A genetic algorithm encoded with the structural information of amino acids and dipeptides for efficient conformational searches of oligopeptides

Journal of Computational Chemistry
Xiao RuZijing Lin

Abstract

The genetic algorithm (GA) is an intelligent approach for finding minima in a highly dimensional parametric space. However, the success of GA searches for low energy conformations of biomolecules is rather limited so far. Herein an improved GA scheme is proposed for the conformational search of oligopeptides. A systematic analysis of the backbone dihedral angles of conformations of amino acids (AAs) and dipeptides is performed. The structural information is used to design a new encoding scheme to improve the efficiency of GA search. Local geometry optimizations based on the energy calculations by the density functional theory are employed to safeguard the quality and reliability of the GA structures. The GA scheme is applied to the conformational searches of Lys, Arg, Met-Gly, Lys-Gly, and Phe-Gly-Gly representative of AAs, dipeptides, and tripeptides with complicated side chains. Comparison with the best literature results shows that the new GA method is both highly efficient and reliable by providing the most complete set of the low energy conformations. Moreover, the computational cost of the GA method increases only moderately with the complexity of the molecule. The GA scheme is valuable for the study of the conformations ...Continue Reading

References

Jun 2, 1995·Journal of Molecular Biology·B H Park, M Levitt
Apr 1, 1996·Current Opinion in Structural Biology·J T Pedersen, J Moult
Sep 15, 1988·Physical Review A: General Physics·A D Becke
Sep 5, 2003·Journal of Molecular Modeling·Paul WingetTimothy Clark
Sep 1, 2005·Journal of Molecular Modeling·Paul Winget, Timothy Clark
Jun 2, 2006·The Journal of Physical Chemistry. a·Julie A Anderson, Gregory S Tschumper
Sep 7, 2006·Journal of Computational Chemistry·Stefan Grimme
Nov 3, 2006·The Journal of Physical Chemistry. a·Sanliang LingMaciej Gutowski
Jan 25, 2008·Proteins·Bin XueYaoqi Zhou
Sep 23, 2009·The Journal of Physical Chemistry. a·Svetlana Stepanenko, Bernd Engels
Dec 15, 2010·Proceedings of the National Academy of Sciences of the United States of America·Lauren L Porter, George D Rose
Jan 6, 2011·Proceedings of the National Academy of Sciences of the United States of America·Joze GrdadolnikFranc Avbelj
Mar 23, 2011·Theoretical Chemistry Accounts·Yaoqi ZhouHongxing Lei
Aug 1, 2013·Proteins·Timothy NugentDavid T Jones
Jan 11, 2014·The Journal of Physical Chemistry. a·Mariana RossiVolker Blum
Aug 29, 2014·PloS One·Harinder SinghGajendra P S Raghava

❮ Previous
Next ❯

Citations


❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.