HIPPO: HIstogram-based Pseudo-POtential for scoring protein-ssRNA fragment-based docking poses.

Background: The RNA-Recognition motif (RRM) is a protein domain that binds single-stranded RNA (ssRNA) and is present in as much as 2% of the human genome. Despite this important role in biology, RRM-ssRNA interactions are very challenging to study on the structural level because of the remarkable flexibility of ssRNA. In the absence of atomic-level experimental data, the only method able to predict the 3D structure of protein-ssRNA complexes with any degree of accuracy is ssRNA'TTRACT, an ssRNA fragment-based docking approach using ATTRACT.

ProtNAff: protein-bound Nucleic Acid filters and fragment libraries.

Motivation: Atomistic models of nucleic acids (NA) fragments can be used to model the 3D structures of specific protein-NA interactions and address the problem of great NA flexibility, especially in their single-stranded regions. One way to obtain relevant NA fragments is to extract them from existing 3D structures corresponding to the targeted context (e.g.