Journal
NUCLEIC ACIDS RESEARCH
Volume 43, Issue W1, Pages W425-W430Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkv493
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Funding
- European Research Council [RNA+P = 123D]
- Polish Ministry of Science [Iuventus Plus] [0570/IP1/2011/71]
- REGPOT Grant FishMed, European Commission (EC) [316125]
- 'Ideas for Poland' Fellowship, Foundation for Polish Science
- EC Structural Funds [POIG.02.03.00-00-003/09]
- FishMed, EC [316125]
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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.
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