** DGSOL ** is a software package for solving large
distance geometry problems in macromolecular modeling.
** DGSOL ** has been developed for both sequential and
parallel architectures.

Distance geometry problems are interesting mathematical problems with important applications in computational biology, the interpretation of NMR data, and the determination of protein structure. Distance geometry problems are difficult to solve. From a complexity viewpoint, obtaining an approximate solution to a distance geometry is NP-hard. From an optimization viewpoint, distance geometry problems have many local minimizers.

** DGSOL ** solves distance geometry problems with a global
continuation algorithm, with Gaussian smoothing of a merit function
that only depends on the sparse distance data.
Several minimizers are traced in the continuation process,
and the best minimizer is selected as the global minimizer.
In the current release of
**DGSOL**, a variable-metric limited-memory code is used
to trace the minimizers.
More robust algorithms will be added in future releases.

For additional information on the solution of distance geometry problems with global continuation and Gaussian smoothing, see

- Jorge Moré and Zhijun Wu,
**Distance geometry optimization for protein structures,**Journal on Global Optimization, 15 (1999), pp. 219-234. - Jorge Moré and Zhijun Wu,
**Epsilon-optimal solutions to distance geometry problems via global continuation,**in Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding, P. M. Pardalos, D. Shalloway, and G. Xue, eds., pages 151-168, American Mathematical Society, 1996. - Jorge Moré and Zhijun Wu,
**Issues in large-scale global molecular optimization,**in Large Scale Optimization with Applications: Molecular Structure and Optimization, Lorenz T. Biegler, Thomas F. Coleman, Andrew R. Conn and Fadil N. Santosa, eds., IMA Volumes in Applied Mathematics and Applications 94, pages 99-122, Springer-Verlag, 1997. - Jorge Moré and Zhijun Wu,
**Smoothing techniques for macromolecular global optimization,**in Nonlinear Optimization and Applications, G. Di Pillo and F. Giannessi, eds., pages 297-312, Plenum Press, 1996. - Jorge Moré and Zhijun Wu,
**Global continuation for distance geometry problems,**SIAM J. Optim. 7, no. 3 (August 1997), pp. 814-836.

** DGSOL ** is written in C and Fortran.
The parallel version uses the
MPICH message-passing library for communication.

The current release of ** DGSOL ** can be obtained by downloading
the compressed file
dgsol-1.3.tar.gz.
The
README
file contains instructions on how to install the software.