Comparison between molecular dynamic based and knowledge based potentials for protein side chains

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
Marcos R Betancourt

Abstract

Parameterizing protein coarse-grained models from atomic-level force fields is a relatively new and promising approach in protein modeling. Here, dihedral angle potentials for the amino acid side chains are derived using molecular dynamic simulations. These are compared to those obtained using the traditional knowledge based approach, where the potentials are obtained from known protein structures. Side chain potentials consist of two- or three-dimensional dihedral angle histograms with a 20 degrees resolution. The simulations for the amino acids are carried out in explicit water using variants of the united atom Gromos force field, in the all-atom OPLS-AA/L force field, and in implicit solvent using variants of the Amber force field. It was found that the knowledge-based and molecular dynamic potentials are significantly correlated, with correlation coefficients in the upper 0.70. Nevertheless, in energy minimization tests performed on a group of proteins keeping the backbones fixed, the knowledge-based potentials generate angles that correspond closer to the angles in native structures (about 20% closer), for either buried and solvent exposed residues. Furthermore, in tests using high-resolution proteins, the prediction accur...Continue Reading

References

Mar 20, 1993·Journal of Molecular Biology·R L Dunbrack, M Karplus
Aug 1, 1997·Protein Science : a Publication of the Protein Society·R L Dunbrack, F E Cohen
Aug 22, 2003·Protein Science : a Publication of the Protein Society·Adrian A CanutescuRoland L Dunbrack
Aug 22, 2003·Protein Science : a Publication of the Protein Society·Dmitry N IvankovAlexei V Finkelstein
Apr 2, 2005·Protein Science : a Publication of the Protein Society·Chu WangDavid Baker
Oct 4, 2005·Journal of Computational Chemistry·David A CaseRobert J Woods
Oct 8, 2005·Journal of Computational Chemistry·David Van Der SpoelHerman J C Berendsen
Feb 14, 2006·Structure·Ian W DavisJane S Richardson
Jul 21, 2006·Artificial Intelligence in Medicine·Roberto SantanaJose A Lozano
Mar 27, 2007·Current Opinion in Structural Biology·Gary S AytonGregory A Voth
Apr 3, 2007·Biophysical Journal·Jian ZhouGregory A Voth
Jul 10, 2007·The Journal of Physical Chemistry. B·Nathalie BasdevantTap Ha-Duong
Aug 19, 2008·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Chen YanoverYair Weiss
Aug 30, 2008·Current Opinion in Structural Biology·Paul SherwoodMark S P Sansom
May 27, 2009·The Journal of Chemical Physics·Marcos R Betancourt, Sheyore J Omovie
Oct 13, 2009·The Journal of Physical Chemistry. B·Marcos R Betancourt

❮ Previous
Next ❯

Citations

Jan 12, 2011·The Journal of Chemical Physics·Marcos R Betancourt
Sep 29, 2011·Biophysical Journal·Tsuyoshi Terakawa, Shoji Takada
Feb 7, 2016·Biopolymers·Marcos R Betancourt

❮ Previous
Next ❯

Methods Mentioned

BETA
x-ray
nuclear magnetic resonance

Software Mentioned

Gromacs
Amber
DeclareMathSizes
AA
Gromos
OPLS

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.

Related Papers

PLoS Computational Biology
Ronald D HillsGregory A Voth
Proceedings of the National Academy of Sciences of the United States of America
Emmanuel TrizacP G Wolynes
© 2021 Meta ULC. All rights reserved