Tuszynska Irina, Magnus Marcin, Jonak Katarzyna, Dawson Wayne, Bujnicki Janusz M
Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland Institute of Informatics, University of Warsaw, Banacha 2, PL-02-097 Warsaw, Poland.
Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland.
Nucleic Acids Res. 2015 Jul 1;43(W1):W425-30. doi: 10.1093/nar/gkv493. Epub 2015 May 14.
Protein-RNA and protein-DNA interactions play fundamental roles in many biological processes. A detailed understanding of these interactions requires knowledge about protein-nucleic acid complex structures. Because the experimental determination of these complexes is time-consuming and perhaps futile in some instances, we have focused on computational docking methods starting from the separate structures. Docking methods are widely employed to study protein-protein interactions; however, only a few methods have been made available to model protein-nucleic acid complexes. Here, we describe NPDock (Nucleic acid-Protein Docking); a novel web server for predicting complexes of protein-nucleic acid structures which implements a computational workflow that includes docking, scoring of poses, clustering of the best-scored models and refinement of the most promising solutions. The NPDock server provides a user-friendly interface and 3D visualization of the results. The smallest set of input data consists of a protein structure and a DNA or RNA structure in PDB format. Advanced options are available to control specific details of the docking process and obtain intermediate results. The web server is available at http://genesilico.pl/NPDock.
蛋白质 - RNA和蛋白质 - DNA相互作用在许多生物过程中发挥着重要作用。对这些相互作用的详细理解需要了解蛋白质 - 核酸复合物的结构。由于通过实验确定这些复合物既耗时，在某些情况下可能也徒劳无功，因此我们专注于从单独结构出发的计算对接方法。对接方法被广泛用于研究蛋白质 - 蛋白质相互作用；然而，只有少数方法可用于构建蛋白质 - 核酸复合物模型。在此，我们描述了NPDock（核酸 - 蛋白质对接）；这是一个用于预测蛋白质 - 核酸结构复合物的新型网络服务器，它实现了一个计算工作流程，包括对接、姿势评分、最佳评分模型的聚类以及最有前景解决方案的优化。NPDock服务器提供了用户友好的界面和结果的3D可视化。最小的输入数据集由PDB格式的蛋白质结构和DNA或RNA结构组成。还提供了高级选项来控制对接过程的特定细节并获得中间结果。该网络服务器可在http://genesilico.pl/NPDock上获取。
