From owner-chemistry@ccl.net Fri Aug 15 14:59:00 2014 From: "Richard Wood richard.wood.:.purduecal.edu" To: CCL Subject: CCL: Need help Message-Id: <-50397-140815104809-19156-+tfAF2FVONKn1f6SCfcotg{=}server.ccl.net> X-Original-From: "Richard Wood" Date: Fri, 15 Aug 2014 10:48:08 -0400 Sent to CCL by: "Richard Wood" [richard.wood{}purduecal.edu] Hi all, Does anybody know of a free software tool that will allow the user to open a protein structure and place a small molecule (i.e., a ligand) anywhere the user wants it to be and then save the resulting structure for further calculations? I ask this because I am working with a ligand-protein system and I was trying to doc the ligand but it would not go where it was predicted to bind. I was trying to reproduce the work of others, but their protein was deemed "proprietary" but their institution and so I was using a different protein structure to start with. Richard From owner-chemistry@ccl.net Fri Aug 15 15:33:00 2014 From: "Andreas Bender, PhD Andreas.Bender:_:cantab.net" To: CCL Subject: CCL: UK QSAR Meeting - Sep 30 __ CCDC & Department of Chemistry, Cambridge University Message-Id: <-50398-140815152046-29118-EWO6mca0CN5/e8YdUsNrtA__server.ccl.net> X-Original-From: "Andreas Bender, PhD" Content-Type: multipart/alternative; boundary=20cf307d0290b5d60d0500afea20 Date: Fri, 15 Aug 2014 20:20:40 +0100 MIME-Version: 1.0 Sent to CCL by: "Andreas Bender, PhD" [Andreas.Bender-*-cantab.net] --20cf307d0290b5d60d0500afea20 Content-Type: text/plain; charset=UTF-8 Dear All, We would like to cordially invite you to the Autumn 2014 UK QSAR meeting, which will be hosted on September 30th by the Cambridge Crystallographic Data Centre (CCDC) as well as the Department of Chemistry of the University of Cambridge. The UK QSAR & Chemoinformatics Group in the UK has a history of more than 20 years of bringing scientists from in and around the computational drug discovery and medicinal chemistry fields together for their biannual informal meetings, which are regularly attended by 100-150 attendees. Membership is complimentary and open to all with related interests; for more information please see http://www.ukqsar.org/. Topics of the oral presentations at the Autumn 2014 meeting will range from conformer generation and fragment-based screening library design to analysing ligand-protein interactions, ligand-based bioactivity data analysis and using gene expression data for drug repurposing. In addition there will be a poster session with flash talks and poster prizes, sponsored by the CCDC. Please indicate on the registration form if you would like to contribute a poster to the meeting. Attendance of the event is free, and for further details on the program and on how to register please see http://www.ukqsar.org/2014/07/07/autumn-2014/. Looking forward to seeing you in September! Best wishes, Steve Maginn (CCDC) and Andreas Bender (Department of Chemistry) -- Andreas Bender, PhD Lecturer for Molecular Informatics Centre for Molecular Informatics, Cambridge University Institute: http://www-ucc.ch.cam.ac.uk Group: http://www.ch.cam.ac.uk/group/bender/index Personal: http://www.andreasbender.de --20cf307d0290b5d60d0500afea20 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

Dear All,

We would like to cordially invite you to the Autumn 2014 UK = QSAR meeting, which will be hosted on September 30th by the Cambridge Cryst= allographic Data Centre (CCDC) as well as the Department of Chemistry of th= e University of Cambridge.

The UK QSAR & Chemoinformatics Group in the UK has a his= tory of more than 20 years of bringing scientists from in and around the co= mputational drug discovery and medicinal chemistry fields together for thei= r biannual informal meetings, which are regularly attended by 100-150 atten= dees. Membership is complimentary and open to all with related interests; f= or more information please see http://ww= w.ukqsar.org/.

Topics of the oral presentations at the Autumn 2014 meeting = will range from conformer generation and fragment-based screening library d= esign to analysing ligand-protein interactions, ligand-based bioactivity da= ta analysis and using gene expression data for drug repurposing. In additio= n there will be a poster session with flash talks and poster prizes, sponso= red by the CCDC. Please indicate on the registration form if you would like= to contribute a poster to the meeting.

Attendance of the event is free, and for further details on = the program and on how to register please see http://www.ukqsar.org/2014/07/07/autumn-2014/<= /a>.

Looking forward to seeing you in September!

Best wishes,
Steve Maginn (CCDC) and Andreas Bender (Department of Chemistry)

--
Andreas Bender, PhD
Lecturer for Molecular Informatics
Centre for Molecular Informatics, Cambridge University
Institute: http://www-ucc.ch.cam.ac= .uk
Group: http://www.ch= .cam.ac.uk/group/bender/index
Personal: http://www.andreasbender.= de

--20cf307d0290b5d60d0500afea20-- From owner-chemistry@ccl.net Fri Aug 15 16:20:00 2014 From: "Sergio Manzetti sergio.manzetti]-[outlook.com" To: CCL Subject: CCL: Re. CCL: Need Help Message-Id: <-50399-140815153435-4078-G1enabkfcY1aW/o2GzE/SQ%server.ccl.net> X-Original-From: "Sergio Manzetti" Date: Fri, 15 Aug 2014 15:34:34 -0400 Sent to CCL by: "Sergio Manzetti" [sergio.manzetti|outlook.com] Yes, Swiss PDB VIewer: http://spdbv.vital-it.ch/ > From: owner-chemistry ~~ ccl.net > To: sergio.manzetti ~~ gmx.com > Subject: CCL: Need help > Date: Fri, 15 Aug 2014 10:48:08 -0400 > > > Sent to CCL by: "Richard Wood" [richard.wood{}purduecal.edu] > Hi all, > > Does anybody know of a free software tool that will allow the user to open a protein structure and place a small molecule (i.e., a ligand) anywhere the user wants it to be and then save the resulting structure for further calculations? > > I ask this because I am working with a ligand-protein system and I was trying to doc the ligand but it would not go where it was predicted to bind. I was trying to reproduce the work of others, but their protein was deemed "proprietary" but their institution and so I was using a different protein structure to start with. > > Richard> From owner-chemistry@ccl.net Fri Aug 15 16:54:00 2014 From: "Elaine Meng meng::cgl.ucsf.edu" To: CCL Subject: CCL: Need help (manual docking, saving results) Message-Id: <-50400-140815160727-30280-Tusys1kBy86rYyA8G7Vv2Q###server.ccl.net> X-Original-From: "Elaine Meng" Date: Fri, 15 Aug 2014 16:07:25 -0400 Sent to CCL by: "Elaine Meng" [meng]![cgl.ucsf.edu] Hi Richard, Im pretty sure you could do it in all the major packages, but Ill tout the one I work on: Chimera, which is free for any noncommercial use. You could open the structures from two files and move one relative to the other, for example by freezing one and moving only the other, alternating with both movable so you can see everything from another direction. Then when/if you get it where you want it, you could either save as separate files, with one set of coordinates relative to the other, or merge into one model and save as a single file. Chimera writes PDB, Mol2, and Amber prmtop files. In Chimera, after opening the files, the freezing/unfreezing would be done by unchecking/checking the Active checkboxes in the model panel. You can show the model panel by choosing it from the Favorites menu, top-level in Chimera. The model panel also includes the merging function as copy/combine in the righthand buttons. Home page, see quick links on left for download http://www.rbvi.ucsf.edu/chimera/index.html Modifying and saving structures http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html Mouse manipulation, freezing/unfreezing (activation) http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html Model Panel http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html To guide your manual docking you can add distance monitors, do clash checking, etc. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco From owner-chemistry@ccl.net Fri Aug 15 18:00:00 2014 From: "Andrew Orry andy{}molsoft.com" To: CCL Subject: CCL: Need help Message-Id: <-50401-140815165330-13229-rFdwrv37CCmUMecNbYd9AQ*_*server.ccl.net> X-Original-From: Andrew Orry Content-Type: multipart/alternative; boundary="------------000702040900040802040806" Date: Fri, 15 Aug 2014 13:53:40 -0700 MIME-Version: 1.0 Sent to CCL by: Andrew Orry [andy|-|molsoft.com] This is a multi-part message in MIME format. --------------000702040900040802040806 Content-Type: text/plain; charset=windows-1252; format=flowed Content-Transfer-Encoding: 7bit Hi Richard, You can manually dock ligands using ICM-Browser which is a free download here: http://www.molsoft.com/icm_browser.html To manually dock: * Use File/Open or PDB Search tab to read in the receptor and ligand. * Right click on the ligand and choose the option "Move Rotate Separately" * Change torsions manually as shown here http://www.molsoft.com/gui/move-structure.html#torsion-angles * Save as PDB http://www.molsoft.com/gui/save-file.html Thanks, Andy -- Andrew Orry Ph.D. Senior Research Scientist MolSoft LLC Tel: 858-625-2000 x108 Fax: 858-625-2888 www.molsoft.com www.twitter.com/MolSoft On 8/15/2014 7:48 AM, Richard Wood richard.wood.:.purduecal.edu wrote: > Sent to CCL by: "Richard Wood" [richard.wood{}purduecal.edu] > Hi all, > > Does anybody know of a free software tool that will allow the user to open a protein structure and place a small molecule (i.e., a ligand) anywhere the user wants it to be and then save the resulting structure for further calculations? > > I ask this because I am working with a ligand-protein system and I was trying to doc the ligand but it would not go where it was predicted to bind. I was trying to reproduce the work of others, but their protein was deemed "proprietary" but their institution and so I was using a different protein structure to start with. > > Richard> --------------000702040900040802040806 Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: 7bit Hi Richard,

You can manually dock ligands using ICM-Browser which is a free download here:
http://www.molsoft.com/icm_browser.html

To manually dock:

Use File/Open or PDB Search tab to read in the receptor and ligand.
Right click on the ligand and choose the option "Move Rotate Separately"
Change torsions manually as shown here http://www.molsoft.com/gui/move-structure.html#torsion-angles
Save as PDB http://www.molsoft.com/gui/save-file.html

Thanks,
Andy

-- 
Andrew Orry Ph.D.
Senior Research Scientist
MolSoft LLC
Tel: 858-625-2000 x108
Fax: 858-625-2888
www.molsoft.com
www.twitter.com/MolSoft

On 8/15/2014 7:48 AM, Richard Wood richard.wood.:.purduecal.edu wrote:

Sent to CCL by: "Richard  Wood" [richard.wood{}purduecal.edu]
Hi all,

Does anybody know of a free software tool that will allow the user to open a protein structure and place a small molecule (i.e., a ligand) anywhere the user wants it to be and then save the resulting structure for further calculations?

I ask this because I am working with a ligand-protein system and I was trying to doc the ligand but it would not go where it was predicted to bind.  I was trying to reproduce the work of others, but their protein was deemed "proprietary" but their institution and so I was using a different protein structure to start with.

RichardE-mail to subscribers: CHEMISTRY(~)ccl.net or use:
      http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST(~)ccl.net or use
      http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs 
Conferences: http://server.ccl.net/chemistry/announcements/conferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtmlhttp://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/

--------------000702040900040802040806--