PEEK — Protein Engineering Efficiency Kit
A focused toolkit for the everyday molecular-biology workflow: silent mutations, primer design, and a visual map of exactly what your edits do to the plasmid — built on reproducible, algorithmic science.
The Backstory
PEEK grew out of research conducted by Kevin Ghobadi in protein engineering. Planning even a straightforward silent mutation — identifying a valid site, verifying codon preservation, designing primer pairs, and confirming melting temperatures — required moving between multiple disconnected tools that frequently produced inconsistent results. The individual calculations were sound, but the lack of an integrated workflow introduced unnecessary room for error.
Kevin developed PEEK to address that directly, bringing the core steps of the process into a single, cohesive platform. Nathan Kura joined the project early and contributed substantially across both the computational and interface sides of the tool. The underlying methods — nearest-neighbor thermodynamics, codon adaptation scoring, restriction-site analysis — are fully documented, so any result the tool produces can be independently verified. Kevin's work was also informed by access to research resources at Washington University in St. Louis, which helped ensure the tool reflects the realities of practical experimental work.
What We Believe
Reproducibility first. The same inputs will always produce the same outputs, and the underlying formulas are documented so any result can be checked independently.
Transparent methods. Every value the tool reports derives from a specific, established algorithm — nothing is estimated or inferred without a documented basis.
Utility over complexity. Features are included because they make the cloning workflow more accurate and efficient, not to add scope.
What's Inside
Silent Mutations + CAI
Find codon-preserving changes that introduce restriction sites, scored with codon adaptation index and structure penalties.
Primer Design
Design enzyme-insertion, amino-acid-insertion, and Q5 site-directed mutagenesis primers with NEB-matched Tm calculations.
Sequence Visualizer
See your plasmid as a circular map and a base-level view — pick a mutation from the sidebar and watch the primer arrows appear.
The Team
