This article describes the development and implementation of algorithms
to study diffusion in biomolecular systems using continuum mechanics
equations. Specifically, finite element methods have been developed
to solve the steady-state Smoluchowski equation to calculate ligand
binding rate constants for large biomolecules. The resulting software
has been validated and applied to mouse acetylcholinesterase. Rates
for inhibitor binding to mAChE were calculated at various ionic strengths
with several different reaction criteria. The calculated rates were
compared with experimental data and show very good agreement when
the correct reaction criterion is used. Additionally, these finite
element methods require significantly less computational resources
than existing particle-based Brownian dynamics methods.
%0 Journal Article
%1 Song_2004_2017
%A Song, Yuhua
%A Zhang, Yongjie
%A Shen, Tongye
%A Bajaj, Chandrajit L
%A McCammon, J. Andrew
%A Baker, Nathan A
%D 2004
%J Biophys. J.
%K 15041644 Acetylcholinesterase, Algorithms, Animals, Computer Gov't, Mice, Models, Molecular, Non-P.H.S., Non-U.S. P.H.S., Research Simulation, Software, Support, U.S.
%N 4
%P 2017--2029
%T Finite element solution of the steady-state Smoluchowski equation
for rate constant calculations.
%U http://www.biophysj.org/cgi/content/full/86/4/2017
%V 86
%X This article describes the development and implementation of algorithms
to study diffusion in biomolecular systems using continuum mechanics
equations. Specifically, finite element methods have been developed
to solve the steady-state Smoluchowski equation to calculate ligand
binding rate constants for large biomolecules. The resulting software
has been validated and applied to mouse acetylcholinesterase. Rates
for inhibitor binding to mAChE were calculated at various ionic strengths
with several different reaction criteria. The calculated rates were
compared with experimental data and show very good agreement when
the correct reaction criterion is used. Additionally, these finite
element methods require significantly less computational resources
than existing particle-based Brownian dynamics methods.
@article{Song_2004_2017,
abstract = {This article describes the development and implementation of algorithms
to study diffusion in biomolecular systems using continuum mechanics
equations. Specifically, finite element methods have been developed
to solve the steady-state Smoluchowski equation to calculate ligand
binding rate constants for large biomolecules. The resulting software
has been validated and applied to mouse acetylcholinesterase. Rates
for inhibitor binding to mAChE were calculated at various ionic strengths
with several different reaction criteria. The calculated rates were
compared with experimental data and show very good agreement when
the correct reaction criterion is used. Additionally, these finite
element methods require significantly less computational resources
than existing particle-based Brownian dynamics methods.},
added-at = {2009-06-03T11:20:58.000+0200},
author = {Song, Yuhua and Zhang, Yongjie and Shen, Tongye and Bajaj, Chandrajit L and McCammon, J. Andrew and Baker, Nathan A},
biburl = {https://www.bibsonomy.org/bibtex/2ae710fa306d34e8c8bfbc877598763ce/hake},
description = {The whole bibliography file I use.},
file = {Song_2004_2017.pdf:Song_2004_2017.pdf:PDF},
interhash = {5ec4c0b6d07bd315e539a4840ca7233c},
intrahash = {ae710fa306d34e8c8bfbc877598763ce},
journal = {Biophys. J.},
keywords = {15041644 Acetylcholinesterase, Algorithms, Animals, Computer Gov't, Mice, Models, Molecular, Non-P.H.S., Non-U.S. P.H.S., Research Simulation, Software, Support, U.S.},
month = Apr,
number = 4,
pages = {2017--2029},
pmid = {15041644},
timestamp = {2009-06-03T11:21:32.000+0200},
title = {Finite element solution of the steady-state Smoluchowski equation
for rate constant calculations.},
url = {http://www.biophysj.org/cgi/content/full/86/4/2017},
volume = 86,
year = 2004
}