Changelog

Latest updates, features, and enhancements to the EM Web Server.

v10.12.0 May 27th, 2026
  • Released Emap2lig: a deep-learning-based computational tool designed to automatically predict ligand densities in cryo-EM maps and model small-molecule ligands directly into those predicted densities.
v10.11.0 May 11th, 2026
  • You can now paste or type sequences directly into the fasta field; no file required.
v10.10.0 April 20th, 2026
  • We’ve introduced a "Like" system, allowing authenticated users to thumbs-up public jobs. We also added public/private visibility settings; currently, only developer jobs can be set to public. Explore and like public jobs!
v10.9.0 March 31st, 2026
  • CryoZeta large complex cycle mode: Now CryoZeta can handle larger complexes with the cycle mode. This mode makes it possible to model as long as the longest chain is less than 2700.
v10.8.0 March 26th, 2026
  • Released DMcloudComplex: A macromolecular structure modeling tool using point cloud matching with diffusion model and 3D U-net (CryoREAD) for cryo-EM maps at 3-10Å resolution.
v10.7.1 March 17th, 2026
  • Updated CryoZeta: The code was optimized so that it can handle larger inputs.
v10.7.0 February 17th, 2026
  • Released CryoZeta: A new tool for Cryo-EM complex modeling supporting up to 10 Å resolution.
v10.6.1 February 15th, 2026
  • Upgraded map visualization and contour level setting for job submission.
v10.6.0 December 18th, 2025
  • A new note section is now available on the 'View Job' page via the Notes tab. In the 'Job Manager', you can quickly preview notes by hovering over any job entry.
v10.5.4 September 21st, 2025
  • Updated example results for DAQ-Refine.
v10.5.3 September 5th, 2025
  • Updated DiffModeler's input parsing logic. Now it can handle mix of PDB/CIF files.
v10.5.2 August 22nd, 2025
  • The DiffModeler computation was migrated to a more powerful cluster for better throughput.
v10.5.1 August 14th, 2025
  • Added email field in the review request section. This allows a better communication with the users and developer team.
v10.5.0 June 9th, 2025
  • No need to provide zip files and config files for the DiffModeler anymore! Now users can simply upload single chain pdb files and the number of copies.
v10.4.1 May 27th, 2025
  • DiffModeler's cif output is now compatible with the Biopython parser.
v10.4.0 May 20th, 2025
  • DeepMainMast Fastmode is now available. Fast mode performs fitting using DMcloud protocol and fill the loops using DeepMainmast. It does not include rosetta, and output is two full-atom structures without Ca only models.
  • Users now can filter the jobs by the job-id. Direct search for the exact job-id is also available.
v10.3.1 March 20th, 2025
  • Added Youtube Tutorial for DAQ-Score. Available in the Job Submission page and the Tutorial page.
  • DiffModeler cif output now can be used with Coot.
v10.3.0 February 24th, 2025
  • DMcloud, a macromolecular structure modeling tool using point cloud matching with diffusion model, is now available!
v10.2.2 February 3rd, 2025
  • Users can download enhanced map from DiffModeler and DiffModeler(seq)
v10.2.1 January 22nd, 2025
  • Emap2sec+ now outputs a .pml file and the .pdb file. You can now open the .pml file directly to analyze the results in PyMol.
  • Added Youtube Tutorial for DiffModeler. Available in the Job Submission page and the Tutorial page.
v10.2.0 November 25th, 2024
  • Improved map rendering speed for most methods.
  • Added descriptions for the DAQ-finder.
  • Added a check in DeepMainMast to verify that AF2 sequences match the FASTA file.
v10.1.0 November 14th, 2024
  • The webpage now checks the format of FASTA files.
v10.0.1 November 1st, 2024
  • Added YouTube tutorial for CryoREAD
  • Youtube tutorial is available in the Tutorial section and in the Job Submission page for CryoREAD
v10.0.0 October 29th, 2024
  • DAQFinder now has the option to search for sequence in UniProt. It also supports to search on PDB95 or user input FASTA file.
  • DiffModeler(seq) now filters out DNA sequences.
v9.0.0 August 21st, 2024
  • Added a YouTube video for the EM server tutorial.
v8.0.0 August 6th, 2024
  • Added ability to visualize input map with the inputted contour level. The contour level can be changed dynamically to choose the best one. This feature is added for: DeepMainmast, CryoREAD, ComplexModeler, Emap2sec, Emap2sec+, Mainmast, DiffModeler and DiffModeler(seq).
v7.5.0 August 5th, 2024
  • Added comprehensive/clear status to all future jobs.
  • Statuses currently present: "Queued", "Running", "Failed", "Success". Followed by a reviewer message if it is present.
v7.0.0 June 26th, 2024
  • Implemented mobile responsiveness. The whole website can be accessed and used through the user's mobile.
v6.0.0 May 9th, 2024
  • New DAQFinder algorithm for finding unknown proteins in your molecular map.
  • Complete Redesign of EMServer.
  • Better looking and clearer homepage, contact page, view job page and navigation bar.
v5.0.0 April 28th, 2024
  • CryoREAD (a de novo DNA/RNA structure modeling tool) can now handle maps up to 10 Å resolution.
  • CryoREAD was originally developed for modeling for maps up to 5 Å resolution, but now we upgraded the neural network to better predict nucleotides up to 10 Å.
v4.0.5 March 28th, 2024
  • Tutorials for Main Algorithms added. They can be accessed by clicking the "Tutorial" button on the navigation bar.
  • The tutorial outlines the workflow of the algorithm, input/output files, job submission and information on submitting for review.
v4.0.0 December 13th, 2023
  • Overall web design updated.
  • Added Instructions, How To Interpret and RoadMap (table outlining all of our algorithms). The instructions can be viewed for each algorithm at the job submission page.
  • You can also view the instructions at the job viewing page. The instructions mainly outline how to interpret.
v3.5.0 November 11th, 2023
  • Users no longer have to be logged in to submit a job.
  • The job they submitted will be remembered once they register.
  • We still highly recommend registering for notifications and easy access.
v3.0.0 October 26th, 2023
  • Update to the overall design of the webserver.
  • Mostly visual changes to the home page and tutorial page.
v2.5.0 October 24th, 2023
  • The contour level can now be changed for maps from the side panel. From the View Job page click the ellipsis ("...") to the right of "Isosurface" within the volume section.Subsequently, click the ellipsis ("...") next to "Type" within the isosurface settings. Finally, adjust the iso-value to the appropriate values to visualize the map online.
v2.0.0 August 22nd, 2023
  • Maps can now be visualized for all Algorithms by clicking the "View Map" button on the top right of the viewer.
  • Clicking the same button again will hide the map.
v1.0.0 June 26th, 2023
  • Initial Release and Deployment.