Georgia Institute of TechnologyCenter for the study of systems biology
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AMBER (ff99) Benchmarking

Reference: L.Wroblewska and J. Skolnick; Can a physics-based, all-atom potential find a protein's native structure among misfolded structures? I. Large scale AMBER benchmarking; J.Comp.Chem.; 2007; in press, DOI: 10.1002/jcc.20720


Benchmark protein lists:

All-atom decoys (660MB)

"tar xvf decoys99.tar" will create the directory "decoys99" containing decoys for the 50-set.

Each decoy set (PDBid.tar.bz2 file) is a compressed directory containing:

  • 1040 decoys (min.#.pdb)
  • native pdb (nat.pdb)

"tar jxvf PDBid.tar.bz2" will uncompress the archive and generate the PDBid directory.

The 1040 structures are minimized snapshots from 2ns molecular dynamics simulations (AMBER/GBSA, ff99, igb=1). For structures 1-1000, the starting structure was a decoy generated with coarse-grained potential. Structures 1001-1020 are snapshots from molecular dynamics of the native structure. Structures 1021-1040 are snapshots from molecular dynamics of native that was reduced to coarse- grained model prior to the simulation, and reconstructed to all-atom model reconstruction using the same procedure as was used for the decoys.

Detailed information about the dataset and the simulations may be found in the AMBER benchmarking publication. Please cite reference above when using the dataset.