Version History Webserver

  • Current Version 3.1.2, release March 2018
    • Sulfur bridges can be taken into account in LRIP/RIPlig and MD simulations (not tCONCOORD): paris CYX residues with SG atoms placed at the distance less than 3A considered as sulfur bridges.
    • All log files as well as JOB_ID.txt file are included in the archive file that can be downloaded
    • Some bugs in analysis of trajectories in dcd format are fixed
    • LRIP simulations with of a trajectory with a part of the structure replaced by a loop (for example, in GPCR) are possible
    • New procedure for selectrion of a central pocket is implemented
    • A standalone version with as set of examples can be obtained upon request
  • Version 3.0.1, release Jan. 2017
    • Fix for problem where negative coordinates in ligand center caused trapp pocket to fail.
    • Changed default for pocket run parameter: 'H-atoms to be generated for uploaded structures/trajectories' to false, as this is normally not needed and takes a long time for long trajectories.
  • Version 3, released Dec. 2016
    • Added sequence conservation score calculation and link to ProSAT+
    • Overhauled the user interface, using twitter bootstrap
    • Upgraded the underlying web framework (Play framework) from version 1.2 to 2.5.
    • Switched from Jmol (java dependent) to JSmol (java independent). This allows the results to be viewed without Java plugin in the browser.
    • Size Limit of trajectory upload increased to 500 MB
    • Support of gzipped trajectories
  • Version 2 released Oct. 2014
    • Added the generation of trajectories via various methods: tCONCOORD, L-RIP, RIPlig, Molecular Dynamics or upload (limited to 100MB file size). Link to the old server is available upon request.
  • Version 1 released April 2013
    • Initial version, allowing analysis of uploaded MD trajectories (limited to 100MB file size). Link to the old server is available upon request.

Version History TRAPP tool

  • TRAPP version 3.0, used for Webserver version 3
    1. New alignment procedure used - proteins with substantially different binding site sequences can be used for analysis (i.e. proteins with a mutation, insertion or deletion are possible).
    2. Analysis of pockets at the interface of different chains is now possible (i.e. binding site residues can belong to different chains). Also when using L-RIP, residues in particular chains can be chosen for perturbation.
    3. Computation of pocket descriptors (number of H-bond donors and acceptors, contacts with hydrophobic, polar, aromatic residues, positively- and negatively-charged residues).
    4. Parallelization of TRAPP-structure.
  • TRAPP version 2.4, used for Webserver version 2.
    1. Complete TRAPP workflow implemented (including TRAPP-analysis and TRAPP-structure)
    2. The use of PDB structures with several chains is now possible, but active site residues should belong to the same chain.
    3. Important: now a single word “TER ” means the end of the snapshot; if TER is followed by some other words/numbers, this line means the end of a chain.
    4. Partial parallelization of TRAPP-pocket and TRAPP-analysis.
    5. DCD formated trajectories can be analyzed.
    6. The first/last snapshot and stride can be used in the trajectory analysis.
  • TRAPP version used for Webserver version 1
    1. tracking of the pocket shape for each snapshot/structure in trajectories/ensembles of structures provided by user
    2. identification of transient and conserved pocket regions
    3. splitting transient pocket regions into sub-pockets and tracing their appearence along a trajectory or in an ensemble of structures
    4. identification of residues that contact the pocket in some protein snapshots/structures
    5. computation of the pocket volume as well as protein-exposed and solvent-exposed pocket surface areas