From orry.molsoft from gmail.com Mon Nov 10 19:08:36 2008 From: orry.molsoft from gmail.com (Andrew Orry) Date: Tue Nov 11 15:34:47 2008 Subject: [Protein-crystallography] Protein Structure and Drug Design Workshop - MolSoft February 5-6 2009 Message-ID: <4918CD04.4050602@molsoft.com> **MolSoft ICM Workshop: "Protein Structure and Drug Discovery" February 5th to 6th 2009 La Jolla, CA.** Please see the following invitation to attend MolSoft's (www.molsoft.com) Protein Structure and Drug Design Workshop on February 5th to 6th 2009 in La Jolla, California USA. Please see www.molsoft.com/training.html for more information and a registration form. Our workshops are suitable for chemists and biologists who would like to learn more about computational drug discovery and bioinformatics. No prior knowledge in this field is required to participate. The workshop is presented by Prof. Ruben Abagyan (The Scripps Research Institute) and Dr. Maxim Totrov (MolSoft). The workshops will consist of lectures, demonstrations, and "hands-on" computational experiments and will cover the following topics: - Sequence and Protein Structure Analysis - Protein Modeling and Simulations - Structure Validation and Optimization - Ligand Binding Site Prediction - Small Molecule Docking and Virtual Ligand Screening - Structure-based development of target-specific compound libraries - Cheminformatics, Chemical Clustering, Searching, Superposition etc... - QSAR, Machine Learning - Protein-Protein Docking We will demonstrate and train you in the use of many of our new developments in computational chemistry and biology including: - 3D Ligand Editor - design and optimize ligands interactively - Markush Library Docking - Multiple Receptor Docking (A method to incorporate receptor flexibility) - Automated model building into electron density - Atomic property field chemical superposition - Fast machine learning tools for QSAR - Pharmacophore drawing and searching - Compound library enumeration tools - Screen-grabbing molecular movie making "The objective of this training workshop is to help chemists and biologists solve challenging problems in the area of drug discovery by efficient use of the science and technology present in ICM molecular modeling tools." Prof. Ruben Abagyan (The Scripps Research Institute and Co-Founder of Molsoft LLC) Please see our website at www.molsoft.com for more details or E mail andy@molsoft.com or call (858) 625 2000 ext.108. Please join the ICM Discussion Forum: http://groups.google.com/group/molsoft-icm-forum Latest Newsletter: http://www.molsoft.com/news.html MolSoft is a La Jolla based company that is a primary source of new breakthrough technologies in computational chemistry and biology. Molsoft is committed to solving intellectually challenging problems in drug discovery and computational biology. -- Andrew Orry Ph.D. Senior Scientist MolSoft LLC 3366 North Torrey Pines Court Suite 300 La Jolla, CA 92037 U S A Phone: (858) 625-2000 (x108) Fax: (858) 625-2888 www.molsoft.com From mitrakheirabadi from yahoo.com Wed Nov 12 14:30:17 2008 From: mitrakheirabadi from yahoo.com (Mitra Kheirabadi) Date: Thu Nov 13 11:08:04 2008 Subject: [Protein-crystallography] I want to crystallize one protein with signal peptide on N-terminal, Is it possible? Message-ID: <140112.69149.qm@web36301.mail.mud.yahoo.com> Hi everybody ? I wanna crystallize a 16 kDa protein with signal peptide on the N-terminl, is it correct? Protein?activity is good with signal peptide but I don't know?if this signal peptide effect on 3D structure? Would you please guide me? ? Best ? Mitra?? From clement from bio.mls.eng.osaka-u.ac.jp Thu Nov 13 21:44:57 2008 From: clement from bio.mls.eng.osaka-u.ac.jp (Clement Angkawidjaja) Date: Thu Nov 13 21:45:08 2008 Subject: [Protein-crystallography] Re: I want to crystallize one protein with signal peptide on N-terminal, Is it possible? In-Reply-To: <200811131703.mADH35V16348@net.bio.net> References: <200811131703.mADH35V16348@net.bio.net> Message-ID: Hi Mitra, The answer, like most answers about protein crystallization, is "It depends." The thing is, most proteins with N-terminal signal sequence are not (completely) folded when the signal is intact. But since you mentioned that yours is active with the signal, it MAY crystallize. However, I would suggest that you perform crystallization screening using both the intact and signal sequence-removed constructs. This way you can save a lot of time if one of them does not crystallize well. Regards, Clement Angkawidjaja, Ph.D Assistant professor Laboratory of Molecular Biotechnology Division of Advance Science and Biotechnology GSE Common East 8F 2-1 Yamadaoka, Suita-shi, Osaka, 565-0871, Japan Tel/fax: +81-6-6879-4580 ----- Original Message ----- From: To: Sent: Friday, November 14, 2008 2:03 AM Subject: Xtal-log Digest, Vol 39, Issue 2 > Send Xtal-log mailing list submissions to > xtal-log@net.bio.net > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.bio.net/biomail/listinfo/xtal-log > or, via email, send a message with subject or body 'help' to > xtal-log-request@net.bio.net > > You can reach the person managing the list at > xtal-log-owner@net.bio.net > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Xtal-log digest..." > > > Today's Topics: > > 1. I want to crystallize one protein with signal peptide on > N-terminal, Is it possible? (Mitra Kheirabadi) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 12 Nov 2008 11:30:17 -0800 (PST) > From: Mitra Kheirabadi > Subject: [Protein-crystallography] I want to crystallize one protein > with signal peptide on N-terminal, Is it possible? > To: xtal-log@magpie.bio.indiana.edu > Message-ID: <140112.69149.qm@web36301.mail.mud.yahoo.com> > Content-Type: text/plain; charset=iso-8859-1 > > Hi everybody > > I wanna crystallize a 16 kDa protein with signal peptide on the N-terminl, > is it correct? Protein activity is good with signal peptide but I don't > know if this signal peptide effect on 3D structure? Would you please guide > me? > > Best > > Mitra > > > > > ------------------------------ > > _______________________________________________ > Xtal-log mailing list > Xtal-log@net.bio.net > http://www.bio.net/biomail/listinfo/xtal-log > > End of Xtal-log Digest, Vol 39, Issue 2 > *************************************** From mitrakheirabadi from yahoo.com Wed Nov 12 14:30:17 2008 From: mitrakheirabadi from yahoo.com (Mitra Kheirabadi) Date: Fri Nov 14 11:52:26 2008 Subject: [Protein-crystallography] I want to crystallize one protein with signal peptide on N-terminal, Is it possible? Message-ID: <140112.69149.qm@web36301.mail.mud.yahoo.com> Hi everybody ? I wanna crystallize a 16 kDa protein with signal peptide on the N-terminl, is it correct? Protein?activity is good with signal peptide but I don't know?if this signal peptide effect on 3D structure? Would you please guide me? ? Best ? Mitra?? From mitrakheirabadi from yahoo.com Fri Nov 14 12:59:55 2008 From: mitrakheirabadi from yahoo.com (Mitra Kheirabadi) Date: Sat Nov 15 12:38:09 2008 Subject: [Protein-crystallography] Re: Xtal-log Digest, Vol 39, Issue 3 In-Reply-To: <200811141703.mAEH38V01754@net.bio.net> Message-ID: <793581.41491.qm@web36305.mail.mud.yahoo.com> Dear Clement, ? Hi, ? Thanks for your comment and attention. ? Best wishes --- On Fri, 11/14/08, xtal-log-request@oat.bio.indiana.edu wrote: From: xtal-log-request@oat.bio.indiana.edu Subject: Xtal-log Digest, Vol 39, Issue 3 To: xtal-log@magpie.bio.indiana.edu Date: Friday, November 14, 2008, 8:33 PM Send Xtal-log mailing list submissions to xtal-log@net.bio.net To subscribe or unsubscribe via the World Wide Web, visit http://www.bio.net/biomail/listinfo/xtal-log or, via email, send a message with subject or body 'help' to xtal-log-request@net.bio.net You can reach the person managing the list at xtal-log-owner@net.bio.net When replying, please edit your Subject line so it is more specific than "Re: Contents of Xtal-log digest..." Today's Topics: 1. Re: I want to crystallize one protein with signal peptide on N-terminal, Is it possible? (Clement Angkawidjaja) 2. I want to crystallize one protein with signal peptide on N-terminal, Is it possible? (Mitra Kheirabadi) ---------------------------------------------------------------------- Message: 1 Date: Fri, 14 Nov 2008 11:44:57 +0900 From: "Clement Angkawidjaja" Subject: [Protein-crystallography] Re: I want to crystallize one protein with signal peptide on N-terminal, Is it possible? To: Message-ID: Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Hi Mitra, The answer, like most answers about protein crystallization, is "It depends." The thing is, most proteins with N-terminal signal sequence are not (completely) folded when the signal is intact. But since you mentioned that yours is active with the signal, it MAY crystallize. However, I would suggest that you perform crystallization screening using both the intact and signal sequence-removed constructs. This way you can save a lot of time if one of them does not crystallize well. Regards, Clement Angkawidjaja, Ph.D Assistant professor Laboratory of Molecular Biotechnology Division of Advance Science and Biotechnology GSE Common East 8F 2-1 Yamadaoka, Suita-shi, Osaka, 565-0871, Japan Tel/fax: +81-6-6879-4580 ----- Original Message ----- From: To: Sent: Friday, November 14, 2008 2:03 AM Subject: Xtal-log Digest, Vol 39, Issue 2 > Send Xtal-log mailing list submissions to > xtal-log@net.bio.net > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.bio.net/biomail/listinfo/xtal-log > or, via email, send a message with subject or body 'help' to > xtal-log-request@net.bio.net > > You can reach the person managing the list at > xtal-log-owner@net.bio.net > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Xtal-log digest..." > > > Today's Topics: > > 1. I want to crystallize one protein with signal peptide on > N-terminal, Is it possible? (Mitra Kheirabadi) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 12 Nov 2008 11:30:17 -0800 (PST) > From: Mitra Kheirabadi > Subject: [Protein-crystallography] I want to crystallize one protein > with signal peptide on N-terminal, Is it possible? > To: xtal-log@magpie.bio.indiana.edu > Message-ID: <140112.69149.qm@web36301.mail.mud.yahoo.com> > Content-Type: text/plain; charset=iso-8859-1 > > Hi everybody > > I wanna crystallize a 16 kDa protein with signal peptide on the N-terminl, > is it correct? Protein activity is good with signal peptide but I don't > know if this signal peptide effect on 3D structure? Would you please guide > me? > > Best > > Mitra > > > > > ------------------------------ > > _______________________________________________ > Xtal-log mailing list > Xtal-log@net.bio.net > http://www.bio.net/biomail/listinfo/xtal-log > > End of Xtal-log Digest, Vol 39, Issue 2 > *************************************** ------------------------------ Message: 2 Date: Wed, 12 Nov 2008 11:30:17 -0800 (PST) From: Mitra Kheirabadi Subject: [Protein-crystallography] I want to crystallize one protein with signal peptide on N-terminal, Is it possible? To: xtal-log@magpie.bio.indiana.edu Message-ID: <140112.69149.qm@web36301.mail.mud.yahoo.com> Content-Type: text/plain; charset=iso-8859-1 Hi everybody ? I wanna crystallize a 16 kDa protein with signal peptide on the N-terminl, is it correct? Protein?activity is good with signal peptide but I don't know?if this signal peptide effect on 3D structure? Would you please guide me? ? Best ? Mitra?? ------------------------------ _______________________________________________ Xtal-log mailing list Xtal-log@net.bio.net http://www.bio.net/biomail/listinfo/xtal-log End of Xtal-log Digest, Vol 39, Issue 3 ***************************************