DNA Origami Structure Prediction | The Aksimentiev Group

This service performs a series of brief coarse-grained simulations of a DNA origami object, first at low resolution to produce rapid relaxation of a structure, then at high-resolution to enable mapping to an atomistic structure. A typical simulation will require about 1 hour of runtime. As we have only limited resources, you may need to wait significantly longer in the queue.

Please direct any questions or issues to Chris Maffeo (cmaffeo2@illinois.edu).

Name your job (optional). *

Email the result to this address (optional).

Upload a DNA origami design .json file. Circular strands (without breaks) are not supported.

Select the scaffold sequence. *

m13mp18 (up to 7,249 bases)

Custom

Sequence file

Text file containing nucleotide sequence ('atcg' or 'ATCG'). Pound symbol (#) comments the remainder of a line. Other characters are ignored.

Additional settings

Which version of service to use. *

v0.5: 2020- (several improvements)

v0.4: 2019-2020 (many improvements)

v0.1: 2016-2019

Omit bonds longer than this many nanometers during first simulation step. This option can help relax closed objects. *

All connections drawn between helices are interpretted as crossovers by default. Attempts to convert all crossovers further than this distance (in nm) into an "intrahelical" connection to give a continuous backbone. This option can be used to give a more realistic structure for some closed objects. A negative value is simply ignored.

dsDNA persistence length (nm) *

dsDNA twist persistence length (nm) *

dsDNA helical rise (Angstrom) *

To obtain statistics for our funding agencies, this service collects and stores your IP address, an approximate location derived from the IP address and a timestamp each time a job is submitted. Your email address, if provided, is not associated with other data collected and is deleted from the server once the job completes and an email is sent. Please contact Chris Maffeo (cmaffeo2@illinois.edu) with questions, concerns or requests regarding privacy.