2023-04 |
New tool: PoseEdit is now available in ProteinsPlus!
PoseEdit uses the PoseView algorithm and the InteractionDrawer JavaScript library (https://github.com/rareylab/InteractionDrawer) for the
fully automatic drawing of highly interactive 2D ligand interaction diagrams of binding sites calculated by Protoss, DoGSite3, and GeoMine.
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2023-04 |
GeoMine: Update
- Runtime optimizations
- Database update that includes all PDBs till 23.03.2023
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2023-01 |
New tool: DoGSite3 is now available in ProteinsPlus!
DoGSite3 is the successor of the DoGSiteScorer. We focused on improved binding site
detection
in presence of ligands and optimized parameters for more robust and reliable predictions
and
binding site descriptor calculations.
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2022-10 |
Updated KNIME nodes are now available on ProteinsPlus and on
KNIME hub.
Check out our
KNIME blog post for more information and an example showcase.
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2022-04 |
New tool: LifeSoaks is now available in ProteinsPlus!
LifeSoaks visualizes solvent channels in protein or nucleic acid crystal
structures and computes bottlenecks along them. Knowledge about solvent channels
and potential obstacles on them can be helpful to plan soaking experiments
where small molecules need to be able to traverse the crystal in order to reach
a binding pocket.
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2022-02 |
GeoMine: Update
- Results are now ranked based on RMSD. The RMSD is calculated considering the 3D query
points and the respective result points that match the 3D query points
- New precalculated pockets generated by new DogSite parameters that were optimized
using the datasets 1 and 2 from 10.1371/journal.pcbi.1006483
- New "Result - Query RMSD" filter - This filter returns all matches within the set RMSD
range
- New "Result - Max Number/Pocket" filter - Limits the number of returned matches for
each resulting pocket to a given value
- New "Pocket - Is Multichain" filter - Only pockets that consist/do not consist of
multiple chains are returned
- "Ligand - Similarity" filter now accepts custom SMILES
- Renaming of the "Pocket - No Symmetrical Matches" filter to
"Result - No Symmetrical Matches"
- Runtime optimizations for the search of PDB subselections
- New point type - "Nucleic Acid". With this new point type, a user can now select either
protein or nucleic acid atoms for the 3D query, improving runtime and result quality
- New secondary structure definitions for protein points -
"Helix C Terminus", "Helix N Terminus"
- Precalculated pocket entries in the central pocket tab do now list pocket properties
- Updated paper references
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2022-01 |
New tool: MicroMiner is now available in ProteinsPlus!
MicroMiner searches mutations in protein structure databases like the PDB. Retrieved mutant structures can be
easily analysed and compared to the wild-type through automatically superposed structures. Local mutation
sites can be filtered by RMSD to identify structurally deviations upon mutation.
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2021-09 |
ProteinsPlus: Update
- Structures of the AlphaFold database can now be used entering on the starting page
an UniProt accession number (e.g. Q5VSL9) instead of an PDB code.
Additional ligand molecules can be provided in SDF format.
- The "Advanced search" of ProteinsPlus can now be used
for searching also the AlphaFold database.
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2021-05 |
GeoMine: Update
- New "P-L-Complex - Excluded PDB codes" filter -
Specify a list of PDB codes that are excluded from the search
- Renaming of the point type "Aromatic" to "Aromatic Ring Center"
as interaction feature to highlight that this is no atom feature
- Added feature for the download and upload of query files
- Results of queries are now available up to 14 days
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2021-04 |
GeoMine: Update
- New "Pocket - No Symmetrical Matches" filter - This filter returns only one match
if multiple symmetrical matches were found
- Bugfix in secondary structure point directions. Floating point exceptions are now
captured leading to defined directions for all secondary structure points
- Improvement in pocket prediction: the pocket size is restricted to
reasonable values for the use in GeoMine
SIENA: Improved internal error handling.
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2021-02 |
GeoMine: Update
- GeoMine database update
The database contains all PDBs till 16.12.2020
Exclusion of structures from the database which contain chains with only Calpha
atom coordinates
The radius pockets are substituted by DogSite pockets (empty pockets and ligand pockets).
If a DogSite pocket could not be calculated for a ligand, the radius pocket is stored instead
- New precalculated pockets are available in the "Pockets" tab
These are the same as the ones stored in the database
They can be visualized together with a grid representation
The pockets are calculated and loaded on the fly. This may take a minute
if they were not calculated yet
They are calculated for uploaded .pdb files
- New 3D query features
Protein surface atoms
End/mid alpha carbons and directions of helices and strands
- New textual/numerical filters
Pocket - Has Ligand: Only pockets containing a ligand are searched
Ligand - Similarity: Returns all PDBs with ligands having a given minimal
similarity (CSFP, tCSFP, or ECFPlike) to a ligand of a template pocket.
- Easier 3D query selection in fullscreen mode
- Help pages are up to date
- The mouse hover highlighting of the 3D query in the NGL viewer is synchronized with the tables
- Result pocket .pdb files superimposed onto the query can be downloaded
- Result table content available as .json and .csv files
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2021-01 |
SIENA: Optimization of search results by
- detection of missing coordinates in single residues
- exclusion of structures from the database which contain chains with only Calpha
atom coordinates
REST API: Upload of custom pdb files is now possible. Once the file is uploaded,
it can be used as input for all available tools via the REST API.
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2020-11 |
New tool: JAMDA docking is now available in ProteinsPlus!
JAMDA is a novel and fully automated protein-ligand docking tool.
The docking and scoring performance of JAMDA is in line with the state of the art in the field.
JAMDA has an unprecedented level of automation enabling molecular docking for everyone on the web.
Starting from a protein structure and the molecules to be docked, the structures are preprocessed
and docked automatically. The docking site can be defined by a reference ligand or by pocket residues.
The molecules for docking can be uploaded without any preprocessing, i.e. neither coordinates nor
protonation states are required.
NGL Viewer: The viewer width can be toggled from normal via medium to fullscreen size by pressing
the "Toggle Viewer Size" button in the main menu.
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2020-04 |
New tool: GeoMine is now available in ProteinsPlus!
GeoMine enables textual, numerical and 3D searching with full chemical awareness in protein-ligand
interfaces of the entire PDB dataset. The tool is based on the desktop application Pelikan.
It enables various user-defined queries for on-the-fly binding site comparison for
predicted and ligand-based binding sites in the PDB.
Data from PDB files is preprocessed and stored in a PostgreSQL database which leads to processing times
of queries in the range of seconds to a few minutes.
NGL Viewer: The measurement mode is now available; distances between atoms, bond angles, and dihedral
angles can be displayed in the viewer. Pick to select/deselect 1 to 4 atoms to start a distance, angle
or dihedral measurement.
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