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 CHARMM-HM?
CHARMM (Chemistry at HARvard Macromolecular Mechanics) is one of the oldest and most popular programs for structural simulations in the field of computational chemistry. Despite its widespread usage and extensive features, application towards homology modeling was limited due to lack of potential terms for structural restraints. We have developed the homology modeling version, CHARMM-HM, by incorporating the homology-derived restraints and analytical forces in MODELLER into the CHARMM potential parameters. Comparison with MODELLER showed that the side-chain accuracy improved slightly by 0-5% depending on the choice of optimization methods. Furthermore, we have set up a web server dedicated to automated homology modeling in an effort to facilitate usage. Simple input of sequence or alignment produces the structural models with the quality evaluation scores. With the flexibility of CHARMM and user-friendly web server, CHARMM-HM would be a valuable asset for homology modeling.

 User information
   Enter a name for your project
   Select your result on public or private Public   Private
   Enter your E-mail (Optional) (If you want to recieve job status and result)

 Input data
Type I (Unknown alignment)
 Enter the protein sequence (FASTA format)
 Or upload sequence (Example for FASTA) :
 Identity cutoff (optional: default is 60%)
 
Type II (Known alignment)
 Upload your alignment (Example for PIR MODELLER format + PDB template ) Download


 Simulation options
 1) Select Global Optimizer
SA (Simulated Annealing) REX (Replica Exchage Method) MCM (Monte Carlo Minimization)

2) Number of Structures to Generate (available in SA)


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