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Following are the general energy terms used in the I-TASSER modeling:

• contact_cut.comm: Residue contact cutoff parameters
• contact_profile.comm: Side-chain contacts environment profile
• contact3.comm: Orientation-dependent side-chain contact potential
• CA13.comm: Short-range C-alpha correlation of (i,i+2)
• CA14.comm: Short-range C-alpha correlation of (i,i+3)
• CA15.comm: Short-range C-alpha correlation of (i,i+4)
• CA14s.comm: Short-range C-alpha correlation of (i,i+3) for strands
• CA14h.comm: Short-range C-alpha correlation of (i,i+3) for helices
• CA15s.comm: Short-range C-alpha correlation of (i,i+4) for strands
• CA15h.comm: Short-range C-alpha correlation of (i,i+4) for helices
• CB.comm: C-beta positions
• sidechain.comm: Sidechain center positions

If you have questions about how to use the energy terms, please read the following

Questions & Answers (09/03/2007).
Questions & Answers (11/21/2007).
Questions & Answers (04/19/2008).

A new distance-specific atomic potential (RW) is available at http://zhanglab.dcmb.med.umich.edu/RW.

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References:
1. Yang Zhang, Andrzej Kolinski, Jeffrey Skolnick. Touchstone II: A new approach to ab initio protein Structure Prediction. Biophysical Journal, vol 85, 1145 (2003). [PDF]
2. Yang Zhang, Jeffrey Skolnick. Automated structure prediction of weakly homologous proteins on a genomic scale. Proceedings of the National Academy of Sciences of USA, vol 101, 7594 (2004). [PDF]
3. Sitao Wu, Jeffrey Skolnick, Yang Zhang. Ab initio modeling of small proteins by iterative TASSER simulations BMC Biology, vol 5, 17 (2007). [PDF]