Hi:
I am working with a protein which we have characterized to be a dimer. Homologous proteins are also dimers and the 3D structures are of the dimeric forms. In these proteins, the amino acid sequence of the dimer is represented as A and B chains. Can I model my protein as a dimer by arranging my sequence as A and B chains with a " | " in between? Would appreciate some thoughts. Thanks,
Guru Rao
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Yes, you can. The only difference is chain breaks are listed in the alignment with a "/" (not a "|").
--- Eswar Narayanan, Ph.D Mission Bay Genentech Hall 600 16th Street, Suite N474Q University of California, San Francisco San Francisco, CA 94143-2240 (CA 94158 for courier) Tel +1 (415) 514-4233; Fax +1 (415) 514-4231 http://www.salilab.org/~eashwar
-----Original Message----- From: modeller_usage-bounces@salilab.org [mailto:modeller_usage-bounces@salilab.org] On Behalf Of Rao, Guru Sent: Thursday, November 13, 2003 6:03 AM To: modeller_usage@salilab.org Subject: [modeller_usage] modeling a dimer
Hi:
I am working with a protein which we have characterized to be a dimer. Homologous proteins are also dimers and the 3D structures are of the dimeric forms. In these proteins, the amino acid sequence of the dimer is represented as A and B chains. Can I model my protein as a dimer by arranging my sequence as A and B chains with a " | " in between? Would appreciate some thoughts. Thanks,
Guru Rao
This communication is for use by the intended recipient and contains information that may be privileged, confidential or copyrighted under applicable law. If you are not the intended recipient, you are hereby formally notified that any use, copying or distribution of this e-mail, in whole or in part, is strictly prohibited. Please notify the sender by return e-mail and delete this e-mail from your system. Unless explicitly and conspicuously designated as "E-Contract Intended", this e-mail does not constitute a contract offer, a contract amendment, or an acceptance of a contract offer. This e-mail does not constitute a consent to the use of sender's contact information for direct marketing purposes or for transfers of data to third parties.
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Eswar Narayanan -
Rao, Guru