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Online Journal of Bioinformatics ©
Analysis of
MMFF94x and AMBER99 force fields using aspartic, serine
metallo-proteases and sugar-binding protein
data sets.
Singh H1,
Marla SS2, Verma D3
1,2,3
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, Online
J Bioinformatics, 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.