Fraternalilab/POPScomp
Solvent Accessible Surface Areas of Biomolecules and their Complexes
POPScomp: Solvent Accessible Surface Areas of Biomolecules and their Complexes
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).
Installation
There are 2 ways to (install and) use POPScomp,
please refer to the Wiki for details:
-
Download the POPScomp Docker image
and run the Shiny App on your local computer. The Docker image provides the program suite in fully functional form,
i.e. a Shiny server with integrated POPSC/POPSR as computational backbone.
Please refer to the Wiki
for detailed guidelines on downloading and usage of the Docker image. -
To install from source code, either download the latest POPScomp release or the development version by cloning this POPScomp repository.
Compile/install the program suite and run the Shiny App on your local computer.
git clone --recurse-submodules https://github.com/Fraternalilab/POPScomp.git
Usage
Enter a PDB identifier or upload a custom PDB file and press 'run POPScomp'.
SASA values and related information 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.
Here is a snapshot of the 
.
Documentation
The Wiki contains additional documentation about the POPS model and implementation.
Software Design
This POPScomp repository contains the following components:
POPSC
A GNU Autotools package of the POPS C program that computes SASA for a given structure.
POPSR
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.
Legacy POPScomp Shiny servers
- popscomp.org:3838 : This server has been discontinued in November 2025. popscomp.org points now to this GitHub repository.
- mathbio.crick.mrc.ac.uk/POPSCOMP : Only for a short while the POPS and POPSCOMP servers were supported by the Francis Crick Institute.
- 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.
References
POPScomp software
Implicit solvent
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.
POPS method
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.
POPS server
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.
POPSCOMP method and server
Kleinjung, J. and Fraternali, F.
POPSCOMP: an automated interaction analysis of biomolecular complexes.
Nucleic Acids Research 33 (2005) W342-W346.
Issues
Iussues can be recorded on the Issues page.
License and Copyright
Usage of the software and server is free under the GNU General Public License v3.0.
Copyright Holders, Authors and Maintainers
- 2002-2026 Franca Fraternali (author, maintainer) f.fraternali@ucl.ac.uk
- 2008-2026 Jens Kleinjung (author, maintainer) jens@jkleinj.eu
Contributors
- 2002 Kuang Lin and Valerie Hindie (translation to C)
- 2002 Luigi Cavallo (parametrisation)