OpenScience / Software



Viewmol

Posted on March 1, 2001 by Dan Gezelter

Viewmol is an open source graphical front end for computational chemistry programs. It is able to graphically aid in the generation of molecular structures for computations and to visualize their results. Find Viewmol at: http://viewmol.sourceforge.net/

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Posted in Molecule Viewers and Editors | Leave a comment

TheRate

Posted on March 1, 2001 by Dan Gezelter

TheRate stands for Theoretical Rates. TheRate allows thermal rate constants for unimolecular and bimolecular gas-phase reactions to be calculated directly from an electronic structure molecular orbital and density functional theory. Find TheRate at: http://therate.hec.utah.edu/

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QMOL

Posted on February 28, 2001 by Dan Gezelter

Qmol is a program for viewing molecular structures and animating molecular trajectories. Find QMOL at: http://www.ccl.net/cca/software/MS-WIN95-NT/qmol/index.shtml

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PyMOL

Posted on February 28, 2001 by Dan Gezelter

PyMOL is a molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations. Find PyMOL at: http://pymol.sourceforge.net/

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PomBase

Posted on February 28, 2001 by Dan Gezelter

An AceDB database for the fission yeast Schizosaccharomyces pombe. Find PomBase at: http://www.genedb.org/genedb/pombe/blast.jsp

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PROCHECK

Posted on February 28, 2001 by Dan Gezelter

Checks the stereochemical quality of a protein structure, producing a number of PostScript plots analysing its overall and residue-by-residue geometry. Find PROCHECK at: https://www.ebi.ac.uk/thornton-srv/software/PROCHECK/

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ORTEP

Posted on February 28, 2001 by Dan Gezelter

Oak Ridge Thermal Ellipsoid Plot Program for Crystal Structure Illustrations Find ORTEP at: http://www.ornl.gov/ortep/ortep.html

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PAML

Posted on February 28, 2001 by Dan Gezelter

Phylogenetic Analysis by Maximum Likelihood Find PAML at: http://abacus.gene.ucl.ac.uk/software/paml.html

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PHYLIP

Posted on February 28, 2001 by Dan Gezelter

PHYLIP Phylogeny Inference Package computer programs for inferring phylogenies Find PHYLIP at: http://evolution.genetics.washington.edu/phylip.html

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Populations

Posted on February 28, 2001 by Dan Gezelter

Population genetic software (individuals or populations distances, phylogenetic trees) Find Populations at: http://bioinformatics.org/~tryphon/populations/

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Posted in Population | Leave a comment