¶ Version 1.10.3
¶ Added functionality
- A new option is now available to visually differentiate between experimental and predicted structures: if enabled on the 3decision environement, predicted structures are now highlighted in red on the search result page.
- Image files (e.g. png) associated to structures can now be displayed directly in your web Browser (opens in new tab).
- The limit for the number of structures that can be downloaded as a CSV or XLSX file has been increased to 1000 (previously 400).
¶ API updates [BREAKING CHANGES] 
- The
POST /exports/structureendpoint has been split into two separate endpoints to address performance issues and enhance the user experience:POST /exports/structure-table: allows the user to download structures as acsvorxlsxfile. This endpoint is synchronous and provides a direct response.POST /exports/structure: allows the user to download structures in thePDBorcifformat. This endpoint is asynchronous and will return a job ID (not a JSON like before).
GET domain-events/{jobID}is now the recommended endpoint to retrieve the status of an asynchronous structure export job.- The endpoint
GET /exports/structurethat returns the exported structure file has been renamed toGET /exports/structure/{jobID}
Example scripts for the export of a structure in the PDB-txt format, before and after the breaking changes
1) Request structure export
¶ Breaking Change in the Request
curl -X 'POST' \
-'https://3decision-api.discngine.cloud/exports/structure?output_format=structures-pdb-txt&filename=3decision_exported_structures&download=true' \
+'https://3decision-api.discngine.cloud/exports/structure?output_format=structures-pdb-txt'
¶ Response Body Before:
{
"state": "processing",
"statusEndpoint": "/exports/structure?filename=3decision_exported_structures&download=true&jobId=38ba9733-24c7-47dd-a048-a24cb1008007",
"content": null,
"jobId": "38ba9733-24c7-47dd-a048-a24cb1008007"
}
¶ Response Body After:
e43a1980-a3ae-4e85-b1ed-6c7a6bc460c5
2) Request to get status of async export job
¶ Breaking Change in the Request
curl -X 'GET' \
-'https://3decision-api.discngine.cloud/exports/structure?jobId=81b9aa92-6862-4521-bc5b-6becae9195a4&filename=my_file&download=true' \
+'https://3decision-api.discngine.cloud/domain-events/46ac86a7-d93c-4108-9b20-7e464e12b46a' \
¶ Response Body Before
{
"state": "processing",
"statusEndpoint": "/exports/structure?filename=3dec_5dls&download=true&jobId=81b9aa92-6862-4521-bc5b-6becae9195a4",
"content": {
"stream": null
},
"jobId": "81b9aa92-6862-4521-bc5b-6becae9195a4"
}
or
{
"state":"success",
"statusEndpoint":"/exports/structure?filename=my_file&download=true&jobId=81b9aa92-6862-4521-bc5b-6becae9195a4",
"content":{
"errors":{ "not_transformed":[], "not_exported":[] },
"stream":[ "type":"Buffer", "data":[72,69,65,68,69,82,32,32,32,32,84,82,65,78,83,70,69,82,65,83,69,32,32,32,32,32,32,32,32,32,32,32,32...]}
},
"jobId":"81b9aa92-6862-4521-bc5b-6becae9195a4"
}
¶ Response Body After
{
"state": "processing",
"content": null,
"domainEventType": "structureExport",
"id": "46ac86a7-d93c-4108-9b20-7e464e12b46a"
}
or
{
"state": "success",
"content": {
"file_path": "//privatedata/tmp/tmpml01yzy8/3dec_exported_structures.zip",
"file_names": [
{
"external_code": "5dls",
"file_name": "3dec_5dls.pdb"
}
],
"errors": {
"not_transformed": [],
"not_exported": []
}
},
"domainEventType": "structureExport",
"id": "46ac86a7-d93c-4108-9b20-7e464e12b46a"
}
3) Download the file
¶ Breaking Change in the Request
curl -X 'GET' \
-'https://3decision-api.discngine.cloud/exports/structure?jobId=81b9aa92-6862-4521-bc5b-6becae9195a4&filename=my_file&download=true' \
+'https://3decision-api.discngine.cloud/exports/structure/46ac86a7-d93c-4108-9b20-7e464e12b46a?filename=structures&download=true' \
¶ Response Body Before
{
"state":"success",
"statusEndpoint":"/exports/structure?filename=my_file&download=true&jobId=81b9aa92-6862-4521-bc5b-6becae9195a4",
"content":{
"errors":{ "not_transformed":[], "not_exported":[] },
"stream":[ "type":"Buffer", "data":[72,69,65,68,69,82,32,32,32,32,84,82,65,78,83,70,69,82,65,83,69,32,32,32,32,32,32,32,32,32,32,32,32...]}
},
"jobId":"81b9aa92-6862-4521-bc5b-6becae9195a4"
}
¶ Response Body After
"HEADER TRANSFERASE 07-SEP-15 5DLS \nTITLE IDENTIFICATION OF NOVEL, IN VIVO ACTIVE CHK1 INHIBITORS UTILIZING \nTITLE 2 STRUCTURE GUIDED DRUG DESIGN..."
¶ Bug fixes
- Electron density maps of public structures can now be correctly fetched and displayed again.
- Direct links to the 3decision Workspace now loads the correct pocket number, if present in the URL, and no longer resets it to the default pocket.
- The download of superposed structures coming from a pocket similarity or interaction search now works correctly.
- The endpoint
/structures/info/biomoleculenow returns the NCBI Taxonomy ID underORGANISM_ID(and not the internal organism id). This update is available in version 2 of the endpoint. - The endpoint
/annotations/ligandsnow filters correctly on thesmall_mol_id. - The endpoint
/structures/delete/status/{jobID}now returns the deletion status. - The endpoint
/structures/file/{structure_id}now works correctly on the Swagger documentation page. - In addition, a series of security patches were implemented
¶ Version 1.10.2
¶ Bug fixes
- Structure files with dot(s) in their filename can now be registered again.
- Ligands with residue codes containing an underscore are now correctly parsed and registered.
- When an authentication error occurs, a
401status code is now returned by the API endpoint, instead of500internal error. - The performance issues for pocket similarity searches with over 1000 hits have now been fixed.
¶ Version 1.10.1
¶ Bug fixes
- PDB files that are missing the sequence database identification code in the DBREF section can now be registered and downloaded correctly.
¶ Version 1.10.0
¶ Added functionality
- Support of the PDBx/mmCIF format (referred to as the 'cif' format here below):
- structures in the cif format can now be registered, analyzed and displayed in 3decision (current limit: max 100 000 atoms)
- an enriched cif file is now created whan a structure is registered or updated
- all structures are available for download in the following formats:
- the original structure file
- the enriched cif file format
- the PDB file format (if the structure is compatible with PDB standards)
- Improved display of structure parameters in the Structure Information Panel:
- the structures parameters are now displayed in a new tab called METHODS
- the structure parameters are now categorized and displayed in dedicated sections in order to give a comprehensive overview of the experimental (or modeling) details behind the resolved structure. Both PDBx/mmCIF and ModelCIF categories are parsed.
- Improved RCSB PDB synchronization:
- structures distributed in the PDBx/mmCIF format only are now registered.
- the service now consistently checks and reruns structure updates that failed in previous weekly synchronizations.
- Associated files can now be uploaded in the following formats:
.rtf,.png,.jpg,.logand.fasta.
¶ API updates
- The usage rate limit of an endpoint is now clearly indicated in the API documentation (Swagger) when it differs from the default rate limit. More details on the API endpoints available here
- The default rate limit for 3decision API endpoints has been reduced to 250 calls per minute.
- The API endpoint
POST /structure-files/validationnow validates files in the cif format. - The API endpoints
POST /projects/{project_id}/emailandDELETE /projects/{project_id}/emailare now deprecated. They will be replaced by thePOST /projects/{project_id}/usersandDELETE /projects/{project_id}/usersendpoints in release 1.11. - The deprecated API endpoint
GET /users/{username}/idhas now been removed from the API. - The deprecated API endpoint
POST /exports/pdbhas now been removed from the API. It is replaced by the endpointPOST exports/structure.
¶ Bug fixes
Structure registration:
- The registration of a structure having a ligand with no related chain now returns an informative error.
- Ligand structures having alternate conformations for specific atoms are now correctly processed.
- TIP residues are now considered as water molecules and not as ligands.
- Negative residue range in the chain mapping is now correctly managed by the structure registration page.
Structure files validation:
- Structure file validation endpoint now returns an error in case of missing chain IDs in the input PDB file.
- Structure file validation endpoint now detects duplicated atom names in PDB files.
- Structure file validation endpoint now raises a warning if input PDB file have lines with less than 80 characters.
Interaction detection:
- The interaction detection was enhanced for specific atoms (e.g. Aluminium).
- Already existing interaction detection data is now deleted before registration of new interactions.
Sequence mapping analysis:
- The analysis now merges consecutive undefined mappings (PRO mappings) to avoid the creation of unnecessary PRO biolmol codes.
- The analysis now fully maps the entire sequence, even if the definition (structure file header or sequence mapping payload) only contains the beginning or ending residue number.
- The analysis now works correctly for structures where the start or end residue happens to be unmodeled in the structure.
- If the start or end residue of the sequence mapping contains an insertion code, the analysis now requires the insertion code to be defined in dedicated PDB or cif fields, i.e. insertBegin/insertEnd, or _pdbx_seq_align_beg_ins_code/pdbx_seq_align_end_ins_code, respectively.
- The sequence mapping attribution for undefined short mappings delimited by a sequence gap of more than 10 residues has now been improved
Structure annotation:
- The automatic annotation "ligand warning : NonStandardWedgeConfiguration" has been deactivated
Download:
- The download of PDB structures is now working for collections containing more than 400 structures.
- Collections of several superposed PDB structures can now be downloaded.
Display:
- Structure files opened in a new browser tab now works correctly for PDB files.
- The display of difference Electron Density maps generated from MTZ files now works correctly for all structures
- Long ligand labels are now correctly displayed
- "Ligands" tab was renamed "Ligand from selected pocket"
Privileges:
- The email address is now used for managing privileges on projects. It is also explicitly described in the UI that the email (and not the username) is expected as input.
¶ Version 1.9.3
¶ Performance
- Database query optimization to reinforce application stability.
¶ Version 1.9.2
¶ Performance
- Improved job prioritization system: jobs triggered by the user (e.g. structure registration) are now prioritized over jobs linked to the weekly RSCB PDB structure release.
¶ API updates
- The user can now relaunch structure analyses on individual structures (both public and user structures) via these API endpoint:
/interaction-registration/pocket-detection/ligand-cavity-overlap/pocket-features
¶ Data reprocessing
- Additional experimental methods officially supported by RCSB are available now.
- Missing privileges on several public structures were corrected.
¶ Bug fixes
- Significative improvement on chain superposition.
- The following advanced search options are now exact match searches: Any annotation, Structure annotation, Sequence annotation, Structure residue annotation, Ligand annotation, Ligand ID.
- When exporting a PDB file from the UI, the original PDB file is downloaded. The endpoints
/exports/pdband/exports/structurenow allow the user to choose to export the original pdb file or the modified pdb file (CONECT RECORD are adapted to allow the visualisation in 3decision 3D Viewer). - When downloading ligand (sdf) from the Project Overview, the internal_ID is now displayed in the downloaded file.
- In the Interaction Search panel, the "center view" button now properly centers and zooms the 3D Viewer on the selected interaction.
- The email address is now used for privileges management on user groups. It is also explicitly described in the UI that the email (and not the username) is expected as input.
- The API endpoint
/structure-registrationnow accepts an empty chain array. - The API endpoint
/sequence-mappingnow accepts an empty chain array for user structures. - The API endpoint
/structures/metadatanow returns the proper STRUCTURE_ID information. - The error message pop-up "Failed to retrieve privileges on structure" is no longer triggered when there is no error.
- The PRO_ biomol codes are now centered in the Information Panel's Chain table.
- Special characters are now escaped in the filename of downloaded structure and ligand files (API endpoints
/export).
¶ Version 1.9.1
¶ Bug fix
- In the UI, the file upload of the structure registration now successfully load large files without blocking the structure registration workflow
¶ Version 1.9.0
¶ Added functionality
- Structure Registration from the UI
- Advanced search options in the UI were renamed for clarification
¶ API updates
- The API endpoint 'POST /exports/pdb' is now deprecated. It will be replaced by the 'POST /exports/structure' in the release 1.10
¶ Bug fixes
- When trying to add a structure to a project where it already exists, a clear message will now be displayed
- Calling endpoint
/structure-status/{external_code}on more than 700 structures does not reboot the API anymore /structures/codesAPI endpoint does not return duplicates anymore for structures with several states- In the UI, it is now possible to create projects and groups containing commas in their name
- Structures with non-Uniprot (customed) sequences no longer link to the Uniprot
/projects/<id>/usersendpoint now returns an error with 404 if user does not have access to the project- Download button from the top menu bar now successfully download files
- It is now possible to add a description of an attached file via the
/structures/fileendpoint - When trying to add a structure in the workspace from code (using the button "+ ADD STRUCTURES") and the code does not exist, an error message is displayed
- Structures 8FRL, 8FRM, 8FRN, 8FRO, 8UFG and 8UFH are correctly displayed in the 3D Viewer
- If you get an error opening AF Registration page, and indication of the error is reported and you are directed back to homepage
- Structures without identified BIOMOL can be filtered in search results
- Download structures to CSV now successfully export CSV file even if one of the structures does not have chain mapping
- The structure tab now opens by default in the workspace (not the ligand tab)
- Sequence mapping now works also for structures where computed implicit sequence mapping overlaps with explicit mapping defined in the DBREF section around small sequence gaps (less than 10 residues)
¶ Version 1.8.2
¶ Performance:
- Improved memory management
¶ Version 1.8.1
This version adds the following bugfixes:
- Structures with non conventional filepaths are now included in large-scale structure reprocessing.
- Structures with a success status for the triggered analysis are now included in large-scale structure reprocessing.
- The memory consumption for structure statuses has been reduced.
¶ Version 1.8
¶ Added functionality
- New public API endpoint for PDB Structure File validation (compliance with 3decision registration) (API endpoint description here)
- All AlphaFold Database models for the human proteome are now available in the 3decision database (feature description here)
- In addition to the preregistered human proteome, additional AlphaFoldDB models can now be registered via the user interface (feature description here) and/or from the public API (API endpoint description here
- "My Structures" panel lists the structures by imported date
¶ Bug fixes
- Structure 'CREATED_BY' field is now filled with structure Authors when information is available in structure file (more info here)
- Error message is displayed when privileges on a structure, a project or a usergroup cannot be updated
- Maps are now successfully superposed in the workspace when structures are open from project with unchecked "superpose atomatically" option
- Project list is now properly filtered in advanced search
- Advanced search on annotations now manages query containing special characters
- All related projects (including projects with access inherited through a group) are now visible in structure information panel
- PDB 8eyo has a correct chain mapping
- The "ligands" array is no longer mandatory in the POST /structure-registration API endpoint payload
¶ Data reprocessing
- Structures without ligand in explicit pocket were reprocessed
- Reprocessing of 1nql interactions
¶ Version 1.7.1
¶ Added functionality
- New API endpoint to edit structure annotations:
PUT /structures/{structure_id}/annotations - New version (v2) of the API endpoint
GET /structuresto allow the retrievel of both public and user structures
¶ Bug fixes
- Results can now be exported to Excel even if the collection name exceeds 30 characters
- Public EM maps are now successfully retrieved with the correct isovalue
- File size limit was increased to 300 MB
- The API endpoint
GET /projects/{project_id}/usersnow returns users in the project only if the current user have "manage user“ privileges
¶ Additional updates
- The MarvinJS sketcher was upgraded to version 23.12.0
¶ Version 1.7
¶ Added functionality
- New API endpoints to edit basic metadata of structures (title, label, experimental method and resolution):
/structures/{structure_id}/metadata(Update structure metadata)/structures/metadata(Update structure metadata in batch of structures)
¶ Bug fixes
- Created date and imported date format are enhanced for better readability
- Structure label is now exposed in information browser (general section)
- In the search results page, all ligands are now well depicted.
- When a pdb file is downloaded from the results navigation page, the file has the correct .pdb extension
- The application is not blocked anymore when a file download is running
- Emails used to give user privileges on a group or on a structure is now case insensitive
- The reset project view button in the 3D viewer now resets the view correctly
- Ligand card don't show duplicates anymore in workspace ligands panel when opening private structures from profile > "my structures"
- "Remove from collection" is now effectively removing structures from target collection
- Electron density map is correctly calculated from .mtz file even when a .ccp4 file is present in the Structure Files
- After fetching electron density maps, other structures can be added in the workspace again
- Public EM map are now successfully retrieved
- The bond order of fluorobenzyl groups are now correctly displayed in the 3D-viewer
- Interaction search results now shows only the ligands sharing the interaction pattern, not all ligands of the hit structures
- Interaction search scores are still present on the ligand card when scrolling down the search results list
- Interaction search results for halogen bonds were enhanced (by fixing the halogen bonds typing)
- Interaction search queries were fixed when vectors are close to be colinear
- When superposing interaction search hits, the binding site residues of the superposed structure are now displayed
- The chemical diversity filter is now applied in the interaction search and shows only the structure with the highest score
- Bond order detection during structure registration was fixed for ligands with explicit hydrogens and missing atom charges
- During structure registration, detection of ligand with name UNL was fixed
- In sequence analysis following structure registration, unresolved short sequences do no longer induce errors in the structure sequence mapping
- Structures for which the pdb files contains dots in filename have now pockets properly detected
- The /structure/info/pocket endpoint now returns info even if the structure has pockets without ligands
- The /structures/info/annotation endpoint now returns the annotation_id
¶ Data reprocessing
- Missing public structure were registered
- Pocket detection analysis was re-launched on structures without pocket found in the database.
¶ Performance
- Memory release issue when calling synchronous endpoints was fixed
¶ Documentation
- API swagger documentation endpoints have been sorted in more intuitive categories. Some of the endpoints descriptions were enhanced for better understanding (Not all endpoints are concerned, enhancements will continue in the next releases).
¶ Version 1.6.5
¶ Bug fixes
- The
/structures/infoAPI endpoints now returns 403 when querying a structure without access privilege - The API endpoint
POST /exports/ligandnow only returns structures with access privilege when querying by small_mol_id
¶ Version 1.6.4
¶ Added functionality
- Reprocessing of protein-ligand interactions on private structures.
¶ Version 1.6.3
¶ Bug fixes
- New users are able to register in the app again (broken since version 1.6.2)
¶ Version 1.6.2
¶ Added functionality
- Additional security checks for Authentication on Azure AD B2C (more details on this link)
¶ Version 1.6.1
¶ Added functionality
- Reprocessing of protein-ligand interactions on public structures.
- Additional security checks for Authentication on Azure (more details on this link)
¶ Version 1.6
¶ Added functionality
- Interaction search (Feature description and related Tutorial)
- Electron density map display from .mtz files (Feature description)
¶ Bug fixes
- When the resolution is displayed as a postfilter, it is rounded off at a maximum of two decimals
- After filtering results, only the selected/filtered structures are open in the workspace
- The superposition of structures coming from a similarity search collection is correct
- Structures with missing structure files are now correctly deleted
- The "manage users in project" privilege now has the right description
- In the results navigation page, Table and Target view mode work for a large number of hits.
- Only users with the privilege "manage structure files" can add/delete/edit Structures files
- If you open the information button from the Parameters section of the Pocket Similarity Search menu, you are now directed to the Parameters description section in the 3decision user guide.
- When unzipping errors during PDB files export occur, the server correctly handles them and does not crash
¶ Version 1.5.1
¶ Bug fix
- Performance issues are fixed when requesting large protein families through basic or advanced search
¶ Version 1.5
¶ Added functionality
- When registering a structure in complex with ligands, the protein ligand contacts are processed and displayed in the 3D Viewer
- Ligand bond orders are well displayed in the 3D-viewer
- Uploading a file to a structure or a project is now possible from any file browsing view (Workspace and Project Dashboard)
- Project related files are now accessible directly from the Workspace
- Files tab from Structure Information Browser now displays targeted structure related files only. It includes original structure file in PDB format and a SDF containing all ligands.
- Associated files are sorted alphabetically
- Superpose a structure from the ligand panel (eye-icon enabled)
¶ Bug fixes
- Structures without proteic chains (RNA) are now displayed correctly
- The contacts detection stability has been enhanced:
- for structures containing some unsupported/unregistered entities
- for structures containing unusual atoms like Terbium
- to avoiding fails related to registration of contacts that should not be processed (now): water-water contacts, or protein-protein contacts
- by enhancing the geometrical characterization of atoms
- by detecting better water mediated interaction detection
- When adding a second structure to the workspace, protein ligand contacts are correctly retrieved and displayed
- During contact detection, the SASA calculation is now correct
- All ligands are now displayed in the LIGANDS tab in the workspace
- The user no longer gets disconnected from the application after a period of inactivity
- During the sequence analysis, unresolved short sequences are not responsible of a wrong mapping anymore
- Improved performance when scrolling large search results set opened in a workspace
- Fetching ligand annotations does not slow down the browsing of pocket comparison results anymore
- In the biomolecule tab of Information panel, the correct number of structures is now displayed
- When doing a chemistry search, the hit structures are not duplicated anymore in the search results page
- Adding a structure collection to a project from the workspace now adds the whole collection to the project (and not only a limited number of structures)
- "manage users in project" privilege now has the right description
- Improved performance of ligand file download, fixing various issues in output content
- Pocket comparison search results can now be downloaded as superposed pdb files
- Superimpositioning of close homologs of newly registered structures now works
- Superimpositioning of pocket comparison hits of newly registered structures now works
¶ Version 1.4.3
¶ API updates
GET /structure-status/diagnostic/private(Perform status diagnostic on user structures)GET /structure-status/diagnostic/rcsb(Perform status diagnostic on RCSB structures)POST /structures-to-reprocess/private(Reprocess user structures)POST /structures-to-reprocess/public(Reprocess RCSB structures)
¶ Data reprocessing
- Pocket features on all user structures have been reprocessed to enable Pocket Similarity Search
¶ Version 1.4.2
¶ Bug fixes
- The API endpoint POST/exports/ligand now returns the sdf file even if one of the requested structure does not contain a ligand
- The "manage users in project" privilege now has the right description
- When a user is successfully removed from a group, a success message is now displayed
- When downloading results from the search results page, a popup appears if there is an issue
- The structure privileges list now shows User groups having privileges on that structure
- When post-filters are applied in Table view mode, the Search results are updated
¶ Data reprocessing
- Pocket features on all RCSB structures to enable the Pocket Similarity Search
¶ Version 1.4.1
¶ Added functionality
- Google authentication
¶ Bug fixes
- The scrolling through Workspace structures doesn't mix the order anymore
- Users with delete permission on structure can now delete structures from My Structures panel
- The ligand correction from template is now able to detect obvious missing bonds and create them
- The sequence mapping shown in the Information Browser for structures with gaps was limited to the first fragment of the sequence. Now the whole mapping is correctly displayed
- In Information Browser, the right residue range is shown
- The clipping plane & fog default parameters have been updated to a more focused default view
- The missing detection of explicit pockets for some very specific ligands was corrected
- In Search result page, structure selection is now propagated correctly through the different views and works as expected
- When superposing identical protein structures, the superposed pocket residues are shown in lines in both structures
- For structure registration, dots are allowed for structure file names
- Advanced search by Ligand ID retrieves all structures containing the ligand with the specified identifier
- In the Workspace, the collections panels that are collapsed now displays structures and ligands correctly after being expanded again
- The polar and apolar surface areas are now accurately shown in the PocketBrowser
- User with “manage project reference” privilege only on a project is now able to set a project reference
- The description of available chemistry search methods have been updated in the UI tooltip
- For chemistry similarity search, a slider permits to tune the threshold from 0 to 1 (default value of 0.65)
- When picking residues in the 3D viewer that have identical residue numbers but supplementary insertion codes, only the picked residue gets selected now
- The pocket analysis is more stable now for structure containing non standard atoms or residues (like amino-acids with Deuterium atoms)
- For files with multiple models with inconsistant number of atoms in each model, the first model is considered. This structure was not supported at all before
- The file names for PDB and ligands is now correctly set in structure file panel
- The pocket features have been recalculated for some structures
- Fpocket now considers alternates with distinct residue numbers accurately
- The default clipping planes for EM maps is adjusted
- The tooltip for the ligand postfiltering options has been improved
- The superposition is improved for structures with pocket at the interface of multiple chains
- The sequence mapping analysis no longer fails during the consistency check of sequence information between PDB header sections and sequence derived from modelled residues
- The backend of structure registration has been optimized
- The subpocket search collections are well displayed in the workspace whatever the screen size
- When superposing some subpocket search hits, the hit pocket that is highlighted as sticks is the one identified as hit
- As an output of subpocket search, only ligands that are in the same pocket are displayed in the ligand tab
- During the sequence analysis, unresolved short sequences are not responsible of a wrong mapping anymore
- The superposition of some particular proteins is now corrected
¶ Version 1.4
¶ Added functionality
- Pocket similarity search (Feature description and related Tutorial)
¶ Bug fixes
- The chains are now sorted in alphabetical order in structure information panel
- The protein names on ligand card are displayed correctly for chimeric structures
- The uploaded volume files can be visualized in the 3D Viewer (dns6 format only)
- The structure privileges are inherited properly for a group of users added to a project
- The structures added to Community project can now be shared to other projects by default
- A request limit has been removed when adding structures to a project (that was set at 1000)
- The pocket features analysis works on structures that have more than 1000 pockets
¶ API updates
- The API link has been changed to add Authentication at the same place
¶ Additional changes:
- Non functional menus have been hidden
- The check analysis column is removed in My Structures panel while it's off
¶ Version 1.3.1
¶ Added functionality
- The access is direct to 3decision User Guide through
?button
¶ API updates
- The uploaded file's URL is unique in endpoint
POST /structures/upload
¶ Bug fixes
- The registered viewpoint from project reference is now fetched properly when opening structures in the workspace
- The depiction for big ligands is displayed
- Opening or adding a related structure in the workspace is now possible
- The delete button on user groups on owners line has been removed
- The structure deposition and imported date are displayed correctly
¶ Performance
- Fetching useless data on structure information is avoided now
¶ Version 1.3
¶ Added functionality
- The download and display of the public cryo-EM maps (Tutorial) is now possible
- The search of large sets of structures has been overhauled in the 3decision backend to improve reliability, stability & performance
- LDAP as authentication backend has been enabled
¶ API updates
- Annotation endpoint
POST /annotation-types- when registering structures through the REST API, you can now add your own annotation types and visualize them in the the information panel in the UI
- Sequence registration new endpoint
POST /sequence/register- you can now register your specific sequence in the 3decision database
- the sequence registration REST endpoint returns the biomolecule code
- Delete Structure endpoint
DELETE /structures/{externalCode}
- after deleting a structure through the REST API, the status is now properly returned
- Structure Registration endpoint
POST /structure-registration/- registering structures with a title in the payload (user-provided label) in not superseded anymore by structure file title
- for some structures containing polysaccharide chains with insertion codes, the registration does not fail anymore because of the use of the insertion codes on "non standard" residues
- accept PDB files with atomic charges formatted "-1" or "1-"
¶ Bug fixes
- When displaying protein structures with multiple ligands, the contacts are now displayed for all of the ligands
- When opening a structure from the "My structures" dialog, the structure is now shown by default
- Download Structures and Ligands is possible when the collection contained more than 30 structures
- The protein structures to sequence mappings are now consistent on structures with 2 or more chains in the asymmetric unit
- The protein structures with modified residues in the middle of a chain resulted now in consistent protein structure to sequence mappings shown in the UI
- For specific structures with insertion codes, the correct residues are now shown for pockets in the UI
- The structure parameters below 0 with several decimals are now shown correctly in the structure information panel and structure resolution is now rounded
- The list of accepted file formats for upload with a structure is now updated in the UI
- Exporting pymol sessions is not yet reintegrated into 3decision, so the link to it has been hidden from the UI
- Add structures to project does not fail anymore if one of the structures to be added is already part of the project
- Several partial sequence mappings have been fixed
- One display issue with ligand panel has been fixed
¶ Version 1.2.2
¶ API updates
- Structure registration endpoint
POST /structure-registration:- charge format properly handled for PDB files generated with REFMAC
- Adjusted Structure file creation: when calling the structure registration endpoint: if the parameter "commit" is True: structure files are created during structure registration, if the parameter "commit" is False structures files are not created
- Structure parse info endpoint
GET /structures/parse/info- Structures containing alternative conformations for PDB files generated with REFMAC are parsed without error
- The resolution detection was enhanced to detect new resolution formats from the PDB
- The returned smiles are read from the PDB file and not replaced by the smiles from the RCSB ligands dictionary based on 3 letters residue code
¶ Bug fixes
- Pocket feature calculation
- Structure registration
- Sequence mapping analysis
- Ligand cavity overlap
¶ Version 1.2.1
¶ Bug fixes
- The superimposition of close related structures is now possible
¶ Version 1.2.0
¶ Added functionality
- Ability to set a reference structure for your projects
- Ability to display protein-protein interactions in the 3Dviewer
- Display ligand user annotation on ligand cards
- Updated source for public electron density maps (PDBe to RCSB)
¶ API updates
- POST Structure Documentation (available under API documentation)
POST /structure-registration/
¶ Performance:
- The performance in fetching ligand annotations has been improved
¶ Bug fixes
- Options on sketched ligands have been hidden
- The default color scales have been adjusted (bfactor and hydrophobicity)
- The display issues for ligand user annotation on ligand cards have been corrected
- Redirection to API documentation has been corrected
- The disabled options in ligand action menu have been hidden
- Bug in ligand-cavity overlap analysis has been corrected
- Bug in set ligand contact display menu ligand has been corrected
- The residueCode field is now optional in the ligand section in the structure-registration API endpoint
¶ Version 1.1.1
¶ Added functionality
- Annotation Browser
- Additional file formats for attached files
- Downloading attached files
- Ligand cavity overlap analysis
¶ API updates
- Get ligands annotations
POST /annotations/ligands - Delete a structure
DELETE /structures/{externalCode} - API documentation links
¶ Bug fixes
- Ligand download
- Keep last loaded molecule in molecule editor
- Search results
- Feedbacks feature
- User session ended on opening a new tab
¶ Version 1.0
This version that has been release in 2022 is the application migration from Pipeline Pilot to in-house scientific backend.
This version has the following features :
- Search / Advanced search speed improvement
- Autocomplete search by:
Gene name
Protein name
Protein family
Internal label
Chembl database
Project - User profiles, groups and permissions
- Workspace
Structure information
Structure superposition by pocket
Structure superposition by chain
Contacts display
Electron map density - Attach file upload to a structure
- Replace previous molecule editor (Sketcher now replaced by Marvin)
- Structure export
CSV
XLSX (Excel)
PDB zip
PDB - Ligand export
CSV
XLSX ( Excel)
SDF - Authentication support
Azure
Azure B2C
Okta - API key generation
3decision API
We now provide an API to programmatically perform every action in the interface and some more.
Main API features :
- Search :
Chemistry (Available options: Exact Search, Tautomer Search, Isomer Search, Tautomer + Isomer Search, Substructure Search, Similarity Search)
Annotations
Experimental method
Resolution
Free text - Structure management
- Structure information
- Structure registration
- Docking
- User management
- Project management