TY - JOUR
T1 - Detection of Functionally Important Regions in "Hypothetical Proteins" of Known Structure
AU - Nimrod, Guy
AU - Schushan, Maya
AU - Steinberg, David M.
AU - Ben-Tal, Nir
N1 - Funding Information:
We thank Frank Pettit, Axel Innis, Angela Wilkins, Ivana Mihalek, and Olivier Lichtarge for applying their algorithms to the data set and for helpful discussions. We would like to acknowledge Leonid Brodsky, Sarel Fleishman, Yanay Ofran, Gilad Wainreb, Lei Xie, and Tsaffrir Zor for helpful discussions. This work was supported by the European Commission 6 th Framework Programme (FP6) Integrated Project EuroHear, LSHG-CT-20054-512063.
PY - 2008/12/12
Y1 - 2008/12/12
N2 - Structural genomics initiatives provide ample structures of "hypothetical proteins" (i.e., proteins of unknown function) at an ever increasing rate. However, without function annotation, this structural goldmine is of little use to biologists who are interested in particular molecular systems. To this end, we used (an improved version of) the PatchFinder algorithm for the detection of functional regions on the protein surface, which could mediate its interactions with, e.g., substrates, ligands, and other proteins. Examination, using a data set of annotated proteins, showed that PatchFinder outperforms similar methods. We collected 757 structures of hypothetical proteins and their predicted functional regions in the N-Func database. Inspection of several of these regions demonstrated that they are useful for function prediction. For example, we suggested an interprotein interface and a putative nucleotide-binding site. A web-server implementation of PatchFinder and the N-Func database are available at http://patchfinder.tau.ac.il/.
AB - Structural genomics initiatives provide ample structures of "hypothetical proteins" (i.e., proteins of unknown function) at an ever increasing rate. However, without function annotation, this structural goldmine is of little use to biologists who are interested in particular molecular systems. To this end, we used (an improved version of) the PatchFinder algorithm for the detection of functional regions on the protein surface, which could mediate its interactions with, e.g., substrates, ligands, and other proteins. Examination, using a data set of annotated proteins, showed that PatchFinder outperforms similar methods. We collected 757 structures of hypothetical proteins and their predicted functional regions in the N-Func database. Inspection of several of these regions demonstrated that they are useful for function prediction. For example, we suggested an interprotein interface and a putative nucleotide-binding site. A web-server implementation of PatchFinder and the N-Func database are available at http://patchfinder.tau.ac.il/.
KW - PROTEINS
UR - http://www.scopus.com/inward/record.url?scp=57049094420&partnerID=8YFLogxK
U2 - 10.1016/j.str.2008.10.017
DO - 10.1016/j.str.2008.10.017
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AN - SCOPUS:57049094420
SN - 0969-2126
VL - 16
SP - 1755
EP - 1763
JO - Structure
JF - Structure
IS - 12
ER -