Hi, I would like to contribute with something at the UGM. I'm not currently sure about what. However,I can't see the email of any of the coordinators in the PDF or the summary mail I get from the mailinglist.
Best Regards Esben Jannik Bjerrum cand.pharm, Ph.D /Sent from my Ubuntu Touch Phone Phone +45 2823 8009 http://dk.linkedin.com/in/esbenbjerrum http://www.wildcardconsulting.dk On Monday, April 4, 2016 10:12 AM, "[email protected]" <[email protected]> wrote: ----- Forwarded Message ----- Send Rdkit-discuss mailing list submissions to [email protected] To subscribe or unsubscribe via the World Wide Web, visit https://lists.sourceforge.net/lists/listinfo/rdkit-discuss or, via email, send a message with subject or body 'help' to [email protected] You can reach the person managing the list at [email protected] When replying, please edit your Subject line so it is more specific than "Re: Contents of Rdkit-discuss digest..." Today's Topics: 1. blog post: Thinking about an RDKit support model (Greg Landrum) 2. mmFF minimization in context of two ligands/binding pocket (Steven Combs) 3. Re: mmFF minimization in context of two ligands/binding pocket (Maciek W?jcikowski) 4. Re: mmFF minimization in context of two ligands/binding pocket (Paolo Tosco) 5. REMINDER: 5th RDKit UGM 26-28 October 2016 in Basel (Nadine Schneider) Dear all, Some of you may not have seen this on LinkedIn or Twitter, so I'm posting here too: https://medium.com/@greg.landrum_t5/thinking-about-an-rdkit-support-model-782cfeb576a3#.n4e5u2tjx Note: I posted that yesterday! it's not a 1st of April joke! :-) I don't necessarily want to spam this list with this stuff, but I do want to be sure that these things get seen. If you find this irritating, let me know off-list. If I get a few of those, I will stop sending these pointers. Best,-greg Hi, Is it possible to do a minimization in mmFF in context of two small-molecules or a single small molecule and sidechains from a binding pocket? From what I gather, I have two options: 1) Make a single RWMol object with the ligand and all residues from the binding pocket, then run mmFF on the combine molecule. The steps would look like this -use combineMols() for all residues -use mmFF on the complex 2) Use a hacked version of MCS from here: http://rdkit.blogspot.com/2013/12/using-allchemconstrainedembed.html Is there a better way of doing this? I am using the C++ api. Steven CombsHi Steven, No. 1) is exactly what I'm doing to preform rigid protein minimization of ligands. I use ff.AddFixedPoint() to fix all protein atoms (you could omit the desired side chains). For better performance I also use following params: ff = AllChem.MMFFGetMoleculeForceField(comp, ff_mp, nonBondedThresh=10., ignoreInterfragInteractions=False) where comp is complex Mol, ff_mp are force-field molecular properties. PS. There is no C++ API to my knowledge, although Greg/Paolo might have something in his undocumented wizard hat ;) ---- Pozdrawiam, | Best regards, Maciek Wójcikowski [email protected] 2016-04-01 17:29 GMT+02:00 Steven Combs <[email protected]>: Hi, Is it possible to do a minimization in mmFF in context of two small-molecules or a single small molecule and sidechains from a binding pocket? From what I gather, I have two options: 1) Make a single RWMol object with the ligand and all residues from the binding pocket, then run mmFF on the combine molecule. The steps would look like this -use combineMols() for all residues -use mmFF on the complex 2) Use a hacked version of MCS from here: http://rdkit.blogspot.com/2013/12/using-allchemconstrainedembed.html Is there a better way of doing this? I am using the C++ api. Steven Combs ------------------------------------------------------------------------------ Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. http://pubads.g.doubleclick.net/gampad/clk?id=278785471&iu=/4140 _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss Dear Steven, just to add up a small bit to Maciek's reply, you may find some examples how to use the RDKit MMFF94 C++ API in Code/ForceField/MMFF/testMMFFForceField.cpp and in Code/ForceField/MMFF/testMMFFHelpers.cpp. All of the constraints are available from C++, a search for "fixed atoms" in Code/ForceField/MMFF/testMMFFForceField.cpp will point you to an example how to set fixed atoms. To minimize a ligand in the context of a protein pocket I would combine the ligand and the relevant residues in a ROMol, set the desired contraints and then minimize. Please do not hesitate to get back to me if you run into trouble. Cheers, p. On 01/04/2016 16:29, Steven Combs wrote: Hi, Is it possible to do a minimization in mmFF in context of two small-molecules or a single small molecule and sidechains from a binding pocket? From what I gather, I have two options: 1) Make a single RWMol object with the ligand and all residues from the binding pocket, then run mmFF on the combine molecule. The steps would look like this -use combineMols() for all residues -use mmFF on the complex 2) Use a hacked version of MCS from here: http://rdkit.blogspot.com/2013/12/using-allchemconstrainedembed.html Is there a better way of doing this? I am using the C++ api. Steven Combs ------------------------------------------------------------------------------ Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. http://pubads.g.doubleclick.net/gampad/clk?id=278785471&iu=/4140 _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss Dear RDKitters This is a reminderfor the 5th RDKit User GroupMeeting taking place from 26-28 October in Basel, Switzerland. Registration for the RDKit UGM is still open and free: https://www.eventbrite.com/e/5th-rdkit-user-group-meeting-tickets-22539677783 Please find a detailed announcement attached. We are looking for people who are willing to dopresentations, talktorials or posters on the first two days. If you'reinterested in contributing, please send us an email soon. Lighting talks don't need to be arranged too far in advance;we will start collecting the list of people interested in doing those shortlybefore the event. Hope to see many of you at this year’s UGM,Christian, Nik, and Nadine ------------------------------------------------------------------------------ _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
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