PrISM

PrISM is an integrated computational system where computational tools are implemented for protein sequence and structure analysis and modeling. All the tools are currently coded in FORTRAN.

Download software

Click here to download PrISM.

System requirements

PrISM package is available in SGI-irix. PrISM.1 package is available in Intel-linux.

Minimum system requirement:

  • 128 Mb memory.
  • 1Gb free hard disk space (Current PrISM takes ~500 Mb).
  • Linux-Intel or sgi IRIX operation system using tcsh or csh shell (csh is default in sgi; tcsh can be set in linux system by changing bash to tcsh in /etc/passwd).
  • To prevent stack overflow in some PrISM modules, increase the stack size by adding the line "limit stack 128000" in your ~/.cshrc.
  • X-window server in Linux-Intel system to view protein structures using RasMol.

Note: Does not work on Red Hat 5 or later.

Documentation

Manual in pdf form

References

Yang AS, Honig B. Sequence to structure alignment in comparative modeling using PrISM. Proteins. 1999;Suppl 3:66-72.

Yang AS, Honig B. An integrated approach to the analysis and modeling of protein sequences and structures. I. Protein structure alignment and quantitative measure for protein structural distance. J Mol Biol. 2000 Aug 18;301(3):665-78.

Yang AS, Honig B. An integrated approach to the analysis and modeling of protein sequences and structures. II. On the relationship between sequence and structural similarity for proteins that are not obviously related in sequence. J Mol Biol. 2000 Aug 18;301(3):679-89.

Yang AS, Honig B. An integrated approach to the analysis and modeling of protein sequences and structures. III. A comparative study of sequence conservation in protein structural families using multiple structural alignments. J Mol Biol. 2000 Aug 18;301(3):691-711.

Yang AS, Wang LY. Local structure-based sequence profile database for local and global protein structure predictions. Bioinformatics. 2002 Dec;18(12):1650-7.
(PrISM.1 - related PrISM scripts for this work: inter/runhis/savehis/buildLSBSP.his, inter/runhis/savehis/localMatchAssess.his')

Yang AS. Structure-dependent sequence alignment for remotely related proteins. Bioinformatics. 2002 Dec;18(12):1658-65. (PrISM.1 - related PrISM scripts for this work: inter/runhis/savehis/SDSApsiBLAST.his, inter/runhis/savehis/alignAssess.his')

Yang AS, Wang LY. Local structure prediction with local structure-based sequence profiles. Bioinformatics. 2003 Jul 1;19(10):1267-74. (PrISM.1 - related PrISM scripts for this work: inter/runhis/savehis/seg9pepLSBSP1.his, inter/runhis/savehis/LSBSP1pred.his')

' Need to download the PrISM.1 system to read these files. These scripts files and the output files in the same directory show examples for the computational protocols used in the published work.

Acknowledgments

PrISM is supported by a funding from the National Science Foundation and National Institutes of Health Grant # DBI-9904841 and 5 R37 GM30518.

Developed in the Honig Lab. Current version maintained by An-Suei Yang.