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GROMOS
A general-purpose molecular dynamics computer simulation package for the study of biomolecular systems.
http://www.igc.ethz.ch/GROMOS/
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Ascalaph DNA
Program for creating models of nucleic acids and their complexes with low-molecular-weight and protein ligands.
http://www.agilemolecule.com/Ascalaph/Ascalaph_DNA.html
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GrAfSS: Graph Theoretic Applications for Structure Searching
Graph theoretic methods for the analysis of structural relationships in biological macromolecules.
http://grafss.imfr.net/
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