Mason Lab tools

Protein-protein interaction tools:

InsiliCoil - A software platform designed to accelerate coiled coil research by providing high-throughput, user-friendly screening technologies for CC inhibitor design and bioengineering. Arora, J. and Mason, J. M., 2025. "InsiliCoil: An Integrated Software Suite for Coiled Coil Design, Prediction and Therapeutic Engineering". ACS Synthetic Biology [Online], in press. DOI: 10.1021/acssynbio.5c00678

Note that the below software has now been superseded by Insilicoil, which contains all modules and more:

bCIPA Library Screen: Screens a library of sequences against a single defined target. The tool will generate the predicted thermal melting temperatures (and core/electrostatic /helical propensity components) with the option to output sequences which have a greater affinity than a specified minimum.

bCIPA Interactome Screen: Screen all interactions between a selection of defined sequences. This includes an option to colour code interactome Tm values according to affinity (Refs: Crooks et al. J. Mol. Biol., 2016 and Crooks et al. Biochemistry., 2017).

bCIPA Set vs Set Screen: Screen the interactions between one set of sequences and another set of sequences, including colour coding Tm values according to affinity.

Find Pairs / Find Quadruples: Users input a library of sequences and screen the resulting interactome to identify two (i.e. four peptides), four (i.e eight peptides), or even higher numbers of pairs of leucine zippers that are specific within each others presence. Users can also input desired parameters for their specific pairs (maximum homodimer T_m, minimum desired T_m, maximum undesired T_m, minimum delta T_m) depending on their requirements. Options for Find Quadruples will appear once Find Pairs has identified sequences that meet the given requirements (Refs: Crooks et al. J. Mol. Biol., 2016 and Crooks et al. Biochemistry., 2017).

Library Design tools:

Generate Library Sequences : A tool to generate a list of all given sequences within a peptide library. Data can be entered at the peptide or DNA level. This tool additionally integrates with Isomasses such that once a library is generated it is possible to rank predicted best binders and their masses for a given leucine zipper target sequence (Refs: Crooks et al. J. Mol. Biol., 2016 and Crooks et al. Biochemistry., 2017).

Build Library: As above but in reverse. A tool to list degenerate sequence positions and their residue options given a list of hypothetical library members

Isomasses: Lists the mass of every member in a given peptide library

Other Biology Tools:

Concentration Calculator: Find the concentration and amount of protein in a sample from the A₂₈₀ and the protein mass.

Library Cloning: To help with calculations involved in cloning libraries.

Mass Calculator: Find the mass of a protein from the amino acid sequence, and other associated calculations.

Downloads

Useful External Links:

Reverse and/or complement DNA sequences

Protein Reverse Translate

Drawcoil - creates helical wheel diagrams for coiled coils.

Seq2logo – peptide sequence logo generator