Forcefield_NCAA: AMBER Forcefield Parameters for Non-canonical Amino Acids

Forcefield_NCAA is a set of self-consistent AMBER forcefield parameters for non-canonical amino acids. It allows you to design and derivatize peptides containing NCAAs for use as drugs.

Instructions to Download and Use Forcefield_NCAA in AMBER

Download and read the instructions for use.

Download and unzip FF_NCAA.

Go to the Multiple Modification Submission Page

Submit Protein Structure to Be Derivatized

Currently can modify positions 2 through N-1
(optional)
 

Publications

If using the parameters or this web server, please cite the associated publications, which describe the details of our method.

Khoury, G.A., Smadbeck, J., Tamamis, P., Vandris, A.C., Kieslich, C.A., and Floudas, C.A. Forcefield_NCAA: Ab Initio Charge Parameters to Aid in the Discovery and Design of Therapeutic Proteins and Peptides with Unnatural Amino Acids and Their Application to Complement Inhibitors of the Compstatin Family. ACS Synthetic Biology 2014 DOI: 10.1021/sb400168u

Khoury, G.A., Thompson, J.P., Smadbeck, J., Kieslich, C.A., and Floudas, C. A. Forcefield_PTM: Ab Initio Charge and AMBER Forcefield Parameters for Frequently Occurring Post-Translational Modifications. Journal of Chemical Theory and Computation 2013, 9 (12) 5653-5674. DOI: 10.1021/ct400556v

This webserver uses the AMBER11 package.

Related Work

For charge parameters and torsion corrections for 32 frequently occurring post-translational modifications and a corresponding web interface, please visit Forcefield_PTM.

Acknowledgements

CAF acknowledges support from The National Institutes of Health grant number R01GM052032, and the National Science Foundation. GAK is grateful for support by a National Science Foundation Graduate Research Fellowship under grant number DGE-1148900.