PREFMD

Protein structure REFinement via Molecular Dynamics

Improvement of the global structure of template-based models via MD and structural averaging (as seen in CASP).

L. Heo, M. Feig: Bioinformatics  (2017)
M. Feig, V. Mirjalili: Prot. Struct. Funct. Bioinf.  (2016) 84 (Suppl. 1), 282-292
A typical example:
Initial model (blue) PDB
Refined model (green) PDB
Native structure red) PDB RCSB

In the form below, provide a PDB file containing a single chain (300 residues max.). If an email address is provided, the result will be sent once the refinement is completed (expect 24-72 hours). Otherwise, the results can be retrieved via a link given after submission.