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PSST-2.0

Protein Data Bank Sequence Search Tool

  • Application Note
  • Published:
Applied Bioinformatics

Abstract

PSST-2.0 (Protein Data Bank [PDB] Sequence Search Tool) is an updated version of the earlier PSST (Protein Sequence Search Tool), and the philosophy behind the search engine has remained unchanged. PSST-2.0 is a Web-based, interactive search engine developed to retrieve required protein or nucleic acid sequence information and some of its related details, primarily from sequences derived from the structures deposited in the PDB (the database of 3-dimensional [3-D] protein and nucleic acid structures). Additionally, the search engine works for a selected subset of 25% or 90% non-homologous protein chains. For some of the selected options, the search engine produces a detailed output for the user-uploaded, 3-D atomic coordinates of the protein structure (PDB file format) from the client machine through the Web browser. The search engine works on a locally maintained PDB, which is updated every week from the parent server at the Research Collaboratory for Structural Bioinformatics, and hence the search results are up to date at any given time.

Availability: PSST-2.0 is freely accessible via http://pranag.physics.iisc.ernet.in/psst/ or http://144.16.71.10/psst/

Contact: Kanagaraj Sekar (sekar@physics.iisc.ernet.in)

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References

  1. Bernstein FC, Koetzle TF, Williams GJB, et al. The Protein Data Bank: a computer based archival file for macromolecular structures. J Mol Biol 1977; 112: 535–42

    Article  PubMed  CAS  Google Scholar 

  2. Saravanan S, Ajmalkhan A, Sekar K. PSST: protein sequence search tool: a web based interactive search engine. Curr Sci 2000; 78(5): 550–2

    CAS  Google Scholar 

  3. Wishart DS, Boyko RF, Willard L, et al. SEQSEE: a comprehensive program suite for protein sequence analysis. Comput Appl Biosci 1994; 10: 121–32

    PubMed  CAS  Google Scholar 

  4. Bairoch A, Apweiler R. The SWISS-PROT protein sequence databank and its supplement TrEMBL in 1998. Nucleic Acids Res 1998; 26: 38–42

    Article  PubMed  CAS  Google Scholar 

  5. Barker WC, Garavelli JS, Haft DH, et al. The PIR: international protein sequence database. Nucleic Acids Res 1998; 28: 27–32

    Article  Google Scholar 

  6. Bairoch A. The ENZYME database in 2000. Nucleic Acids Res 2000; 28: 304–5

    Article  PubMed  CAS  Google Scholar 

  7. Hobohm U, Sander C. Enlarged representative set of protein structures. Protein Sci 1994; 3(3): 522–4

    Article  PubMed  CAS  Google Scholar 

  8. Murzin AG, Brenner SE, Hubbard T, et al. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995; 247: 536–40

    PubMed  CAS  Google Scholar 

  9. Balaji S, Srinivasan N. Use of a database of structural alignments and phylogenetic trees in investigating the relationship between sequence and structural variability among homologous proteins. Protein Eng 2001; 14: 219–26

    Article  PubMed  CAS  Google Scholar 

  10. Sankaranarayanan R, Sekar K, Banerjee R, et al. A novel mode of carbohydrate recognition in jacalin, a Moraceae plant lectin with a beta-prism fold. Nat Struct Biol 1996; 3: 596–602

    Article  PubMed  CAS  Google Scholar 

  11. Sheik SS, Aggarwal SK, Poddar A, et al. A FAST pattern matching algorithm. J Chem Inf Comput Sci 2004; 44(4): 1251–6

    Article  PubMed  CAS  Google Scholar 

  12. Grubb SC. Ploticus 2.04 data display engine. Software, documentation and examples 1998

  13. Ramachandraiah G, Chandra NR. Sequence and structural determinants of man-nose recognition. Proteins 2000; 39: 358–64

    Article  PubMed  CAS  Google Scholar 

  14. Walker JE, Saraste M, Runswick MJ, et al. SEQSEE: a comprehensive program suite for protein sequence analysis. EMBO J 1982; 1: 945–51

    PubMed  CAS  Google Scholar 

Download references

Acknowledgments

The authors gratefully acknowledge the use of the Bioinformatics Centre, the interactive graphics-based molecular modelling facility and the Supercomputer Education and Research Centre. We are also grateful to the Department of Biotechnology, Ministry of Science and Technology and the Government of India for their enduring financial support. One of the authors, C. Mayilarasi, thanks the Bioinformatics Centre for providing an opportunity to undergo summer internship under K. Sekar.

The authors have no conflicts of interest that are directly relevant to the content of this article.

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Authors and Affiliations

  1. Bioinformatics Centre, Indian Institute of Science, Bangalore, 560 012, India

    Parthiban Ananthalakshmi, Krishnan Samayamohan, Chellapandi Chokalingam, Chandran Mayilarasi &  Kanagaraj Sekar

  2. Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore, India

    Kanagaraj Sekar

Authors
  1. Parthiban Ananthalakshmi
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  2. Krishnan Samayamohan
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  3. Chellapandi Chokalingam
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  4. Chandran Mayilarasi
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  5. Kanagaraj Sekar
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Correspondence to Kanagaraj Sekar.

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Ananthalakshmi, P., Samayamohan, K., Chokalingam, C. et al. PSST-2.0. Appl-Bioinformatics 4, 141–145 (2005). https://doi.org/10.2165/00822942-200504020-00008

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  • DOI: https://doi.org/10.2165/00822942-200504020-00008

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