Potentials 'R' Us web-server for protein energy estimations with coarse-grained knowledge-based potentials.
BACKGROUND
Knowledge-based potentials have been widely used in the last 20 years for fold recognition, protein structure prediction from amino acid sequence, ligand binding, protein design, and many other purposes. However generally these are not readily accessible online.


RESULTS
Our new knowledge-based potential server makes available many of these potentials for easy use to automatically compute the energies of protein structures or models supplied. Our web server for protein energy estimation uses four-body potentials, short-range potentials, and 23 different two-body potentials. Users can select potentials according to their needs and preferences. Files containing the coordinates of protein atoms in the PDB format can be uploaded as input. The results will be returned to the user's email address.


CONCLUSIONS
Our Potentials 'R' Us server is an easily accessible, freely available tool with a web interface that collects all existing and future protein coarse-grained potentials and computes energies of multiple structural models.
Feng
Yaping
Y
Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011-0320, USA.
Kloczkowski
Andrzej
A
Jernigan
Robert L
RL
D000595:Amino Acid Sequence; D001185:Artificial Intelligence; D003198:Computer Simulation; D004735:Energy Transfer; D020407:Internet; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011381:Programming Languages; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
D011506:Proteins