The EM2NA Web Server is an automatic de novo nucleic-acid structure determination web server for near-atomic-resolution cryo-EM maps using a deep learning-based framework. Users are required to provide an EM density map in MRC2014 format with optional nucleic-acid sequences in FASTA format. EM2NA supports modeling from NA-only, protein-NA complex, single-chain or multi-chain cryo-EM maps. If you have any question or suggestion about EM2NA Web Server, don't hesitate to contact us at the first time.
The maximum size of the upload MRC file is limited to 500 Mb. After the user-specified EM density map is uploaded, NGL Viewer is used to display the input EM density map, where users can adjust the contour level.
The nucleic acid sequences are optional for EM2NA. Users can upload their sequence(s) file in FASTA format or simply paste the sequence(s) into the box. By either way the input sequence(s) will be displayed in the box. If you have multiple sequences, they should be written in one .fasta file. The input sequence(s) should only contain A/G/C/U/T (upper cases), and other characters are NOT supported.
Users can modify their EM2NA job by changing the advanced settings:
Nucleic acid type is used to specify the target nucleic acid type.
By default, "AUTO" is used and EM2NA automatically determine the type
according to the input sequence and/or modeled structure.
"RNA" stands for the RNA struture and
"DNA" is for the DNA structure.
If your map contains both DNA and RNA, just use the default "AUTO" mode.
Running mode is used to control the EM2NA running style.
By default, the "Normal speed" mode is used.
"Fast speed" will have a shorter running time at some expense of accuracy
by setting a larger density map chunking stride during modeling.
Users can provide their email address to the EM2NA server. Once the submitted job is finished, the users will be notified by a reminder email. The name of submitted jobs can also be specified by users.
After clicking the Start EM2NA button, the job will be submitted to the server. Since the EM map file often have a large size, the job submission may take sometime. After the job is successfully submitted, the page will be redirected to the job status page. At this time, users may bookmark the page and access the results at a later time. The job status page will automatically refresh every 10s to show the job runing process. There are two job statuses for a successful submission, PENDING or RUNNING. A PENDING job means that it has been successfully submitted to the job system and temporarily waiting for resources. If the web server is down for regular maintenance, the submitted job will also be in PENDING status and the job will be scheduled to run once the server is up. A RUNNING job means that it has be allocated computing resources and is running on the server. After the job is finished, the job status page will turn to job result page. If users provided a valid email address, they may also receive an email notifying the job completion.
After an EM2NA job is completed, the EM2NA Web Server provides users a web interface to interactively view the built structure models via NGL Viewer. The average local confidence score of the built EM2NA model is listed in the table. The EM2NA server provides multiple results for download: all-atom models and predicted probability maps.