1. What is Pinecone?

Pinecone is Serotiny’s web-based software that helps you design novel protein constructs from verified functional protein domains. You can upload your own proteins by importing the sequence for the for their functional domains. You can also browse through Popular verified proteins, or search those that have been published as Public Proteins.

Once you source the domains you’ll need, design your new protein construct by dragging domains to your protein’s domain table, arranging them in the correct order - between the N and C terminus. When your design is complete, add it to your cart and submit your design for production - we’ll help you order your design in the deliverable you need, from a supplier of your choice.

2. Will my protein work?

There is no certainty that any given protein construct design will function as intended, especially when the design is novel. Pinecone helps reduce risk in protein design by showing you how other scientists have used particular protein domains, but it does not predict protein folding, or otherwise algorithmically predict protein function.

There are many factors that determine what properties a specific protein design will have when it is expressed.

3. What are verified proteins?

A verified protein domain is an amino acid sequence which has an articulable function cited in a published work. Popular Proteins are verified.

4. Can I see the sequence?

Yes. You can view the amino acid sequence for a protein. If you’re designing a cassette that includes non-coding regions, you can also view their DNA sequence. After you’ve place an order, you will receive a report with sequence details of your construct design.

5. What sequences should I import?

Pinecone enables rapid design of proteins by focusing on the protein domain, or basic functional unit. To make the best use of Pinecone, import a basic protein domain separately, and curate it with a function. Importing and curating each domain of a protein construct individually enables you to quickly make high-level design decisions and keep track of large construct function.

Additionally, you can design a cassette - a genetic construct that includes both proteins (coding regions) and non-coding regions such as promoters, terminators, etc. You can upload your own non-coding regions as DNA sequences by selecting the ‘non-coding’ tab during import. This will ensure your sequence imports as DNA and does not translate into amino acids.

6. Are sequences in-frame?

Yes. Sequences pulled from Public Proteins and Popular Proteins are all in-frame. Additionally, Pinecone will not let you import an out-of-frame protein sequence.

7. Do sequences have start/stop codons?

Sequences pulled from Public Proteins and Popular Proteins are all free of stop codons. If you need start/stop codons in your construct, you will be able to add them at the order menu. When you import new sequences Pinecone will automatically remove stop codons from sequences you upload, but it is best practice to upload stop codon-free sequences. Because it is sometimes difficult to establish whether a Methionine functions as a start codon or whether it is part of the coding sequence for a protein, some sequences may have a start codon. If you are uncertain, you can view the sequence to confirm.

When designing a cassette containing both coding and and non-coding regions, each coding region, by definition, will automatically contain a start/stop codon. You should avoid using the cassette designer to create protein fusions, because each coding region incorporated into your cassette will contain a start/stop codon. Rather, if you are building a protein fusion use the protein designer, and then incorporate that fusion into your cassette.

8. Where can I order from?

Because every supplier has a different expertise Serotiny will propose the cheapest supplier capable of fulfilling your specific order. Currently we can fulfill orders for Genscript, IDT, and Twist but please let us know if there’s another supplier you’d like to order from.

9. What deliverables can I order?

Currently, suppliers can deliver dsDNA, plasmid DNA (cloning vectors, expression vectors or a custom vector provided by you) and purified protein. Depending on your deliverable requirements, we will match you with an appropriate supplier. In addition to a report from Serotiny detailing your designs and their sequences, suppliers will provide you with sequence details for the delivered product.

10. How much DNA do I get?

Typically, suppliers deliver to you about 4 micrograms of lyophilized DNA. This mostly depends on the particular supplier. If you need more, let us know.

11. How do I make an order?

After you select your deliverable details, Pinecone will automatically calculate an estimate of the supplier’s price to produce your design. While Pinecone is in Beta we will confirm your order details with you before accepting payment or submitting your order to the supplier. Once your order details are confirmed Serotiny will accept payment for both it and the supplier, and communicate your order details to the supplier for production.

Serotiny recognizes that many of its customers have pre-established relationships with suppliers. Just let us know and we’ll make sure your particular payment arrangement or discount is used.

12. How much does Serotiny charge?

Serotiny’s software, Pinecone, is free to use. When you order your constructs for production, Serotiny charges you a fee based on the dollar value of your order from the supplier. Serotiny’s fee is of 15% of the supplier’s price to produce your design.

13. What methods of payment?

Serotiny currently accepts both credit card and purchase order.

14. Can I publish my proteins?

Yes. When you upload a new sequence to Pinecone you will have the option to choose from two levels of privacy for your new protein and its curation:

Private - only you will have access to this protein. Select ‘Private’ if you do not want other users to have access to your protein.

Public - other Pinecone users will have access. After selecting ‘Public’, you will have the chance to confirm.

After designing a new construct, you can also click ‘Make this protein Publicly Accessible’. Once public, other Pinecone users will be able to view and incorporate your published protein into their own designs. By publishing your proteins, you can distribute your designs and knowledge, and receive credit for your work.

We understand that not everyone is in a position to publish their work in Pinecone; when you keep your proteins private, they are not accessible by other users.

15. Can I keep my proteins private?

Yes. When you upload a new sequence to Pinecone you will have the option to choose from two levels of privacy for your new protein and its curation:

Private - only you will have access to this protein. Select ‘Private’ if you do not want other users to have access to your protein.

Public - other Pinecone users will have access. After selecting ‘Public’, you will have the chance to confirm.

If you have particularly sensitive data, let us know. We can help create the right protein design infrastructure for your needs.

16. Who has access to my data?

When you select ‘Private’ while uploading a sequence, the sequence and curation details are accessible by only you and Serotiny. Of course, when you place an order for manufacture, Serotiny must communicate sequence details to the manufacturer.

17. Can I use my own sequences?

Yes. Go to Import>From a Sequence. You can import your own sequences, either DNA or Amino Acid, through our import function. Importing a sequence makes a protein domain that you can incorporate into a larger protein construct. You can also import sequences from databases such as Uniprot by clicking Import>From a Database.

18. Can I use non-coding sequences?

Yes. Use the cassette designer to design a genetic construct containing both coding and non-coding regions. If you have more specific requirements, let us know.

19. Can I mutate a protein?

Yes. Go to Design>Mutation Set to mutate your protein of interest. You will create a mutation instruction to generate your desired mutant or set of mutants. After creating your mutation, you can either add particular mutants to your library or you can order your entire mutant set for production.

20. What if published data is incorrect?

Let us know. Serotiny will consult with the original author and publication to reconcile the inaccuracy.

21. What is the turnaround from suppliers?

Turnaround time depends on the supplier, base-pair count, and complexity of your order. Currently, turnaround for dsDNA ranges from 2-8 days. Plasmid DNA ranges from 8-20 days.

22. How can I contact Serotiny?

Contact us at info@serotiny.bio