From owner-chemistry@ccl.net Sun Aug 26 17:23:01 2012 From: "Marc Baaden baaden . smplinux.de" To: CCL Subject: CCL: prediction of peptide structures and protein-protein docking Message-Id: <-47471-120826165812-419-idjr5HF6EhHiYKDiQm8/BQ|server.ccl.net> X-Original-From: Marc Baaden Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Sun, 26 Aug 2012 22:59:42 +0200 Mime-Version: 1.0 Sent to CCL by: Marc Baaden [baaden,,smplinux.de] Dear Guiyu Zhao, You may want to try the Pepfold server: http://bioserv.rpbs.univ-paris-diderot.fr/PEP-FOLD/ The current version should work for peptides up to 36 amino acids. Kind regards, Marc Baaden >>> "Guiyu Zhao guiyu.zhao(0)astrazeneca.com" said: >> >> Sent to CCL by: "Guiyu Zhao" [guiyu.zhao{:}astrazeneca.com] >> Dear CCL colleagues, >> >> I'm trying to fulfill a request from my colleagues about a 17-membered pept ide. They want to get a rough idea about the peptide's 3D structure and, i f possible, the binding pose with a cell receptor. >> >> I feel the task is chellenging for me not only because I'm a modeler on sma ll molecules and not familiar with protein modeling, but also because we a re lack of commercial tools to do peptide structure prediction and protein -protein docking. So first of all, is there any free tool to do such calcu lations? RosettaDcok and BioLuminate from Schrodinger Inc. are not availab le to me. Then, is it reallistic to model a peptide's 3D structure without knowing anything about its secondary structure (my colleagues only provid ed me its sequence)? >> >> Thank you in advance for any response. >> >> Kind regards, >> Guiyu Zhao>> >> Marc Baaden -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:baaden---smplinux.de - http://www.baaden.ibpc.fr FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217