Dear Patrick Timmons ,

Presumably you are familiar with most of them, but my suggestions are:

PEP2D:

Singh, H., Singh, S., & Raghava, G. P. S. (2019). Peptide Secondary Structure Prediction using Evolutionary Information. bioRxiv, 558791.

https://webs.iiitd.edu.in/raghava/pep2d/

PEPstr:

Kaur, H., Garg, A., & Raghava, G. P. S. (2007). PEPstr: a de novo method for tertiary structure prediction of small bioactive peptides. Protein and peptide letters, 14(7), 626-631.

https://webs.iiitd.edu.in/raghava/pepstr/home.html

PEPFOLD:

Shen, Y., Maupetit, J., Derreumaux, P., & Tufféry, P. (2014). Improved PEP-FOLD approach for peptide and miniprotein structure prediction. Journal of chemical theory and computation, 10(10), 4745-4758.

https://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-FOLD/

PEP-LOOK:

Thomas, A., Deshayes, S., Decaffmeyer, M., Van Eyck, M. H., Charloteaux, B., & Brasseur, R. (2009). PepLook: an innovative in silico tool for determination of structure, polymorphism and stability of peptides. In Peptides for Youth (pp. 459-460). Springer, New York, NY.

http://peplook.gembloux.ulg.ac.be/ (looks inactive at the time I checked)

Not exclusively for peptides but often used for this purpose:

PSIPRED:

McGuffin, L. J., Bryson, K., & Jones, D. T. (2000). The PSIPRED protein structure prediction server. Bioinformatics, 16(4), 404-405.

http://bioinf.cs.ucl.ac.uk/psipred/

JPred4 (minimum lenght is 20 AA):

Drozdetskiy, A., Cole, C., Procter, J., & Barton, G. J. (2015). JPred4: a protein secondary structure prediction server. Nucleic acids research, 43(W1), W389-W394.

http://www.compbio.dundee.ac.uk/jpred4/index.html

SOPMA:

Geourjon, C., & Deleage, G. (1995). SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments. Bioinformatics, 11(6), 681-684.

https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_sopma.html

CONCORD:

Wei, Y., Thompson, J., & Floudas, C. A. (2012). CONCORD: a consensus method for protein secondary structure prediction via mixed integer linear optimization. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, 468(2139), 831-850.

http://helios.princeton.edu/CONCORD

(and indirectly I used I-Tasser (https://zhanglab.ccmb.med.umich.edu/I-TASSER/ ) giving the FASTA sequence of the entire protein and then look at particular regions of round 18 AA long).

Pretty sure there are more, but anyway this is my contribution to your list.

Best regards.

PS. FYI I did a little comparison of several prediction programs using 18-20 AA long sequences:

Article The role and significance of potential lipid-binding regions...

Perhaps out of topic but this study made use of the Heliquest program (https://heliquest.ipmc.cnrs.fr/ ), perhaps interesting to have a little look at.

Dear Patrick Timmons ,

Presumably you are familiar with most of them, but my suggestions are:

PEP2D:

Singh, H., Singh, S., & Raghava, G. P. S. (2019). Peptide Secondary Structure Prediction using Evolutionary Information. bioRxiv, 558791.

https://webs.iiitd.edu.in/raghava/pep2d/

PEPstr:

Kaur, H., Garg, A., & Raghava, G. P. S. (2007). PEPstr: a de novo method for tertiary structure prediction of small bioactive peptides. Protein and peptide letters, 14(7), 626-631.

https://webs.iiitd.edu.in/raghava/pepstr/home.html

PEPFOLD:

Shen, Y., Maupetit, J., Derreumaux, P., & Tufféry, P. (2014). Improved PEP-FOLD approach for peptide and miniprotein structure prediction. Journal of chemical theory and computation, 10(10), 4745-4758.

https://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-FOLD/

PEP-LOOK:

Thomas, A., Deshayes, S., Decaffmeyer, M., Van Eyck, M. H., Charloteaux, B., & Brasseur, R. (2009). PepLook: an innovative in silico tool for determination of structure, polymorphism and stability of peptides. In Peptides for Youth (pp. 459-460). Springer, New York, NY.

http://peplook.gembloux.ulg.ac.be/ (looks inactive at the time I checked)

Not exclusively for peptides but often used for this purpose:

PSIPRED:

McGuffin, L. J., Bryson, K., & Jones, D. T. (2000). The PSIPRED protein structure prediction server. Bioinformatics, 16(4), 404-405.

http://bioinf.cs.ucl.ac.uk/psipred/

JPred4 (minimum lenght is 20 AA):

Drozdetskiy, A., Cole, C., Procter, J., & Barton, G. J. (2015). JPred4: a protein secondary structure prediction server. Nucleic acids research, 43(W1), W389-W394.

http://www.compbio.dundee.ac.uk/jpred4/index.html

SOPMA:

Geourjon, C., & Deleage, G. (1995). SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments. Bioinformatics, 11(6), 681-684.

https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_sopma.html

CONCORD:

Wei, Y., Thompson, J., & Floudas, C. A. (2012). CONCORD: a consensus method for protein secondary structure prediction via mixed integer linear optimization. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, 468(2139), 831-850.

http://helios.princeton.edu/CONCORD

(and indirectly I used I-Tasser (https://zhanglab.ccmb.med.umich.edu/I-TASSER/ ) giving the FASTA sequence of the entire protein and then look at particular regions of round 18 AA long).

Pretty sure there are more, but anyway this is my contribution to your list.

Best regards.

PS. FYI I did a little comparison of several prediction programs using 18-20 AA long sequences:

Article The role and significance of potential lipid-binding regions...

Perhaps out of topic but this study made use of the Heliquest program (https://heliquest.ipmc.cnrs.fr/ ), perhaps interesting to have a little look at.

Dear Rob Keller ,

Many thanks for your thorough response. I was indeed familiar with some of those services, but a number of those are new to me.

Thanks you for suggesting your comparison between them, I will be sure to take a look at that as well!

Best wishes,

Patrick

Dear Patrick

we developed an algorithm to predict new peptides from transcriptomic databases, we also predict structures

is not a service but sure we could be of help

kind regards

Jean paul