2021-2032 All Rights Reserved. Online Journal of Bioinformatics. You may not store these pages in any form except for your own personal use. All other usage or distribution is illegal under international copyright treaties. Permission to use any of these pages in any other way besides the before mentioned must be gained in writing from the publisher. This article is exclusively copyrighted in its entirety to onlinejournals@gmail.com publications. This article may be copied once but may not be, reproduced or re-transmitted without the express permission of the editors. Linking: To link to this page or any pages linking to this page you must link directly to this page only here rather than put up your own page.


Online Journal of Bioinformatics

Established 1995

ISSN  1443-2250


Volume 22 (3): 199-208, 2021.

Near-native protein folding structure simulation


Stefka Fidanova


IPP - Bulgarian Academy of Science, Acad. G. Bonchev str, Soa, Bulgaria.




Fidanova S., Near-native protein folding structure simulation, Onl J Bioinform., 22 (3): 199-208, 2021. Protein folding is a fundamental problem in computational molecular biology and biochemical physics. Optimization is based on homologous and hydrophobic-polar (HP) protein model. We used structure elements to predict tertiary structure by HP model on a cubic lattice to determine least energy conformation. The main secondary structures are α helix and β sheets with hydrophobic (H) and polar (P) binary chain monomer. To find most non-consecutive H-H contacts we consider only polypeptide chain with hydrophobic monomers so that minimal energy equates to most H-H. Amino acid sequences determines protein folds for a unique 3D structure with >30% similarity of different structure and function. Conversely, proteins with similar functions and structures can have low AA sequence similarity. Even simplified lattice models cannot find correct structure. Author describes 6 models of helices and sheets hydrophobic-polar (HP) lattices for predicting folding in long chain proteins.


Keywords: Protein folding, Hydrophobic, 3D HP model.