Kleinjung Jens, Fraternali Franca
Bioinformatics Unit, Faculty of Sciences, Vrije Universiteit De Boelelaan 1081A, 1081HV, Amsterdam, The Netherlands.
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W342-6. doi: 10.1093/nar/gki369.
Large-scale analysis of biomolecular complexes reveals the functional network within the cell. Computational methods are required to extract the essential information from the available data. The POPSCOMP server is designed to calculate the interaction surface between all components of a given complex structure consisting of proteins, DNA or RNA molecules. The server returns matrices and graphs of surface area burial that can be used to automatically annotate components and residues that are involved in complex formation, to pinpoint conformational changes and to estimate molecular interaction energies. The analysis can be performed on a per-atom level or alternatively on a per-residue level for low-resolution structures. Here, we present an analysis of ribosomal structures in complex with various antibiotics to exemplify the potential and limitations of automated complex analysis. The POPSCOMP server is accessible at http://ibivu.cs.vu.nl/programs/popscompwww/.
生物分子复合物的大规模分析揭示了细胞内的功能网络。需要计算方法从现有数据中提取关键信息。POPSCOMP服务器旨在计算由蛋白质、DNA或RNA分子组成的给定复杂结构的所有组件之间的相互作用表面。该服务器返回表面积掩埋的矩阵和图表，可用于自动注释参与复合物形成的组件和残基，确定构象变化并估计分子相互作用能。该分析可以在每个原子水平上进行，或者对于低分辨率结构在每个残基水平上进行。在这里，我们展示了核糖体结构与各种抗生素复合物的分析，以例证自动复合物分析的潜力和局限性。可通过http://ibivu.cs.vu.nl/programs/popscompwww/访问POPSCOMP服务器。
