The POPScomp program computes the Solvent Accessible Surface Area (SASA) of a given PDB structure. If the structure is a complex, i.e. composed of more than one chain containing protein or RNA/DNA, POPScomp computes additionally the SASA buried between chains. The name 'POPS' is derived from Parameter OPtimised Surfaces, because its parametrisation was performed by regression against a large set of protein and RNA/DNA structures. Details of those routines are explained in the published papers. (Note: POPScomp embodies both methods, POPS and POPSCOMP).
There are 3 ways to (install and) use POPScomp, please refer to the Wiki for details:
- Use the free POPScomp Shiny server at popscomp.org without installation.
- Download the POPScomp Docker image and run the Shiny App on your local computer.
- To install from source code, either download the latest release or the development version by cloning this POPScomp repository. Compile/install the program suite and run the Shiny App on your local computer.
Enter a PDB identifier or upload a custom PDB file and press 'run POPScomp'. Results will be shown as tables for different resolutions: Atom, Residue, Chain and Molecule. Download individual results via the buttons underneath the tables or bundled via the 'Download All Results' button.
Please refer to the Wiki for documentation.
This POPScomp repository contains the following components:
A GNU Autotools package of the POPS C program that computes SASA for a given structure.
An R package to
- split complexes into single and pair components to compute buried SASA using POPSC and
- provide a Shiny App as interface to the POPSC program.
A POPScomp Docker image is available that provides the program suite in fully functional form, i.e. pre-compiled POPSC, RStudio with POPSR and all dependencies installed. Please refer to the Wiki for detailed guidelines on downloading and usage of the Docker image.
A Make pipeline to run POPScomp over the PDB database and to feed the JSON output into the Elixir FunPDBe project. To include newly added PDB structures, the pipeline is run via a cron @weekly job on a virtual Ubuntu machine hosted on a Synology DS218+ computer. This directory has been included purely as a reference for the FunPDBe project and is not intended as a user-facing application. However, some users might find the pipeline or parts of it useful for their own purposes.
POPScomp Shiny server at popscomp.org
Publically available server with an intuitive user interface. Results will be stored on the server until midnight (GMT). For permanent storage, please download your results via the 'Download' buttons.
POPScomp is part of the FunPDBe resources.
- mathbio.nimr.mrc.ac.uk/POPSCOMP : This was the original address of the POPS and POPSCOMP servers in the Division of Mathematical Biology at the NIMR institute, which has been closed in 2015 and became a part of the Francis Crick Institute.
- mathbio.crick.mrc.ac.uk/POPSCOMP : Only for a short while the POPS and POPSCOMP servers were supported by the Francis Crick Institute.
Users publishing results obtained with the program and its applications should acknowledge its use by citation.
Kleinjung, J. and Fraternali, F.
Design and Application of Implicit Solvent Models in Biomolecular Simulations.
Current Opinion in Structural Biology 25 (2014) 126-134.
Fraternali, F. and van Gunsteren, W.F.
An efficient mean solvation force model for use in molecular dynamics simulations of proteins in aqueous solution.
Journal of Molecular Biology 256 (1996) 939-948.
Fraternali, F. and Cavallo, L.
Parameter optimized surfaces (POPS): analysis of key interactions and conformational changes in the ribosome.
Nucleic Acids Research 30 (2002) 2950-2960.
Cavallo, L., Kleinjung, J. and Fraternali, F.
POPS: A fast algorithm for solvent accessible surface areas at atomic and residue level.
Nucleic Acids Research 31 (2003) 3364-3366.
Kleinjung, J. and Fraternali, F.
POPSCOMP: an automated interaction analysis of biomolecular complexes.
Nucleic Acids Research 33 (2005) W342-W346.
Please feel free to open an issue on the Issues page if you have any difficulty with POPScomp. We have no formal procedure to process contributed code, but we will revise code submitted via pull requests and will acknowledge authors accordingly.
Usage of the software and server is free under the GNU General Public License v3.0.
- 2002-2021 Franca Fraternali (author, maintainer) franca.fraternali@kcl.ac.uk
- 2008-2021 Jens Kleinjung (author, maintainer) jens@jkleinj.eu
- 2002 Kuang Lin and Valerie Hindie (translation to C)
- 2002 Luigi Cavallo (parametrisation)