PrISM References

From Honiglab_public

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References:

  • Yang, A. S. & Honig, B. (1999). Sequence to structure alignment in comparative modeling using PrISM. Proteins Suppl 3, 66-72.
  • Yang, A. S. & Honig, B. (2000). 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 301(3), 665-678.
  • Yang, A. S. & Honig, B. (2000). 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 301(3), 679-690.
  • Yang, A. S. & Honig, B. (2000). 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 301(3), 691-712.
  • Yang, A. S. & Wang, L. (2002). Local structure-based sequence profile database for local and global protein structure predictions. Bioinformatics 18(12): 1650-1657.
    (PrISM.1 - related PrISM scripts for this work: inter/runhis/savehis/buildLSBSP.his, inter/runhis/savehis/localMatchAssess.his')
  • Yang, A. S. (2002). Structure-dependent sequence alignment for remotely related proteins. Bioinformatics 18(12): 1658-1665.
    (PrISM.1 - related PrISM scripts for this work: inter/runhis/savehis/SDSApsiBLAST.his, inter/runhis/savehis/alignAssess.his')
  • Yang, A. S. & Wang, L (2003). Local structure prediction with local structure-based sequence profiles. Bioinformatics 19(10):1267-1274.
    (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.


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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.

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