©1996-2009 All Rights Reserved. Online
Journal of Bioinformatics . You may not store these pages in any form
except for your own personal use. All other usage or distribution is illegal
under international copyright treaties. Permission to use any of these pages in
any other way besides the before mentioned must
be gained in writing from the publisher. This article is exclusively
copyrighted in its entirety to OJB publications. This article may be copied
once but may not be, reproduced or re-transmitted
without the express permission of the editors. This journal satisfies the
refereeing requirements (DEST) for the Higher Education Research Data
Collection (Australia). Linking:To
link to this page or any pages linking to this page you must link directly to
this page only here rather than put up your own page.
OJB®
Online
Journal of Bioinformatics ©
Volume 8 (1):45-55, 2007.
Analysis of MMFF94x and AMBER99 force fields
using aspartic, serine metallo-proteases
and sugar-binding protein data sets.
Singh H,
Marla SS, Verma D
Biotechnology and Bioinformatics
Department,
ABSTRACT
Singh H,
Marla SS, Verma D, Analysis of MMFF94x and AMBER99
force fields using aspartic, serine, metallo-proteases
and sugar-binding protein data sets, Onl J Bioinform., 8 (1) 45-55, 2007. Force fields
vary in that they are developed to be applied to different aspects of
bio-organic chemistry. They are all developed differently and with specific
sets of data. It has been found that although there are significant differences
in modern day force fields, they all perform at the same magnitude of
precision. Although there are differences but each one has its own strength due
to the intended application during development and the data sets used to derive
and parameterize them. In this work MMFF94x &
AMBER99 force fields were applied for energy minimization on proteins belonging
to different classes e.g. Aspartic Proteases, Serine Proteases, Metallo-proteases, Sugar-binding proteins. Since both the
force fields are successful in their respective terms, a question remains
unanswered; Out of the two, MMFF94 & AMBER, which force field should we use
for energy minimization of proteins? In this study we have tried to evaluate
this question by dividing the proteins in their respective classes, finding
their initial and final energies and finally applying statistical techniques
(paired test). This was done by using MOE (Molecular Operating Environment)
software Package from Chemical Computing Group. It was observed that the
selection of force field should be on the basis of class of protein to which
that protein belongs.
Keywords- Forcefields,
AMBER99, MMF94X.
FULL-TEXT (SUBSCRIPTION OR PURCHASE TITLE $25USD)