Iowa State University
Plant Sciences Institute

Laurence H. Baker Center for Bioinformatics and Biological Statistics


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 computer.
You can click these potentials listed as following to learn more:
four-body, general-four-body, short-range, Qa, Qm, Qp, HLPL, SKOb, SKOa, SJKG, MJPL, MJ3h, MJ2h, TS, BT, BFKV, TD, TEl, TEs, RO, MS, MJ1, MJ3, GKS, VD, BL, MSBM


Please upload one protein pdb file.  If you want to upload a set of pdb files, zip them and then submit your *.zip file. The names for your pdb files should be less than 60 characters. Here is an example show you how this server works. Download here!  
The protein PDB files are analyzed at a coarse grained level as follows: the geometric center of all side-chain heavy atoms from one residue is calculated to represent this residue, or if the PDB file has only backbone atoms, then the Ca atom is used to represent the residue.


Please choose potentials. You can choose all potentials by clicking this option button 'All', or any combination of potentials

All

Four-body general-four-body Short-range Qa Qm Qp HLPL SKOb SKOa SJKG MJPL MJ3h MJ2h TS

BT BFKV TD TEl TEs RO MS MJ1 MJ3 GKS VD MSBM

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The correlations between pairwise two-body potentials

Four-body, general four-body and short-range potentials have different characteristics with two-body potentials.
The correlation coefficients among two-body potentials are shown as the following figure, and you can also refer to this paper. (Pokarowski P et al. Proteins 59, 49, 2005)

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.