What's new?

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.

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

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.

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.

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

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.

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

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.

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.

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.