PaDEL ws descriptors engine
This web app implements a web server to compute PaDEL descriptors in a more efficient way in the framework of eTOXlab and eTOX project
In the latest version 2.21 (21/07/2014). The software currently calculates 1875 descriptors (1444 1D, 2D descriptors and 431 3D descriptors) and 12 types of fingerprints (total 16092 bits).
eTOXlab is a modelling framework to develop and deploy QSAR models in production environments. One of the major goals of eTOXlab is the robustness of the platform.
To acomplish this goal the eTOXlab pipeline processess molecules individually. But this has a major performance penalty when computing PaDEL descriptors due to PaDEL commandline mode startup delay and JVM startup delay.
So we developed the PaDEL ws descriptors engine that maintains a in-memory ready PaDEL descriptor computation engine.
By calling the web server we can compute descriptors for the molecules needed without the need to reload PaDEL engine for every individual molecule.
In the current implementation the input molecules must be located in a local folder of the PaDEL ws descriptors engine. The ouput files containing the descriptors computed are also stored locally in the web server. A possible improvement is to provide an upload molecule mechanism
We can measure de difference in computation time.
Using the original PaDEL commnd-line interface:
| Molecule | Computation method | Computation time |
|---|---|---|
| mol1 | PaDEL command-line | time ./test_cl_single_molecule.sh real 0m2.487s user 0m5.606s sys 0m0.442s |
| Set of 141 molecules | PaDEL command-line | time ./test_cl_folders.sh real 6m35.709s user 15m28.519s sys 1m1.071s |
Using the PaDEL ws descriptors engine:
| Molecule | Computation method | Computation time |
|---|---|---|
| mol1 | PaDEL ws descriptors engine | time ./test_ws_single_molecule.sh real 0m0.260s user 0m0.005s sys 0m0.015s |
| Set of 141 molecules | PaDEL ws descriptors engine | time ./test_ws_folders.sh real 0m52.643s user 0m0.398s sys 0m0.946s |
The throughput of descriptor computation is increased by 7x (test dataset).
If you want to obtain further information please contact the author Oriol López Massaguer oriol.lopez@upf.edu
Copyright 2017 Oriol Lopez
PaDEL ws descriptors engine is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation version 3.
PaDEL ws descriptors engine is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with PaDEL ws descriptors engine. If not, see http://www.gnu.org/licenses/.
The research leading to these results has received support from the Innovative Medicines Initiative (IMI) Joint Undertaking under grant agreement n° 115002 (eTOX), resources of which are composed of financial contribution from the European Union’s Seventh Framework Programme (FP7/2007-2013) and EFPIA companies’ in kind contributions.