ProBiS

ProBiS is a computer software which allows prediction of binding sites and their corresponding ligands for a given protein structure. Initially ProBiS was developed as a ProBiS algorithm by Janez Konc and Dušanka Janežič in 2010[1] and is now available as ProBiS server, ProBiS CHARMMing server, ProBiS algorithm and ProBiS plugin. The name ProBiS originates from the purpose of the software itself, that is to predict for a given Protein structure Binding Sites and their corresponding ligands.

ProBiS
Developer(s)Insilab (National Institute of Chemistry Slovenia)
Initial release2010 (2010)
Written inC++, Java Script, PHP
Operating systemUnix-like, Windows
TypeWeb server, plugin, algorithm, database
Websiteprobis.cmm.ki.si

Description

ProBiS software started as ProBiS algorithm that detects structurally similar sites on protein surfaces by local surface structure alignment using a fast maximum clique algorithm. The ProBiS algorithm was followed by ProBiS server which provides access to the program ProBiS that detects protein binding sites based on local structural alignments. There are two ProBiS servers available, ProBiS server and ProBiS CHARMMing server. The latter connects ProBiS and CHARMMing servers into one functional unit that enables prediction of protein−ligand complexes and allows for their geometry optimization and interaction energy calculation. The ProBiS CHARMMing server with these additional functions can only be used at National Institutes of Health, USA. Otherwise it acts as a regular ProBiS server. Additionally a ProBiS PyMOL plugin and ProBiS UCSF Chimera plugin have been made. Both plugins are connected via the internet to a newly prepared database of pre-calculated binding site comparisons to allow fast prediction of binding sites in existing proteins from the Protein Data Bank. They enable viewing of predicted binding sites and ligands poses in three-dimensional graphics.

Protein building sites tools
An example output of the ProBiS software for detecting structurally similar binding sites.
An example output of the ProBiS software for pairwise alignment of two proteins.
Detect structurally similar binding sites
This tool takes as an input a query protein or a binding site. The ProBiS algorithm structurally compares the query independently of sequence or fold with a database of non-redundant protein structures. The output of this tool are a 3D query protein colored by degrees of structural conservation from blue (unconserved) to red (structurally conserved) in Jmol viewer and a table of similar proteins.
Pairwise local structural alignment
This tool takes as an input two proteins or binding sites. The ProBiS algorithm compares structures based on geometry as well as physicochemical properties and returns their local structural alignment.
ProBiS web server RESTful Web Services
The ProBiS web server features RESTful (Representational State Transfer) web services to make the binding site similarities and local pairwise alignments for any PDB protein structure easily accessible from any script.
ProBiS-Database access
ProBiS-Database can be accessed directly from ProBiS (CHARMMing) server, ProBiS-Database widget, which can be included in any web page to provide access to the ProBiS-Database, or RESTful Web Services, which make ProBiS-Database easily accessible from any script.

History
  • ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment (March 2010)[1]
  • ProBiS: A web server for detection of structurally similar protein binding sites (February 2010)[2]
  • ProBiS-Database: Precalculated Binding Site Similarities and Local Pairwise Alignments of Pdb Structures (December 2011)[3]
  • ProBiS - 2012: Web server and web services for detection of structurally similar binding sites in proteins (February 2012)[4]
  • Parallel-ProBiS: Fast Parallel Algorithm for Local Structural Comparison of Protein Structures and Binding Sites (March 2012)[5]
  • ProBiS-ligands: a web server for prediction of ligands by examination of protein binding sites (February 2014)[6]
  • ProBiS-Charmming: Web Interface for Prediction and Optimization of Ligands in Protein Binding Sites (August 2015)[7]
gollark: Well, if you made dales compile to C, you could make the compiler bit in any language you wanted and the C would run "anywhere".
gollark: Rust has `mem::forget` and such.
gollark: I don't agree with "impossible", since you can probably just patch your program's code in memory to fix problems with C++.
gollark: No.
gollark: Idea: make Dale dales (this IS the defined name for dale build script things) compile to C, for purposes.

References
  1. Janez Konc; Dušanka Janežič (2010). "ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment". Bioinformatics. 26 (9): 1160–1168. doi:10.1093/bioinformatics/btq100. PMC 2859123. PMID 20305268.
  2. Janez Konc; Dušanka Janežič (2010). "ProBiS: A web server for detection of structurally similar protein binding sites". Nucleic Acids Research. 38 (Web Server issue): W436–W440. doi:10.1093/nar/gkq479. PMC 2896105. PMID 20504855.
  3. Tomo Česnik; Joanna Trykowska Konc; Matej Penca; Dušanka Janežič (2012). "ProBiS-Database: Precalculated Binding Site Similarities and Local Pairwise Alignments of Pdb Structures". Journal of Chemical Information and Modeling. 52 (2): 604–612. doi:10.1021/ci2005687. PMC 3287116. PMID 22268964.
  4. Janez Konc; Dušanka Janežič (2012). "ProBiS - 2012: Web server and web services for detection of structurally similar binding sites in proteins" (PDF). Nucleic Acids Research. 40 (Web Server issue): W214–21. doi:10.1093/nar/gks435. PMC 3394329. PMID 22600737.
  5. Janez Konc; Matjaz Depolli; Roman Trobec; Kati Rozman; Dušanka Janežič (2012). "Parallel-ProBiS: Fast Parallel Algorithm for Local Structural Comparison of Protein Structures and Binding Sites" (PDF). Journal of Computational Chemistry. 33 (27): 2199–2203. doi:10.1002/jcc.23048. PMID 22718529.
  6. Janez Konc; Dušanka Janežič (2014). "ProBiS-ligands: a web server for prediction of ligands by examination of protein binding sites". Nucleic Acids Research. 42 (Web Server issue): W215–20. doi:10.1093/nar/gku460. PMC 4086080. PMID 24861616.
  7. Janez Konc; Benjamin T. Miller; Tanja Štular; Samo Lešnik; H. Lee Woodcock; Bernard R. Brooks; Dušanka Janežič (2015). "ProBiS-Charmming: Web Interface for Prediction and Optimization of Ligands in Protein Binding Sites". Journal of Chemical Information and Modeling. 55 (11): 2308–2314. doi:10.1021/acs.jcim.5b00534. PMID 26509288.
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