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Applied Bioinformatics

, Volume 4, Issue 2, pp 147–150 | Cite as

ProLysED

An Integrated Database and Meta-server of Bacterial Protease Systems
  • Mohd Firdaus Raih
  • Hafiza Aida Ahmad
  • Mohd Yunus Sharum
  • Norazah Azizi
  • Rahmah MohamedEmail author
Application Note

Abstract

Bacterial proteases are an important group of enzymes that have very diverse biochemical and cellular functions. Proteases from prokaryotic sources also have a wide range of uses, either in medicine as pathogenic factors or in industry and therapeutics. ProLysED (Prokaryotic Lysis Enzymes Database), our meta-server integrated database of bacterial proteases, is a useful, albeit very niche, resource. The features include protease classification browsing and searching, organism-specific protease browsing, molecular information and visualisation of protease structures from the Protein Data Bank (PDB) as well as predicted protease structures.

Availability: ProLysED is integrated into the ProLysES (Prokaryotic Lysis Enzymes Site) website at http://genome.ukm.my/prolyses/. Access to the ProLysED database is free for academic users upon registration.

Contact: M. Firdaus Raih (prolysed@cgat.ukm.my or mfirr@pkrisc.cc.ukm.my)

Keywords

Protein Data Bank Perl Script Enzyme Commission Enzyme Commission Number Protein Data Bank File 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgments

We acknowledge the National Biotechnology and Bioinformatics Network (NBBnet), Malaysia, which is hosting ProLysED, and funding from the Microbial Genomics for Gene and Natural Product Discovery IRPATOPDOWN grant (09-02-02-002 BTK/TD/03) from the Ministry of Science, Technology and Innovation, Malaysia. We thank Fuad Muhammad and Noraslinda for miscellaneous technical input and feedback.

The authors have provided no information on conflicts of interest directly relevant to the content of this article.

References

  1. 1.
    Rao MB, Aparna AM, Ghatge MS, et al. Molecular and biotechnological aspects of microbial proteases. Microbiol Mol Biol Rev 1998; 62: 597–635PubMedGoogle Scholar
  2. 2.
    Rawlings ND, O’Brien EA, Barrett AJ. MEROPS: the protease database. Nucleic Acids Res 2002; 30: 343–6PubMedCrossRefGoogle Scholar
  3. 3.
    Boeckmann B, Bairoch A, Apweiler R, et al. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res 2003; 31: 365–70PubMedCrossRefGoogle Scholar
  4. 4.
    Berman HM, Westbrook J, Feng Z, et al. The Protein Data Bank. Nucleic Acids Res 2000; 28: 235–42PubMedCrossRefGoogle Scholar
  5. 5.
    Rost B. PHD: predicting 1D protein structure by profile based neural networks. Methods Enzymol 1996; 266: 525–39PubMedCrossRefGoogle Scholar
  6. 6.
    Kelley LA, MacCallum RM, Sternberg MJE. Enhanced genome annotation using structural profiles in the program 3D-PSSM. J Mol Biol 2000; 299: 499–520PubMedCrossRefGoogle Scholar
  7. 7.
    Karplus K, Barrett C, Hughey R. Hidden Markov models for detecting remote protein homologies. Bioinformatics 1998; 14: 846–56PubMedCrossRefGoogle Scholar
  8. 8.
    McGuffin LJ, Bryson K, Jones DT. The PSIPRED protein structure prediction server. Bioinformatics 2000; 16: 404–5PubMedCrossRefGoogle Scholar
  9. 9.
    Benson DA, Karsch-Mizrachi I, Lipman DJ, et al. GenBank. Nucleic Acids Res 2003; 31: 23–7PubMedCrossRefGoogle Scholar
  10. 10.
    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: 536–40PubMedGoogle Scholar
  11. 11.
    Laskowski RA. PDBsum: summaries and analyses of PDB structures. Nucleic Acids Res 2001; 29: 221–2PubMedCrossRefGoogle Scholar
  12. 12.
    Orengo CA, Michie AD, Jones S, et al. CATH: a hierarchic classification of protein domain structures. Structure 1997; 5: 1093–108PubMedCrossRefGoogle Scholar
  13. 13.
    Altschul SF, Madden TL, Schaffer AA, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997; 25: 3389–402PubMedCrossRefGoogle Scholar
  14. 14.
    Sali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 1993; 234: 779–815PubMedCrossRefGoogle Scholar
  15. 15.
    Altschul SF, Gish W, Miller W, et al. Basic local alignment search tool. J Mol Biol 1990; 215: 403–10PubMedGoogle Scholar

Copyright information

© Adis Data Information BV 2005

Authors and Affiliations

  • Mohd Firdaus Raih
    • 1
    • 2
  • Hafiza Aida Ahmad
    • 2
  • Mohd Yunus Sharum
    • 2
  • Norazah Azizi
    • 2
  • Rahmah Mohamed
    • 1
    • 2
    Email author
  1. 1.School of Biosciences and Biotechnology, Faculty of Science and TechnologyUniversiti Kebangsaan MalaysiaBangiMalaysia
  2. 2.Malaysia Genome InstituteUniversiti Kebangsaan Malaysia - Malaysia Technology Development Corporation (UKM-MTDC) Smart Technology CentreBangiMalaysia

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