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DelPhi is a program which uses finite difference method to solve the Poisson-Boltzmann equation for molecules of arbitrary shape and charge distribution.
Submitted: Oct 18, 2000
The main purpose of the program DynaFit is to perform nonlinear least-squares regression of chemical kinetic, enzyme kinetic, or ligand-receptor binding data. The experimental data can be either initial reaction velocities in dependence on the concentration of varied species (e.g., inhibitor concentration vs. velocity), or the reaction progress curves (e.g., time vs. absorbance).
Submitted: Oct 08, 2000
Genometric Analysis Simulation Program (G.A.S.P.)  
The Genometric Analysis Simulation Program (G.A.S.P.) is a software tool that can generate samples of family data based on user specified genetic models. Data generated can be as simple as a single sample of random individuals with a single normally distributed trait or as complex as thousands of samples of extended families with multiple traits based on a linear combination of major locus, polygenic, common sibship environment and covariate components. Traits can be generated based on a number of user specified components, and components can be unique to a single trait or shared by multiple traits.
Submitted: Oct 20, 2000
DIRAC is a FORTRAN (and a bit of C) code for relativistic molecular calculations based on the Dirac-Coulomb Hamiltonian. It solves the the 4-component Dirac-Hartree-Fock (DHF) equations by the Self Consistent Field (SCF) iterative procedure and provides tools for analysis of the converged wave function.
Submitted: Oct 18, 2000
Raster3D is a set of tools for generating high quality raster images of proteins or other molecules. The core program renders spheres, triangles, cylinders, and quadric surfaces with specular highlighting, Phong shading, and shadowing. It uses an efficient software Z-buffer algorithm which is independent of any graphics hardware. Ancillary programs process atomic coordinates from Brookhaven PDB files into rendering descriptions for pictures composed of ribbons, space-filling atoms, bonds, ball+stick, etc. Raster3D can also be used to render pictures composed in other programs such as Molscript in glorious 3D with highlights, shadowing, etc. Output is to pixel image files with 24 bits of color information per pixel.
Submitted: Oct 08, 2000
The Oak Ridge Thermal Ellipsoid Plot (ORTEP) program is a computer program for drawing crystal structure illustrations. Ball-and-stick type illustrations of a quality suitable for publication are produced with either spheres or thermal-motion probability ellipsoids, derived from anisotropic temperature factor parameters, on the atomic sites. The program also produces stereoscopic pairs of illustrations which aid in the visualization of complex arrangements of atoms and their correlated thermal motion patterns.
Submitted: Sep 12, 2000
This software calculates the free energies of solvation in aqueous solutions, charge models for partial atomic charges of gas-phase molecules and of solutes in alkane solvents and models for free energies of solvation and partial atomic charges in water or in any organic solvent.
Submitted: Sep 05, 2000
CINEMA is a Colour INteractive Editor for Multiple Alignments. The program allows visualisation and manipulation of both protein and DNA sequences.
Submitted: Sep 04, 2000
Statistical Genetics Software  
MENDEL is a program for the genetic analysis of human pedigree data under models involving a small number of loci. FISHER is a program for the genetic analysis of classical biometric traits like blood pressure or height that are caused by a combination of polygenic inheritance and complex environmental forces. SEARCH is a subprogram for function minimization. SPERM is a program for the analysis of sperm typing data.
Submitted: Sep 19, 2000
The TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for polypeptides.
Submitted: Sep 15, 2000
The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package. GAMESS is maintained by the members of the Gordon research group at Iowa State University.
Submitted: Sep 05, 2000
SHELX is a set of programs for crystal structure determination from single-crystal diffraction data.
Submitted: Dec 10, 2000
Test_shotgun is a Fortran program which simulates a shotgun sequencing project. It is a handy tool for estimating not only how much work must be done (or remains to be done) for a given project, but also how much it will cost. It simulates projects up to 1 Mbp directly in memory. For projects larger than that it simulates it in 1 Mbp region and then scales the results. It is known to compile and run on OpenVMS, Digital Unix, and IRIX.
Submitted: Sep 30, 2000
ASAD is a software package developed for creating and integrating chemistry schemes in atmospheric models without the need to write any FORTRAN code to solve the chemical rate equations.
Submitted: Dec 21, 2000
The bioWidgets toolkit is a collection of Java Beans(tm) used for development of graphics applications and/or applets in the genomics domain.
Submitted: Oct 17, 2000

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