ABACUS2: Protein Sequence Design


To design amino acid sequences that are intended to fold into a user-provided backbone structure. This is achieved by optimizing the ABACUS (A Backbone-based Amino aCid Usage Survey) statistical energy function with respect to the sequence.

For detailed descriptions of the method, please read the references.

If you only need to score the compatibility between an existing sequence and a backbone structure using the ABACUS model, you may use the ABACUS Score service.


* indicates required fields

*
i A file containing atomic coordinates of the target backbone in PDB format. The residue types in this file will be ignored unless the sequence-identity-with-input restraint is requested. Please make sure that the residue ID fields contain only integers (no character contents such as those indicating inserted positions).

Number of sequences to be designed :

* (allowed value: 1 to 100)
i Different designed sequences will be obtained by optimizing different random initial sequence s.

Restrain the sequence identity between designed sequences to be around:

(allowed value: 0.5 to 0.9)
i An extra sequence restraining energy term will be applied.

Restrain the identity of designed sequences with input PDB sequence to be around:

(allowed value: 0 to 1)
i An extra sequence restraining energy term will be applied.

If you would like to restrict the allowed residue types at some backbone positions, define position-specific residue type sets here:

Job Name:
i You can use this name to distinguish between different requests.

Your Email:

i An email will be sent to this address after finishing the job.


After submission, the calculation will be carried out on our servers. You will be navigated to a page waiting for it to finish. That page will be automatically updated with downloadable results after the calculation is finished.

If you have any problem or suggestion, please contact <hb080@mail.ustc.edu.cn>.




References:

  • Xiong P, Wang M, et al. Protein design with a comprehensive statistical energy function and boosted by experimental selection for foldability[J]. Nature communications, 2014, 5: 5330.
  • Xiong P, et al. Increasing the Efficiency and Accuracy of the ABACUS Protein Sequence Design Method[J]. Bioinformatics, 2020, 36(1): 136-144.