Downloads

Create Library: A downloadable tool to generate a list of all given sequences within a peptide library. Data is entered at the peptide level. Data is outputted into a single text file. (Windows only .exe file within the zip file). (Refs: Crooks et al. J Mol Biol, 2016; Crooks et al. Biochemistry., 2017; Lathbridge and Mason, Biochemistry., 2018; Yu et al RSC Chem Biol 2021).

In silico PCA (isPCA) and in silico CANDI (isCAN): Used to derive high affinity (isPCA) and specific (isCAN) parallel and dimeric coil coils given a target and user defined off-targets. The user screens a library (L) of sequences (up to hundreds of millions) against a single defined target (T), and can additionally specify a number of competitors (C). The software will identify highest affinity sequences for the given target (LT) while choosing those of lowest homodimeric stability (LL) as well as considering target homodimer stability (TT) and off-target stability (LC). The tool will generate the predicted thermal melting temperatures (T_m values, and core/electrostatic /helical propensity components) with the option to output sequences, which have a greater affinity (deltaT_m) than a specified minimum. (Windows only .exe file within the zip file).

For isPCA and isCAN use please cite:

• Lathbridge, A and Mason J.M. Computational Competitive and Negative Design to Derive a Specific cJun Antagonist. Biochemistry. 57(42), 6108-18 (2018).
• Lathbridge, A., Michalowska, A., Mason, J.M. Coupling Computational and Intracellular Screening and Selection Towards Co-compatible cJun and cFos Antagonists. Biochemistry 59(4), 530-540 (2020).
• Yu, M., Ghamsari, L., Rotolo, J.A., Kappel, B.J. and Mason, J.M. Combined Computational and Intracellular Peptide Library Screening: Towards a Potent and Selective Fra1 Inhibitor. RSC Chem Biol 2, 656-668 (2021).

Please contact Jody Mason for feedback on the above software: j.mason@bath.ac.uk