KNOWLEDGE-BASED POTENTIAL SERVER FOR PROTEINS at coarse grained level
There are two very different types of energy function: physics-based effective potential
function and knowledge-based effective function (Lazaridis & Karplus, Curr Opin Struct Biol,
10, 139, 2000). The knowledge-based potential function implicitly incorporates many physical
interactions, such as hydrophobic, electrostatic, and cation-pi interactions, and these derived
potentials do not necessarily fully reflect true energies but rather effective ones that may be
averaged over many details. The most successful protein structure predictions
usually use knowledge-based
potentials in their force fields for threading or ab initio protein structure prediction by
analyzing results of the Critical Assessment of Techniques for Protein Structure Prediction
(Pillardy et al. Proc Natl Acad Sci USA, 98, 2329, 2001; Skolnick et al.
Proteins, 53, 469, 2003).
This server is designed to use
four-body contact potentials, short-range potentials, and two-body
potentials to calculate energies for the pdb
files you submitted, or you can also ask for the source codes to run in your own
You can click these potentials listed as following to learn more:
Please refer your questions/comments about this server to
Yaping Feng associated with the Jernigan group.
We only test the server using Windows Internet Explorer. We are not sure if
other web browsers work as well.