ProPores2 is a web service and stand-alone tool for identifying and visualizing void spaces in protein structures.
PoreID: Identifies all surface pores, cavities and tunnels in protein structure files (PDB format) and their lining residues.
AxisTrace: Determines the axis of void spaces identified by PoreID.
GateOpen: Rotates the shared lining residues of two neighbouring void spaces to open putative connections.
In addition to the webservice, ProPores2 is also freely available as a stand-alone tool for Windows, Linux and MacOs. The source code is hosted on GitHub, where you can also download the latest release.
The GitHub Wiki documents the technical aspects and usage of ProPores2, including the installation of the stand-alone tool, the options and parameters used by both the webservice and the stand-alone tool, as well as solutions some known problems.
For further background information, research context and a detailed discussion of the methodology, please refer to our two publications below.
Should you run into technical difficulties with ProPores2 that cannot be solved with the help of the documentation, the fastest way to receive help is to open a ticket on GitHub. That is also the best way to contact us if you would like to report a bug, leave feedback and suggestions, or make a feature request.
Alternatively, you can contact Prof. Dr. Volkhard Helms directly.
If you use ProPores2 in your work, please cite:
Hollander, M, Rasp, D, Aziz, M, Helms, V (2021). ProPores2: Web Service and Stand-Alone Tool for Identifying, Manipulating, and Visualizing Pores in Protein Structures. J Chem Inf Model, 61, 4:1555-1559. DOI: 10.1021/acs.jcim.1c00154. pubs.acs.org/doi/10.1021/acs.jcim.1c00154
The original approach was designed by Po-Hsien Lee and published as:
Lee, PH, Helms, V (2012). Identifying continuous pores in protein structures with PROPORES by computational repositioning of gating residues. Proteins, 80, 2:421-32. ncbi.nlm.nih.gov/pubmed/22095919
ProPores1 was implemented by Po-Hsien Lee (2011) in Perl. ProPores2 is a faster and more memory-efficient C++ implementation by Markus Hollander and Moomal Aziz. The ProPores web service was developed by Livia Rasp and Markus Hollander. It uses the following external software, frameworks and databases:
Wang, Kw and Hall, CK (2019). Characterising the throat diameter of through-pores in network structures using a percolation criterion. Molecular Physics, 117:23-24, 3614-3622. DOI: 10.1080/00268976.2019.1654140. tandfonline.com/doi/full/10.1080/00268976.2019.1654140
Ariz-Extreme, I, Hub, JS (2017). Potential of Mean Force Calculations of Solute Permeation Across UT-B and AQP1: A Comparison between Molecular Dynamics and 3D-RISM. J Phys Chem B, 121, 7:1506-1519. DOI: 10.1021/acs.jpcb.6b11279. pubs.acs.org/doi/full/10.1021/acs.jpcb.6b11279
Johnson, QR, Lindsay, RJ, Nellas, RB, Shen, T (2016). Pressure-induced conformational switch of an interfacial protein. Proteins, 84, 6:820-7. DOI: 10.1002/prot.25031. onlinelibrary.wiley.com/doi/10.1002/prot.25031
Nguyen, D, Helms, V, Lee, PH (2014). PRIMSIPLR: prediction of inner-membrane situated pore-lining residues for alpha-helical transmembrane proteins. Proteins, 82, 7:1503-11. DOI: 10.1002/prot.24520, onlinelibrary.wiley.com/doi/10.1002/prot.24520
Benkaidali, L, é, F, Maouche, B, Siregar, P, Benyettou, M, Maurel, F, Petitjean, M (2014). Computing cavities, channels, pores and pockets in proteins from non-spherical ligands models. Bioinformatics, 30, 6:792-800. DOI: 10.1093/bioinformatics/btt644. academic.oup.com/bioinformatics/article/30/6/792/286861
Sehnal, D, á, R, Berka, K, Pravda, L, á, V, š, P, Ionescu, CM, Otyepka, M, a, J (2013). MOLE 2.0: advanced approach for analysis of biomacromolecular channels. J Cheminform, 5, 1:39. DOI: 10.1186/1758-2946-5-39. link.springer.com/article/10.1186/1758-2946-5-39
Johnson, QR, Nellas, RB, Shen, T (2012). Solvent-dependent gating motions of an extremophilic lipase from Pseudomonas aeruginosa. Biochemistry, 51, 31:6238-45. DOI: 10.1021/bi300557y. pubs.acs.org/doi/10.1021/bi300557y
Berka, K, k, O, Sehnal, D, s, P, á, V, Jaiswal, D, Ionescu, CM, á, R, Koca, J, Otyepka, M (2012). MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels. Nucleic Acids Res, 40, Web Server issue:W222-7. DOI: 10.1093/nar/gks363. academic.oup.com/nar/article/40/W1/W222/1071280