Resources

Original description of the SCREPs database:

[1] M. Maxwell, E.A.B. Undheim, M. Mobli, Secreted Cysteine-Rich Repeat Proteins "SCREPs": A Novel Multi-Domain Architecture, Front Pharmacol 9 (2018) 1333.

[2] Liu, J., Maxwell, M., Cuddihy, T., Crawford, T., Bassetti, M., Hyde, C., ... & Mobli, M. (2022). ScrepYard: an online resource for disulfide‐stabilised tandem repeat peptides. Protein Science, e4566.

Inspired by discoveries by:

[2] A. van de Locht, D. Lamba, M. Bauer, R. Huber, T. Friedrich, B. Kröger, W. Höffken, W. Bode, Two heads are better than one: crystal structure of the insect derived double domain Kazal inhibitor rhodniin in complex with thrombin, The EMBO journal 14(21) (1995) 5149-5157.

[3] C.J. Bohlen, A. Priel, S. Zhou, D. King, J. Siemens, D. Julius, A bivalent tarantula toxin activates the capsaicin receptor, TRPV1, by targeting the outer pore domain, Cell 141(5) (2010) 834-45.

[4] I.R. Chassagnon, C.A. McCarthy, Y.K.Y. Chin, S.S. Pineda, A. Keramidas, M. Mobli, V. Pham, T.M. De Silva, J.W. Lynch, R.E. Widdop, L.D. Rash, G.F. King, Potent neuroprotection after stroke afforded by a double-knot spider-venom peptide that inhibits acid-sensing ion channel 1a, Proc Natl Acad Sci U S A 114(14) (2017) 3750-3755.

Using the following resources:

• Uniprot 

  Bateman, A., Martin, M. J., Orchard, S., Magrane, M., Agivetova, R., Ahmad, S., ... & UniProt Consortium. (2020). UniProt: the universal protein knowledgebase in 2021. Nucleic Acids Research.

• BLAST 2.10.1+

  Boratyn, G. M., Camacho, C., Cooper, P. S., Coulouris, G., Fong, A., Ma, N., ... & Zaretskaya, I. (2013). BLAST: a more efficient report with usability improvements. Nucleic acids research, 41(W1), W29-W33.

• SignalP 5.0

  Armenteros, J. J. A., Tsirigos, K. D., Sønderby, C. K., Petersen, T. N., Winther, O., Brunak, S., ... & Nielsen, H. (2019). SignalP 5.0 improves signal peptide predictions using deep neural networks. Nature biotechnology, 37(4), 420-423.

• CDHIT 4.8.1

  Chen, Q., Wan, Y., Lei, Y., Zobel, J., & Verspoor, K. (2016, December). Evaluation of CD-HIT for constructing non-redundant databases. In 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) (pp. 703-706). IEEE.

• INTERPROSCAN 5.48-83.0

  Jones, P., Binns, D., Chang, H. Y., Fraser, M., Li, W., McAnulla, C., ... & Hunter, S. (2014). InterProScan 5: genome-scale protein function classification. Bioinformatics, 30(9), 1236-1240.