Loop Scoring with DFIRE Potential
PDB file:
Or PDB ID(lower case):
Protein Loop Region:
Starting residue position:
Length of loop:
usage: for example, in pdb file 1aaj, there is only one chain. (Note: please input a structure which has only one chain. ) The loop region is from 82nd PHE to 85th ALA, and thus the length of loop is 4. The input and output are the following:
Input
Starting residue position: 82
Length of loop: 4
Output
REMARK /tmp/_tmp.pdb min=-724.288991 nomin=-655.349239
... pdb formated structure ...
Note
"min=-724.288991" is the DFIRE energy for the loop with sidechain minimization.
"nomin=-655.349239" is the DFIRE energy for the loop without any sidechain minimization.
The output structure is the whole protein structure and the sidechains of amino acid residues on loop are minimized with DFIRE energy.

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