proteolutions was founded in 2020 with the mission to provide a robust and superior gene optimization algorithm for academia and industry that guarantees maximal protein yields from many sequenced expression hosts. proteolutions has optimized a range of DNA sequences for selected users in a beta-test phase, all validating the proteolutions gene optimization approach.

With its official launch in 2025, proteolutions provides a web-based on-demand service to enhance synthetic gene sequences for the optimization of your protein expression in terms of solubility and functionality.

The right DNA is where your project starts and badly optimized DNA is where it prematurely ends. So try our sequences for expressions that failed in the past or your new protein expression project and benefit from our sequence optimization expertise.

With proteolutions, you will drastically reduce the rate of expression failure and increase the chance of high protein yields.

Heterologous gene expression may often feel like a lottery mainly due to the redundancy of the genetic code that allows for a plethora of possible synthetic gene variants (typically > 10⁷⁴) coding for one protein. Current options for gene optimization, like host codon abundance or codon adaptation index, are deployed by various free and proprietary tools, unfortunately with high failure rates due to intrinsic conceptual weaknesses.

Deploying a robust, efficient and universal gene optimization method with a performance way beyond the current state-of the art, proteolutions takes gene optimization to the next level. With numerous real case beta-tests in mammalian and bacterial expression systems, proteolutions now has a proven track record of successfully applied gene optimization, outperforming current protocols by

1. black-and-white results, i.e. rescuing failed expression approaches,

2. markedly increased expression yields up to a factor of 35,

3. increasing the fraction of well-folded and functional protein.

proteolutions is a biotechnology / bioinformatics service provider synergizing the expertise of a biochemist and bioinformatician with twenty years of protein expression experience, a biophysicist yeast geneticist and RNA expert with 35 years of recombinant protein expression and project management experience, a physicist bringing in statistical and informatic knowledge and a software architect deploying a web-based on demand service to the users. All proteolutions co-founders are aware of the great potential for any protein expression endeavour that lies in the right choice of the optimized sequence.

At the moment, proteolutions is specialized in computational codon sequence optimization. We do not offer any laboratory services at this time.

First click on the New Projects link at the top of the screen. This will take you to your New Projects page which provides an overview of all your planned optimization projects. A project can contain one or multiple gene optimization tasks. To add a new project, simply click on the New Project button. If you have already created projects, you can choose to Open them and continue to edit them or Remove them from the list.

If you have selected New Project, this takes you first to the Optimization Information dialog. Here you can provide an informative name for your new project and add detailed notes for your own purposes to it. Once you are done, click on Optimizations > to start adding Optimization tasks to your new project.

Next, on the Project Optimizations page you have the options to either create a New Optimization or Edit or Remove previously created ones.

Creating an Opimization task is a guided process which offers the possibility to model your own sequence parameters for processing by the proteolutions algorithm. Once your are done, click Create and your optimization is added to your project. Proceed the same way to add and edit more optimizations to your project as desired. When you are ready to commence your order, select the Billing > button in your Project Optimizations page.

Note that at this point you need to log in to your proteolutions account if you haven't already. Creating projects and designing optimization tasks requires no login but for us to process your order we need a valid account. If you have no account, creating one is simple and completely free of charge. Your data remains with proteolutionsonly and will not be shared with any other party.

On the Project Billing page you are asked to optionally provide a purchase order number for your internal accounting reference, choose a billing address to deliver your results to and select the payment method you prefer. When the required information is provided, it becomes possible to proceed to the Checkout page of your project.

The Checkout view allows to review your order in detail. After acceptance of all terms and clicking Continue, the sequence transfer agreement (STA) for your order is shown and needs to be accepted to commission your project.

If you are elegible for and have selected payments by invoice, your processing starts immediately and you are taken to the Commisioned Projects view. For other payment methods, you are forwarded to our payment provider Mollie to finish the purchase.

Note that for payment methods bank transfer and direct debit the processing of your sequences will start once the payment has been registered on the proteolutions side, if you choose to pay via credit card or PayPal your optimizations are immediately starting to process.

As soon as sequence optimization is complete, you will be able to download the optimized sequence in the FASTA format. Additionally, the processing result will be sent to you conveniently by email.

Several factors prolong the processing time of your sequence such as growing length of the sequence and higher usage of place holders and exclusion sequences.

Normally, processing a medium sized sequence is expected to take less than one day but we reserve a maximum of 14 days for processing your requests.

The Library lets you manage individual and reusable processing settings via the Exclusion and Exclusion Set pages. More details are available on the respective pages under Library.

The Commissioned Projects section, displaying the counts for Pending, Processing, and Done projects, is available to logged-in users.

It provides a quick overview of

• Pending projects which await payment

• Processing projects which are paid for and are currently being processed

• Completed projects which have been successfully finished processing

The proteolutions codon optimization service was built using an API-first approach. Hence an API to the proteolutions services exists and is utilized in the background of the webservices.

Currently we are evaluating the possibility to make the API publicly available.

If you are interested in using our API, please contact us directly via email at inquiries@proteolutions.com.

Please send your questions to inquiries@proteolutions.com. Thank You.