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Bioinformatics Vol. 17 no. 9 2001
Pages 851-852
© 2001 Oxford University Press

Applications Note

VISTRAJ: exploring protein conformational space

John J. Salama 1, Howard J. Feldman 2,3 and Christopher W. V. Hogue 2,3,*

1 MDS Proteomics Inc., 480 University Ave, Toronto, Ontario, Canada
2 Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8
3 Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Ave, Toronto, Ontario, Canada M5G 1X5

Received on March 19, 2001 ; revised on April 27, 2001 ; accepted on May 30, 2001

Summary: VISTRAJ is an application which allows 3D visualization, manipulation and editing of protein conformational space using probabilistic maps of this space called ‘trajectory distributions’. Trajectory distributions serve as input to FOLDTRAJ which samples protein structures based on the represented conformational space. VISTRAJ also allows FOLDTRAJ to be used as a tool for homology model creation, and structures may be generated containing post-translationally modified amino acids.

Availability: Binaries are freely available for non-profit use as part of the FOLDTRAJ package at ftp://ftp.mshri.on.ca/pub/TraDES/foldtraj/.

Contact: hogue{at}mshri.on.ca

Supplementary Information: The Trajectory Directed Ensemble Sampling (TraDES) web site can be visited at http://bioinfo.mshri.on.ca/trades/. The web-based version of INITTRAJ/FOLDTRAJ may be accessed at http://foldtraj.mshri.on.ca/.

* To whom correspondence should be addressed.


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