Nucleic Acid Structure Analysis Software Release
babcock at mbcl.rutgers.edu
babcock at mbcl.rutgers.edu
Tue May 31 16:52:53 EST 1994
Please: if you know someone who can use the program, forward a copy of this
message to them.
ANNOUNCING THE RELEASE OF A PROGRAM WHICH ANALYSES NUCLEIC ACID
CRYSTALLOGRAPHIC COORDINATE DATA ACCORDINATE TO THE EMBO GUIDELINES
OF 1988.
Several years ago, the European Molecular Biology Organization
published guidelines defining how nucleic acid duplex structures can
be examined. The guidelines defined three rotational and three translational
parameters between the bases comprising a base pair as well as from one base
pair to the next. There are five programs readily distributed in order to
perform the calculations. We are releasing a sixth which was created to be
able to handle not only the calculations of normal duplexes, but also
comparably examine mispaired bases, hoogstein base pairs, looped out bases,
a single base adjacent to a base pair, intercalated drugs for which a
coordinate frame has been defined, etc.
The nucleic acid structure analysis program is written in Fortran and
runs in a UNIX or VMS environment (please specify preference). The program
calculates all of the rotational and translational parameters for complementary
base pairs, neighboring base pairs in Cartesian and helical coordinate frames,
and base to base Cartesian and helical parameters along each strand. A simple
interactive user interface allows for one to specify what file is examined and
which parameters to calculate. The program was designed so that the user needs
to spend a minimal time reading the documentation in order for the program to
run. Full disclosure of the mathematics has been made and published so that the
user can readily understand what their parameters mean.
The mathematics are unique for this type of calculation and aviod many
of the problems previously encountered. In particular, the calculations are
performed by a single rotation not sequential rotations avoiding the use of a
midway coordinate frame for rotational parameter calculations. This ensures
that the magnitude of the rotational parameters is strand free and direction
free. Because a single rotation is used, the equations for each rotational
parameter are equivalent, therefore, a 5 degree rotation about the X axis is
equivalent to a 5 degree rotation about either the Y or the Z axis. This is not
always true of other mathematical formulations presently being used. The
mathematics used for calculating the complementary base parameters is identical
to the math used to calculate the neighboring base/base pair parameters except
that different axes are involved. This is not generally the case of the other
available programs. In addition, since the calculations are bases upon local
considerations, the value of the parameter depends on only the bases involved
and are independent of adjacent bases. This allows for more accurate comparison
of parameters from one structure to another.
Copies of the code can be acquired by e-mailing me at:
Marla at Rutchm.Rutgers.edu.
Dr. Marla Babcock
Dept of Chemistry
Rutgers University
P.O. Box 939
Piscataway, N.J. U.S.A 08855
Useful References:
A users guide to the programs is provided in the paper:
Babcock, M.S., Pednault, E.P.D, and Olson, W.K., "Nucleic Acid
Structure Analysis: A Users Guide to a Collection of New
Analysis Programs," Journal of Biomolecular Structure and
Dynamics, Vol. 11, No. 3, pp 597-628, 1993.
The issues surrounding the definition of nucleic acid structure
parameters and how we address these issues are discussed in:
Babcock, M.S., and Olson, W.K., "A New Program for the
Analysis of Nucleic Acid Structure Interpretation," in
Computation of Biomolecular Structures: Achievements,
Problems, and Perspectives, Soumpasis, D.M., and Jovin, T.M.,
Eds., Springer-Verlag, Heidelberg, pp 65-85, 1993.
The mathematical definitions of the nucleic acid structure parameters
and the methods used to calculate them are presented in:
Babcock, M.S., Pednault, E.P.D, and Olson, W.K., "Nucleic Acid
Structure Analysis: Mathematics for Local Cartesian and
Helical Structure Parameters That are Truly Comparable Between
Structures," Journal of Molecular Biology, Vol. 237,
pp 125-156, 1994.
In order to take into account base-stacking effects and other physical
constraints, the mathematical definitions we have developed contain
parameters called "pivot points", which are the points about which the
bases in a structure buckle, propeller twist, and open. The
statistical analyses that were performed to determine the optimum
positions of the pivot points are presented in:
Babcock, M.S., and Olson, W.K., "The Effect of Mathematics and
Coordinate System on Comparability and 'Dependencies' of
Nucleic Acid Structure Parameters," Journal of Molecular
Biology, Vol. 237, pp 98-125, 1994.
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