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I-TASSER potential
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).
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]
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