Current Version 4.0 with druggabillity implementation, release Sept. 2019.
Only central pocket is considered (no side pockets). If you need this, please use version 3 below without druggability.
Calculates druggability score (Yuan et al, JCIM, 2020).
Change in Licensing. Starting from 4.0 TRAPP webserver and standalone uses EUPL 1.2 (https://eupl.eu/1.2/en/)
Current Version 3.1.2 without druggability implementation, release March 2018 available at https://trapp3.h-its.org/
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+
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
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).
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.
Computation of pocket descriptors (number of H-bond donors and acceptors, contacts with hydrophobic, polar, aromatic residues, positively- and negatively-charged residues).
Parallelization of TRAPP-structure.
TRAPP version 2.4, used for Webserver version 2.
Complete TRAPP workflow implemented (including TRAPP-analysis and TRAPP-structure)
The use of PDB structures with several chains is now possible, but active site residues should belong to the same chain.
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.
Partial parallelization of TRAPP-pocket and TRAPP-analysis.
DCD formated trajectories can be analyzed.
The first/last snapshot and stride can be used in the trajectory analysis.
TRAPP version used for Webserver version 1
tracking of the pocket shape for each snapshot/structure in trajectories/ensembles of structures provided by user
identification of transient and conserved pocket regions
splitting transient pocket regions into sub-pockets and tracing their appearence along a trajectory or in an ensemble of structures
identification of residues that contact the pocket in some protein snapshots/structures
computation of the pocket volume as well as protein-exposed and solvent-exposed pocket surface areas
