PMID: 15244630Jul 13, 2004Paper

Effect of chain connectivity on the structure of Lennard-Jones liquid and its implicationon statistical potentials for protein folding

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
W C LuK M Ho

Abstract

Statistical contact potentials and bead-spring models have been widely used for computational studies of protein folding. However, there has been speculation that systematic error may arise in the contact energy calculations when the statistical potentials are deduced under the assumption that the chain connectivity in proteins can be ignored. To address this issue, we have performed molecular-dynamics simulations to study the structure and dynamics of a simple liquid system in which the beads are either connected or unconnected with springs. Results from the present study provide useful information for assessing the accuracy of the statistical potentials for protein structure simulations.

References

Feb 27, 1975·Nature·M Levitt, A Warshel
Sep 1, 1994·Protein Science : a Publication of the Protein Society·R S DeWitte, E I Shakhnovich
Apr 1, 1993·Proteins·M Pellegrini, S Doniach
Oct 1, 1995·Protein Science : a Publication of the Protein Society·A GodzikJ Skolnick
Mar 29, 1996·Journal of Molecular Biology·P D Thomas, K A Dill
Oct 15, 1996·Proceedings of the National Academy of Sciences of the United States of America·P D Thomas, K A Dill
Dec 20, 1996·Journal of Molecular Biology·L A Mirny, E I Shakhnovich
Apr 1, 1997·Current Opinion in Structural Biology·A E Torda
Apr 1, 1997·Current Opinion in Structural Biology·S VajdaJ Novotny
Mar 26, 1998·Protein Science : a Publication of the Protein Society·L Zhang, J Skolnick
Oct 14, 1998·Journal of Molecular Biology·L A Mirny, E I Shakhnovich
Jul 21, 2001·Biophysical Journal·J Liang, K A Dill
Oct 26, 2005·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Meng QinWei Wang
Nov 23, 1990·Science·J Skolnick, A Kolinski

❮ 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.

Related Papers

The Journal of Chemical Physics
Takashi Uneyama, Yuichi Masubuchi
Journal of Physics. Condensed Matter : an Institute of Physics Journal
Hamed Maleki, Panagiotis E Theodorakis
Journal of Chemical Theory and Computation
Nicholas LeioattsAlan Grossfield
© 2022 Meta ULC. All rights reserved