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INTRODUCTION


By using YASARA, a molecular-graphics, modeling and simulation package, it proved necessary to integrate a new function: the superposition of structure. YASARA doesn't make this function, so we need to find softwares allowing this. The choice of the softwares of superposition was done according to specific criteria.

They must be:
  • using in prompt line
  • using offline
  • easy to use
  • Because of these criteria, only some software was retained:
  • SSM(http://www.ebi.ac.uk/msd-srv/ssm/),
  • FLEXPROT (http://bioinfo3d.cs.tau.ac.il/FlexProt/),
  • MULTIPROT (http://bioinfo3d.cs.tau.ac.il/cgi-bin/pdownload/progdownload.pl?pname=MultiProt),
  • SHEBA (http://rex.nci.nih.gov/RESEARCH/basic/lmb/mms/sheba.htm).

  • Those softwares will give us the opportunity to superpose 2 or several pdb files (several for MULTIPROT), and the result will be seen in YASARA. The plugin only works under linux.