A coarse-grained force field for Protein-RNA docking

Piotr Setny, Martin Zacharias

Research output: Contribution to journalArticlepeer-review

52 Scopus citations

Abstract

The awareness of important biological role played by functional, non coding (nc) RNA has grown tremendously in recent years. To perform their tasks, ncRNA molecules typically unite with protein partners, forming ribonucleoprotein complexes. Structural insight into their architectures can be greatly supplemented by computational docking techniques, as they provide means for the integration and refinement of experimental data that is often limited to fragments of larger assemblies or represents multiple levels of spatial resolution. Here, we present a coarse-grained force field for protein-RNA docking, implemented within the framework of the ATTRACT program. Complex structure prediction is based on energy minimization in rotational and translational degrees of freedom of binding partners, with possible extension to include structural flexibility. The coarse-grained representation allows for fast and efficient systematic docking search without any prior knowledge about complex geometry.

Original languageEnglish
Pages (from-to)9118-9129
Number of pages12
JournalNucleic Acids Research
Volume39
Issue number21
DOIs
StatePublished - Nov 2011
Externally publishedYes

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