Gille Chirstoph, Hoppe Andreas, Holzhütter Herman-Georg
Medical Faculty of the Humboldt University Berlin, Charité Berlin, Institute of Biochemistry, 10117 Berlin, Monbijoustrafsse 2, Germany.
Genome Inform. 2008;20:277-84.
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.
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.
重建的生物网络是源自实验、科学文献、数据库和建模的知识的核心。蛋白质是生物网络中的主要参与者。如果一种蛋白质的功能尚不清楚，通常可以从已经通过实验表征的同源蛋白质中推断出来。由于这样的结论不如实验证据可靠，所以当有实验数据时，应该对其进行充分记录和审查。所得网络的不一致操作可能表明功能分配无效。在这里，我们提出了一种新技术，通过网页链接来引用带注释的序列和三维结构比对。通过点击网页链接，可以在蛋白质查看器STRAP中查看比对结果。对诸如EMBL、KEGG、GENBANK、PDB、PFAM、PRODOM和UNIPROT/SWISSPROT等公共蛋白质数据库的引用编码在网页链接中，而比对缺口是动态计算的。特定位点的注释和三维渲染命令也可能包含在网页链接中。相比之下，只要可以从公共数据库中检索到，诸如活性位点残基、磷酸化位点和配体结合位点等序列特征就无需指定。该方法是为一个用于代谢途径重建的信息管理系统而开发的。比对查看器对于实验人员也可能有意义，因为它可用于记录正在进行实验研究的蛋白质中感兴趣的位点。这些比对网页链接可以包含在项目网站中。
STRAP程序是在GNU许可条件下发布的，当点击比对参考文献时会自动从http://3d-alignment.eu/ 或http://www.charite.de/bioinf/strap/ 下载。
