About PoPS

The PoPS project and contact information

The PoPS project was created and developed by Dr Sarah Boyd as part of her Honours and PhD degrees (Monash University, Melbourne, Australia). The project was inspired by Dr George Rudy (at that time of the Walter and Eliza Hall Institute, Melbourne Australia), and was supervised by Assoc Prof Maria Garcia de la Banda (Monash University), and co-supervised by Dr George Rudy, and Profs Robert Pike and James Whisstock (Monash University).

PoPS is currently maintained and developed by Sarah Boyd, Dr Torsten Seemann (the Victorian Bioinformatics Consortium) and Dr Jiangning Song (Department of Biochemistry and Molecular Biology at Monash University).

Questions about PoPS and the related research should be emailed to Sarah Boyd (Sarah.Boyd{at}monash.edu) or Jiangning Song (Jiangning.Song{at}monash.edu). Please use an informative title, so that your message does not get redirected to spam. There are things missing, especially updated instructions and examples. There is good will to add these things, but in the meantime, please do not hesitate to email your questions.

PoPS is a very large project, with many contributors. Please see the credits list below for the people who have contributed to this work.

How to cite PoPS

If you use PoPS in your work, please cite the extended version of the original PoPS paper:
S.E. Boyd, M. Garcia de la Banda, R.N. Pike, J.C. Whisstock, G.B. Rudy
PoPS: A Computational Tool for Modeling and Predicting Protease Specificity,
J. Bioinform. Comput. Biol. 2005 Jun; vol 3 (3): pp 551-85   [Paper pdf (941Kb)] [PubMed]

The original PoPS paper:
S.E. Boyd, M. Garcia de la Banda, R.N. Pike, J.C. Whisstock, G.B. Rudy
PoPS: A Computational Tool for Modeling and Predicting Protease Specificity,
Proc. IEEE Comput. Syst. Bioinform. Conf., pp 372-381, Stanford, CA, August 2004.   [Paper pdf (425 Kb)]    [PubMed]

The PhD thesis that was based on PoPS:
S.E. Boyd
Computational Modelling and Prediction of Protease Specificity,
Monash University, Melbourne, Australia, June 2005.   [Thesis pdf (4Mb)]

Published research that has cited PoPS

If your work cites PoPS and would like it to appear here, send the details to Sarah Boyd (Sarah.Boyd[@]Infotech.monash.edu.au).

Igarashi Y, Heureux E, Doctor KS, Talwar P, Gramatikova S, Gramatikoff K, Zhang Y, Blinov M, Ibragimova SS, Boyd S, Ratnikov B, Cieplak P, Godzik A, Smith JW, Osterman AL, Eroshkin AM. PMAP: databases for analyzing proteolytic events and pathways. Nucleic Acids Res. 2009; Vol 37 (Database issue): pp D611-8.   [PubMed]

Shakib F, Ghaemmaghami AM, Sewell HF. The molecular basis of allergenicity. Trends Immunol. 2008; Vol 29 (12): pp 633-42.   [PubMed]

Enoksson M, Zhu W, Salvesen GS. Identification of Protease Substrates by Mass Spectrometry Approaches-1. In: The Cancer Degradome: Proteases and Cancer Biology (New York: Springer), pp 67-82.

Chen CT, Yang EW, Hsu HJ, Sun YK, Hsu WL, Yang AS. Protease substrate site predictors derived from machine learning on multilevel substrate phage display data. Bioinformatics. 2008; Vol 24 (23): pp 2691-7.   [PubMed]

Schilling O, Overall CM. Proteome-derived, database-searchable peptide libraries for identifying protease cleavage sites. Nat Biotechnol. 2008; Vol 26 (6): pp 685-94.   [PubMed]

Scott FL, Fuchs GJ, Boyd SE, Denault JB, Hawkins CJ, Dequiedt F, Salvesen GS. Caspase-8 cleaves histone deacetylase 7 and abolishes its transcription repressor function. J Biol Chem. 2008; Vol 283 (28): pp 19499-510.   [PubMed]

Minkiewicz P, Dziuba J, Iwaniak A, Dziuba M, Darewicz M. BIOPEP database and other programs for processing bioactive peptide sequences. J AOAC Int. 2008; Vol 91 (4): pp 965-80.   [PubMed]

Kerr FK, Thomas AR, Wijeyewickrema LC, Whisstock JC, Boyd SE, Kaiserman D, Matthews AY, Bird PI, Thielens NM, Rossi V, Pike RN. Elucidation of the substrate specificity of the MASP-2 protease of the lectin complement pathway and identification of the enzyme as a major physiological target of the serpin, C1-inhibitor. Mol. Immunol. 2008; Vol 45 (3): pp 670-7.   [PubMed]

Bylander J, Li Q, Ramesh G, Zhang B, Reeves WB, Bond JS. Targeted disruption of the meprin metalloproteinase beta gene protects against renal ischemia-reperfusion injury in mice. Am. J. Physiol. Renal Physiol. 2008; Vol 294 (3): F480-90.   [PubMed]

Vincents B, Onnerfjord P, Gruca M, Potempa J, Abrahamson M. Down-regulation of human extracellular cysteine protease inhibitors by the secreted staphylococcal cysteine proteases, staphopain A and B. Biol Chem. 2007; Vol 388 (4): pp 437-46.   [PubMed]

Hostetter DR, Loeb CR, Chu F, Craik CS. Hip is a pro-survival substrate of granzyme B. J. Biol. Chem. 2007; Vol 282 (38): pp 27865-74.   [PubMed]

Furmonaviciene R, Ghaemmaghami AM, Boyd SE, Jones NS, Bailey K, Willis AC, Sewell HF, Mitchell DA, Shakib F The protease allergen Der p 1 cleaves cell surface DC-SIGN and DC-SIGNR: experimental analysis of in silico substrate identification and implications in allergic responses, Clin. Exp. Allergy 2007; vol 37 (2): pp 231-42.   [PubMed]

Timmer JC, Salvesen GS. Caspase substrates. Cell Death Differ. 2007; Vol 14 (1): pp 66-72.   [PubMed]

Shiryaev SA, Ratnikov BI, Chekanov AV, Sikora S, Rozanov DV, Godzik A, Wang J, Smith JW, Huang Z, Lindberg I, Samuel MA, Diamond MS, Strongin AY Cleavage targets and the D-arginine-based inhibitors of the West Nile virus NS3 processing proteinase, Biochem. J. 2006; vol 393: pp 503-511.   [PubMed]

Strongin AY. Mislocalization and unconventional functions of cellular MMPs in cancer. Cancer Metastasis Rev. 2006; Vol 25 (1): pp 87-98.   [PubMed]

Kerr FK, O'Brien G, Quinsey NS, Whisstock JC, Boyd S, Garcia de la Banda M, Kaiserman D, Matthews AY, Bird PI, Pike RN Elucidation of the Substrate Specificity of the C1s Protease of the Classical Complement Pathway, J. Biol. Chem. 2005 Nov 25; vol 280 (47): pp 39510-39514.   [PubMed]

Golubkov VS, Boyd S, Savinov AY, Chekanov AV, Osterman AL, Remacle A, Rozanov DV, Doxsey SJ, Strongin AY Membrane Type-1 Matrix Metalloproteinase (MT1-MMP) Exhibits an Important Intracellular Cleavage Function and Causes Chromosome Instability, J. Biol. Chem. 2005 Jul 1; vol 280 (26): pp 25079-86.   [PubMed]

The Credits List of PoPS contributors

The PoPS project is very large, and has been developed from the contributions of many people, past and present, in many forms including ideas, coding and laboratory work. In alphabetical order, these people are:

Current contributors             Past contributors
Steve Androulakis              Phillip Bird
Maria Garcia de la Banda             Michael Cameron
Natasha Ng             (Suan) Khai Chong
Robert Pike              Dion Kaiserman
Cyril Reboul              Anthony Matthews
Torsten Seemann             David Powell
Jiangning Song              George Rudy
James Whisstock              Laurent Tardiff
             Di Wu