1. Motivation

The TRAPP webserver provides a workflow for simulation, analysis, and visualization of protein cavity dynamics and for detection of transient sub-pockets using protein motion trajectories or ensembles of protein structures obtained either from experiment or from simulations. The TRAPP webserver includes an interface for several methods for generating conformational changes of a binding site and to analyze them.
TRAPP is not designed for identification of all of a protein's binding sites. The binding site regions to be analysed must be defined by the user.

2. Overview

The TRAPP workflow consists of the following tools:
  • TRAPP-structure: Simulation of protein conformational changes (from side-chain rotation to distortion of secondary structure or domain motion). It is a python wrap around several programs for the generation of protein conformational changes (tCONCOORD; L-RIP; RIPlig; NAMD);
  • TRAPP-analysis: Analysis of protein conformational changes. It helps to identify the most flexible parts of a binding site from protein trajectories or structures generated by TRAPP-structure or provided by the user
  • TRAPP-pocket: Analysis, and visualization of protein cavity dynamics and detection of transient pockets/subpockets from protein motion trajectories or ensembles of protein structures obtained either from TRAPP-structure or provided by the user.
    TRAPP-pocket identifies conserved and transient regions of a binding pocket and variations of the binding site composition, size, surface and some other characteristics such as amino acid sequence. It enables the user to trace the opening or closing of particular pocket regions or sub-pockets along each trajectory.
  • Webserver visualization uses JSmol, a protein structure viewer that does not require Java plugins in your browser. However, if there are more than 100 snapshots in a trajectory to be used for pocket simulations - all snapshots will be taken into account in pocket property computations, but not all snapshots will be shown in Jsmol visualization ( the stride is calculated as: int(total_number_of_snapshots)/100 +1 )

3. Frequently Asked Questions

4. Details of the algorithm, input parameters, and results:

5. Current Version

6. Testing Information

Trapp was tested with the following versions of these browsers and operating systems.

Browser/OS Windows 10 Linux (Ubuntu 16.04) Mac OS X (10.11.6)
Firefox 48.0 48.0 48.0
Chrome 54.0.2840.59 52.0.2743.116 -
Safari - - 9.1.3