Nucleic Acids Research, 2006, Vol. 34, Web Server issue W225–W230 doi:10.1093/nar/gkl121 sgTarget: a target selection resource for structural genomics Ana P. C. Rodrigues, Barry J. Grant and Roderick E. Hubbard* Structural Biology Laboratory, University of York, York YO10 5YW, UK Received February 14, 2006; Revised February 22, 2006; Accepted March 13, 2006 ABSTRACT sgTarget (http://www.ysbl.york.ac.uk/sgTarget) is a web-based resource to aid the selection and priori- tization of candidate proteins for structure deter- mination. The system annotates user submitted gene or protein sequences, identifying sequence families with no homologues of known structure, and characterizing each protein according to a range of physicochemical properties that may affect its expression, solubility and likelihood to crystallize. Summaries of these analyses are available for indi- vidual sequences, as well as whole datasets. This type of analysis enables structural biologists to iter- atively select targets from their genomic sequences of interest and according to their research needs. All sequence datasets submitted to sgTarget are avail- able for users to select and rank using their choice of criteria. sgTarget was developed to support indi- vidual laboratories collaborating in structural and functional genomics projects and should be valuable to structural biologists wishing to employ the wealth of available genome sequences in their structural quests. INTRODUCTION The ﬁrst step in any structure determination project is to select the appropriate molecule for study. Selection strategies vary according to the scientiﬁc context and aims of the project. In structural genomics, which aims to determine the structure of all important bio-molecules, the large number of potential candidates complicates the selection process. It is therefore important to identify the molecules for which a structure (normally of a protein) will provide the highest new informa- tion content and, where possible, quantify measures of how tractable each molecule is for structure determination (1,2). Evolutionary constraints can be used to identify proteins that may adopt similar conformations to known protein structures. For these proteins, modeling approaches may provide sufﬁcient information to understand structure and mechanism. Certain sets of protein characteristics can be inferred from its sequence and employed in the identiﬁcation of proteins that may pose problems during the various stages of structure determination. For example, ﬁbrous domains can frustrate single crystal formation protocols and may frequently be identiﬁed by examining the protein’s amino acid sequence (e.g. certain coiled coils). Structural biology groups wishing to select and prioritize targets from raw sequence data may currently use genomic annotation servers, such as PEDANT (3) or 3D-Genomics (4). These automated services contain gene and protein annotations for a number of completed genomes. Although they detail annotations of relevance to the selection pro- cedure no user accessible mechanism exists for generating target lists. sgTarget was speciﬁcally designed to enable structural biologists to submit their sequence of interest and to select and rank targets according to their choice of criteria. A simple web interface can be used to generate and download target lists that may be iteratively reﬁned by users. The resource was developed to assist individual laboratories participating in structural and functional genomics consorti- ums, as necessitated by our laboratory’s involvement in the Structural Proteomics IN Europe (SPINE) consortium (http:// www.spineurope.org/) and the Plasmodium Functional Genomics Initiative (http://www.sanger.ac.uk/PostGenomics/ plasmodium/). THE sgTarget ANNOTATION PIPELINE A sequence annotation pipeline forms the core of the resource. This carries out the determination and prediction of properties and relationships that can be used in the selection of suitable *To whom correspondence should be addressed. Tel: +44 1904 328267; Fax: +44 1904 328266; Email: rod@ysbl.york.ac.uk Present addresses: Ana P. C. Rodrigues, Burnham Institute for Medical Research, La Jolla CA 92037, USA Barry J. Grant, Department of Chemistry & Biochemistry, University of California San Diego, La Jolla CA 92037, USA The Author 2006. Published by Oxford University Press. 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