sequence Data, Protein Conformation, Protein Folding, Proteins
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.

Alternate JournalIn Silico Biology (Gedrukt)
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