Application of the frozen atom approximation to the GB/SA continuum model for solvation free energy

Journal of Computational Chemistry
Olgun GuvenchW Clark Still

Abstract

The generalized Born/surface area (GB/SA) continuum model for solvation free energy is a fast and accurate alternative to using discrete water molecules in molecular simulations of solvated systems. However, computational studies of large solvated molecular systems such as enzyme-ligand complexes can still be computationally expensive even with continuum solvation methods simply because of the large number of atoms in the solute molecules. Because in such systems often only a relatively small portion of the system such as the ligand binding site is under study, it becomes less attractive to calculate energies and derivatives for all atoms in the system. To curtail computation while still maintaining high energetic accuracy, atoms distant from the site of interest are often frozen; that is, their coordinates are made invariant. Such frozen atoms do not require energetic and derivative updates during the course of a simulation. Herein we describe methodology and results for applying the frozen atom approach to both the generalized Born (GB) and the solvent accessible surface area (SASA) parts of the GB/SA continuum model for solvation free energy. For strictly pairwise energetic terms, such as the Coulombic and van-der-Waals ener...Continue Reading

References

Feb 1, 1992·Protein Science : a Publication of the Protein Society·L Wesson, D Eisenberg
May 1, 1987·Proceedings of the National Academy of Sciences of the United States of America·T OoiH A Scheraga
Feb 14, 1971·Journal of Molecular Biology·B Lee, F M Richards
May 1, 1995·Protein Engineering·N Kurochkina, B Lee
Dec 1, 1996·Journal of Molecular Graphics·R R Gabdoulline, R C Wade
Aug 26, 1998·Folding & Design·A G Street, S L Mayo
Apr 1, 1980·Proceedings of the National Academy of Sciences of the United States of America·S J Wodak, J Janin
Apr 1, 1986·Journal of Computational Chemistry·Scott J WeinerDavid A Case
May 1, 1999·Journal of Computational Chemistry·Jörg WeiserW Clark Still

❮ Previous
Next ❯

Citations

May 13, 2010·Journal of Molecular Modeling·Pradeep Kumar NaikHarvinder Singh
May 24, 2011·The Journal of Chemical Physics·Dong-Xia ZhaoZhong-Zhi Yang
Dec 7, 2010·Annual Review of Physical Chemistry·Ilan SamishJeffery G Saven
Nov 16, 2010·Journal of Molecular Graphics & Modelling·Pradeep Kumar NaikHarvinder Singh
Aug 21, 2007·Biochemical and Biophysical Research Communications·Qi-Shi DuKuo-Chen Chou
Aug 20, 2003·Journal of Computational Chemistry·Richard D TaylorJonathan W Essex
Oct 1, 2019·Nucleosides, Nucleotides & Nucleic Acids·Kazuki YamamotoSatoshi Ichikawa

❮ 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.