Mason Lab tools
Protein-protein
interaction tools:
(note
some do not work with firefox)
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 Tm, minimum desired Tm, maximum
undesired Tm, minimum delta Tm) 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.
Useful
External Links:
Reverse
and/or complement DNA sequences
Drawcoil
- creates helical wheel diagrams for coiled coils.
Seq2logo – peptide sequence
logo generator