Berkeley-SC-Ensemble

Rosetta all-atom decoys [Berkeley-SC-Ensemble version]

Updated by Asmit Bhowmick: May 15, 2014

The directory contains alternate high scoring conformations of Rosetta decoys and native state structures for 55 proteins. These alternate conformations were generated using the MC-SCE method developed by our group by placing alternate side chain rotamers on a given backbone. The best generated structure(for each native and its corresponding decoys) from our MC-SCE method was energy-minimized using the all-atom AMBER-ff99SB forcefield with the GB-HPMF solvation model. Currently, PDB files for 24 proteins can be downloaded from the link at the bottom of the page. Additional structures will be added soon.

Relevant Publications and Links-

1) MC-SCE method – Bhowmick,A., Head-Gordon,T. Structural Ensemble Characterization of Protein Native and Misfolded States (Submitted, 2014)

2) GB-HPMF model – Lin, M. S., Fawzi, N. L. & Head-Gordon, T. Hydrophobic potential of mean force as a solvation function for protein structure prediction. Structure 15, 727-740 (2007).

3) Original 2007 Rosetta decoyset link – http://depts.washington.edu/bakerpg/decoys/

Contact for any questions :Asmit Bhowmick (asmit [at] berkeley [dot] edu)

Berkeley_SC_Ensemble