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 Flowchart of CHARMM-HM


A user can choose an option of two types. One is protein sequence written by FASTA format. Another is the combination of protein sequences and its alignments (PIR Modeller format) and template coordinates (PDB format).

1. If you don't know alignment, PSI-BLAST and in-house PDBaa find an appropriate template from the given sequence.

2. PSI-BLAST makes a suitable alignment of template and query sequences.

3. If you know or provide your alignments, you can skip the first two steps (step 1 and 2).

   3-1. Restraints are generated by modeller-9v7 and they are converted to CHARMM readable input.

   3-2. CHARMM-HM generate homology structures with one of global optimization methods.

4. After homology models are generated, various quality scores are measured for a user to choose which one is the best.

 Tutorial example (For detail view, click the step buttons below.)


 License of CHARMM
       Web site of CHARMM license

      Academic users will be allowed to access the server free of charge.
      Private companies need to provide proof that they have an Accelrys CHARMMm license.
      Academic users can obtain CHARMM by contacting The CHARMM Development Project.
      For-profit companies should contact Accelrys Inc.

      Below is the standard reply to inquiries for the CHARMM program.

      We distribute the source code of the CHARMM program with documentation to individual academic research groups for       a $600 licensing fee. CHARMM runs on a variety of UNIX workstations. No graphics are necessary. The license is       issued to the head of a laboratory or research group. Please send a letter with the full name and title of the professor in       charge of your group and formal mailing address. Describe briefly the kind of research for which you intend to use the       CHARMM program and the computers you will be using. The letter should be addressed to:

      The CHARMM Development Project
      Professor Martin Karplus
      Department of Chemistry & Chemical Biology
      12 Oxford Street
      Harvard University
      Cambridge, Massachusetts 02138
      U. S. A.

      Contact Martin Karplus

 License of MODELLER
       Web site of MODELLER license

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