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Nucleic Acids Research Advance Access published online on May 30, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn308
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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3D-Fun: predicting enzyme function from structure

Marcin von Grotthuss1, Dariusz Plewczynski2, Gert Vriend1,* and Leszek Rychlewski2

1CMBI, NCMLS, Radboud University Nijmegen Medical Centre, Geert Grooteplein 26-28, 6525 GA Nijmegen, The Netherlands and 2BioInfoBank Institute, ul. Limanowskiego 24A, 60-744 Poznan, Poland

*To whom correspondence should be addressed. Tel: +31 24 361 9521; Fax: +31 24 361 9395; Email: vriend{at}cmbi.ru.nl

Received February 29, 2008. Revised April 26, 2008. Accepted April 30, 2008.

The ‘omics’ revolution is causing a flurry of data that all needs to be annotated for it to become useful. Sequences of proteins of unknown function can be annotated with a putative function by comparing them with proteins of known function. This form of annotation is typically performed with BLAST or similar software. Structural genomics is nowadays also bringing us three dimensional structures of proteins with unknown function. We present here software that can be used when sequence comparisons fail to determine the function of a protein with known structure but unknown function. The software, called 3D-Fun, is implemented as a server that runs at several European institutes and is freely available for everybody at all these sites. The 3D-Fun servers accept protein coordinates in the standard PDB format and compare them with all known protein structures by 3D structural superposition using the 3D-Hit software. If structural hits are found with proteins with known function, these are listed together with their function and some vital comparison statistics. This is conceptually very similar in 3D to what BLAST does in 1D. Additionally, the superposition results are displayed using interactive graphics facilities. Currently, the 3D-Fun system only predicts enzyme function but an expanded version with Gene Ontology predictions will be available soon. The server can be accessed at http://3dfun.bioinfo.pl/ or at http://3dfun.cmbi.ru.nl/.


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