Data from Publications

Scoing Program

Both papers relied on an in-house scoring program.

Protein-DNA paper

Robertson, T. and Varani, G. "An all-atom, distance-dependent scoring function for the prediction of protein-DNA interactions from structure." Proteins 66(2) 359-374 (2007).

Protein-DNA Docking Decoys

These files allow the reconstruction of the protein-DNA docking decoys used to test the scoring functions. In order to conserve bandwidth and disk space, these decoys are provided as FTDock output files, which can be used in combination with the build program from the FTDock package (available here), to create PDB files for every decoy structure. To do this, you'll need to download both the FTDock output files, as well as the set of PDB structures used to conduct the original docking runs:

Docking Decoy Scores

These files contain the all-atom scores corresponding to the docking decoy sets from the Robertson and Varani (2007) paper. Both "fair" and "unfair" scores are included, in all of the paramterizations tested in the paper, for the best (lowest-RMSD) 2000 decoy structures in each set:

Protein-RNA paper

S. Zheng, T. A. Robertson and G. Varani A knowledge-based potential function predicts the specificity and binding energy of RNA-binding proteins FEBS J. 274 6378-6391 (2007)

Rosetta Decoys

These files contain near native RNA structures in complex with RNA binding proteins generated using Rosetta:

In Progress

Computation (last edited 2013-07-31 21:29:11 by varani-fw63)