©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.
OJBTM
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.
ABSTRACT
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.
FULL TEXT (SUBSCRIBE OR PURCHASE TITLE)