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Journal of Biomedicine and Biotechnology
Volume 2005 (2005), Issue 2, Pages 65-79
http://dx.doi.org/10.1155/JBB.2005.65
Research article

Early-Stage Folding in Proteins (In Silico) Sequence-to-Structure Relation

1Department of Bioinformatics and Telemedicine, Medical Faculty, Jagiellonian University, Kopernika 17, Cracow 31-501, Poland
2Faculty of Chemistry, Jagiellonian University, Ingardena 3, Cracow 30-060, Poland
3Institute of Biochemistry, Medical Faculty, Jagiellonian University, Kopernika 7, Cracow 31-501, Poland

Received 16 September 2004; Revised 3 January 2005; Accepted 5 January 2005

Copyright © 2005 This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

A sequence-to-structure library has been created based on the complete PDB database. The tetrapeptide was selected as a unit representing a well-defined structural motif. Seven structural forms were introduced for structure classification. The early-stage folding conformations were used as the objects for structure analysis and classification. The degree of determinability was estimated for the sequence-to-structure and structure-to-sequence relations. Probability calculus and informational entropy were applied for quantitative estimation of the mutual relation between them. The structural motifs representing different forms of loops and bends were found to favor particular sequences in structure-to-sequence analysis.