Berkeley-SC-Ensemble Decoys
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.
Relevant Publications and Links-
1) A. Bhowmick, T. Head-Gordon (2015). A monte carlo method for generating side chain structural ensembles. Structure 23(1):44-55. doi: 10.1016/j.str.2014.10.011
2) 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). http://DOI:https://doi.org/10.1016/j.str.2007.05.004
3) Original 2007 Rosetta decoyset link – http://depts.washington.edu/bakerpg/decoys/