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model challenge

Joint Challenges Wrap-Up Meeting Oct 6-8

In 2016 EMDataBank ran two community challenges in parallel to create awareness of the need for cryoEM structure validation as a routine process in research studies and publications, and to expedite development of quantitative tools for assessment

Model Challenge Face-to-Face Meeting

Update for the Model Challenge: A face-to-face meeting was held Monday May 29, 2017 to discuss model assessments and how to move forward with completing the challenge.  The challenge has been designed to enable assessment of current approaches to interpretation of higher resolution (3-5Å) cryoEM maps with atomic models, to critically evaluate the map interpretation, model fitting, model refinement, and validation methods that are now coming into use. Initial assessments of the 106 submissions from 16 modellers have been prepared and can be viewed at the model comparison site.  Notes from the May 29 meeting are available in the provided attachment.

Model Challenge Comparison Site

The model challenge assessment period is still in progress.  Interested to see how we the results are being assessed?  Please visit the model-compare pages at http://model-compare.emdatabank.org.  There you can view and compare the submitted models via more than a dozen different whole-model and residue level metrics, as summarized here.

Assessment Phases are Coming Soon

Following two amazing challenge submission finishes in April (66 maps!) and in June (106 models!), we have been working with our respective committees to prepare and organize the data for blinded assessments and to perform preliminary analyses. This process has taken more time than originally anticipated, so we have been making adjustments to assessment phase timelines. For the map challenge, we plan to announce the beginning of the assessment phase in early November.  Watch this space for more details! 

Model Challenge Submission Deadline is Friday June 17

EMDataBank Challenge Modellers, Please complete your model submissions this week--the deadline is this coming Friday at 21:00 UTC. Any questions/issues please let us know (challenges@emdatabank.org). Thanks for participating!

Model Challenge: Symmetry Info Updated

The model challenge guide now holds corrected symmetry center info and BIOMT matrices for the proteasome, GroEL, and β-galactosidase targets. The changes are highlighted with red text and update date.

The previously posted symmetry info had used rounded values for the voxel sizes, yielding inprecise center coordinate and matrix element values. We apologize for the errors.

Model Challenge Submission Deadline Extended

The deadline for model challenge submissions is now changed to Friday June 17 (21:00 UTC).

We hope that this extension will be helpful to all of our challengers.

In addition, please be aware that indicated symmetry centers in the model challenge guide may not be exact. 
This issue was just raised by one participant—we are investigating and will send a further update about this soon.

Further note (4/28): symmetry issue has been resolved

Challenge Submissions Update

The following updates have been made to the challenges site this week:

  1. Model challenge submissions are now open.
  2. Challenge submissions (both map and model) now require login to the challenges site.  Emails have been sent out to all challenger registrants with their login information.
  3. Challenge news is now available via rss feed.

Announcing the 2nd EMDataBank Model Challenge

EMDataBank is pleased to announce the 2015/2016 Model Challenge.

All members of the Scientific Community--at all levels of experience--are invited to participate as Challengers, and/or as Assessors.

Benchmark targets of varying size and complexity have been selected from recently deposited 3DEM structures based on current state-of-the-art detectors and processing methods, in the resolution range 2.2-4.5 Å.

Model Challenge Workshop

The model challenge committee held a weekend workshop on June 20/21 with a selected group of cryoEM specialists and model software developers to share results and develop plans for the model challenge. The outcome of this meeting is the recommendation by this group to launch a community wide challenge to model 5-7 selected cryoEM density maps that have been reported to be determined at 3.0-4.5 Å gold-standard resolution.

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EMDataBank Validation Challenges are supported by NIH National Institute of General Medical Sciences

Please send your challenge questions, comments and feedback to challenges@emdatabank.org

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