Changelog

2.0.4.1 (20-03-2024)

Added

Changed

Fixed

Selection tool gives an error using the generic numbering nomenclature.
Step 3 of the submission form not showing the sdf image of the molecule, mainly basic ions like Calcium, Sodium and Water, among others.

Added

New policy on the pre-submission, point 4 to avoid incomplete submissions: “Step 5 on references can be completed after publication. Please submit the full citation with the DOI once available. Failure to do so may result in automatic closure of the submission without reference completion.”
Update of the submission table style to facilitate the user to take a look into their previous submissions.
Search tool filters can accept regular expressions to filter the data RegEx (e.g. State > Active or Inactive > ^Active, ^ means startswith, in this case only get active results).

Changed

Change of the max upload file size accepted for the server in order to incorporate bigger systems.
Users do not need to use the submission protection key to acces into his submissions if they are the owners. To share with other people you need to continue sharing with them the dynamic id and the submission key.

Fixed

Error with whitespaces on the field of uniprotkbac at the submission form step3.
Emails to notify maintenance blocked by Gmail and not reaching the users.
Error with distance and rmsd tool with new data (not working).
Data login request when the user try to download files of published submissions.

Added

New function on GPCRmd API to get information about the compounds elements simulated in GPCRmd grouped by type.

Changed

Fixed

Added

New topology file format accepted: .cms.
New batch of published simulations from January 2023 to October 2023.
New graph on the statistics homepage section about the accumulated time of simulation in GPCRmd, grouped by GPCRmd community or individual contributions.
New two functions on GPCRmd API to get all the dynamics id by class or by ligand type (Apoform / Complex).
New filtering mode by field using text and download modes to get the data filtered on the search tool.

Changed

Limited the delta values from 0 to 20 nanoseconds in the step 1 of the submission form due to confusions on the units.
New style of graphs on the statistics section at the homepage.

Fixed

Error access to the summary of a submission using the button “See summary” in the submission list.
Bug on meta-analysis tool NGL viewers that not showing the structure correctly.
Error numbering on generic number association with structures with fusion protein in the middle of the pdb (like 5TVN).

Added

Publication page link in the reference section of the simulation report (e.g. https://gpcrmd.org/dynadb/dynamics/id/90/).
API can accept multiple inputs.
Documentation menu button with detailed information for the users related with GPCRmd.

Changed

Fixed

Pockets tool bug not showing data in the table if the user access from the selection tool.
Description empties on the submission forms cause an error before the step 5 in the submission summary.
Minor bugs.

Added

Search tool selector with a dynamic table to select a specific dynamic.
New front-end style of the web.
New GPCRmd API.
Instructions to follow before start the submission process as pre-submission step.
Option on step 4 to upload the simulation protocol in the submission form.
Option on step 5 to retrieve the information of the article using the DOI.
Guide to create and manage the GPCRmd account Link.
Step-by-step guide to submit a submission into GPCRmd Link.
Secret key account parameter for the non-published simulations to give the option to share them using the link and this key.
Trr trajectory file format added to replace the trj format.
GitHub community of GPCRmd (https://github.com/GPCRmd) if some users wants to collaborate.

Changed

Fixed

Removed