Web-links as a means to document annotated sequence and 3D-structure alignments in systems biology.
Reconstructed biological networks are the essence of knowledge originating from experiments, scientific literature, databases and modeling. Proteins are the major players in biological networks. If the function of a protein is not yet known, it can often be deduced from homologous proteins that are already experimentally characterized. As such conclusions are not as reliable as experimental evidences, they should be well documented and reviewed when experimental data is available. Inconsistent operation of the resulting network may indicate invalid functional assignments. Here we present a novel technique to refer to annotated sequence and 3D-structure alignments in terms of Web links. By clicking the Web link the alignment is viewed in the protein viewer STRAP. References to public protein databases such as EMBL, KEGG, GENBANK, PDB, PFAM, PRODOM and UNIPROT/SWISSPROT are encoded in the Web-link whereas the alignment gaps are computed dynamically. Site specific annotations and 3D-rendering commands may also be included in the Web-link. In contrast, sequence features such as active site residues, phosphorylation sites and ligand binding sites do not need to be specified, as long as they are retrievable from public databases. The method has been developed for an information management system that is used for the reconstruction of metabolic pathways. The alignment viewer may also be of interest for experimentalists, as it can be used to document sites of interest in the proteins under experimental investigation. These alignment Web links may be included in project Web sites.


BACKGROUND
The STRAP program is published under the GNU-license condition and is automatically downloaded from http://3d-alignment.eu/ or http://www.charite.de/bioinf/strap/ when an alignment reference is clicked.
Gille
Chirstoph
C
Medical Faculty of the Humboldt University Berlin, Charité Berlin, Institute of Biochemistry, 10117 Berlin, Monbijoustrafsse 2, Germany. christoph.gille@charite.de.
Hoppe
Andreas
A
Holzhütter
Herman-Georg
HG
D000595:Amino Acid Sequence; D001695:Biology / Q000379:methods*; D002477:Cells / Q000737:chemistry / Q000378:metabolism; D019992:Databases as Topic; D030562:Databases, Protein; D006593:Hexokinase / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D008968:Molecular Conformation; D011506:Proteins / Q000737:chemistry / Q000378:metabolism; D016415:Sequence Alignment / Q000379:methods*; D012984:Software
D011506:Proteins; D006593:Hexokinase