Table 1 Comparison of existing ssRNA-protein fragment-based docking methods
From: HIPPO: HIstogram-based Pseudo-POtential for scoring protein-ssRNA fragment-based docking poses
Method | Advantages | Disadvantages |
|---|---|---|
RNA-LIM | Simplicity (single nucleotide representation) | Source code not available for download |
Can predict only global binding site | ||
No orientation of nucleotides | ||
FBDRNA | Simplicity (single nucleotide representation) | Source code not available for download |
Created for design | Poor docking predictions (no success on chains longer than 3 nucleotides) | |
Modified nucleotides accepted | ||
RNP-denovo | Protocol available for download | Requires as input the precise coordinates of at least the first and the last nucleotides |
Gives acceptable RMSDs in top-100 docking poses (fold and dock) | ||
ssRNA'ATTRACT | Protocol available for download | Works at the fragment level |
Gives acceptable RMSDs while performing completely blind docking | Requires a lot of docking poses | |
Produces many models | ||
ssRNA'ATTRACT + HIPPO | Protocol available for download | Works at the fragment level |
Gives acceptable RMSDs while performing completely blind docking | Requires a lot of docking poses | |
Provides enrichment of good models compared to ssRNA'ATTRACT alone |