dear all , I've done homology modeling of a protein using modweb and hhpred .now , how can i do energy minimization or identify the best model? i am about to start homology modeling. Thanks in advance.
Here few of them....
Energy Minimization:
YASARA Energy Minimization Server: http://www.yasara.org/minimizationserver.htm
Chiron portal: http://troll.med.unc.edu/chiron/login.php
PRODRG2: http://davapc1.bioch.dundee.ac.uk/prodrg/
Gromacs energy minimization: http://lorentz.immstr.pasteur.fr/gromacs/minimization_submission.php
Structure Evaluation:
Harmony http://caps.ncbs.res.in/harmony/
ModEval Model Evaluation Server http://modbase.compbio.ucsf.edu/evaluation//
HoPPscore http://hoppscore.lbl.gov/
PROSESS http://www.prosess.ca/
Do you want to perform minimization in order to remove side chain clashes? SCWRL is good for that and quite fast. If you dont want to install any program, you can use CHARMM-GUI for energy minimization online. According to my experience the best way is to use Modeller from the alignments generated from various programs like ClustalW, Muscle, HHPred in case of distant homology. The best scoring servers in the previous CASP9 did actually that and scored their models using PCons, ModFold etc. You may look at the best protein model quality assesment (MQAP) programs in CASP assessment section.
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