I have used the CaPTURE tool for several years now to identify potential cation-pi interactions I might have missed during visual inspection of a model I'm building or perusing. It now seems that the webserver is no longer connected to the PDB, so one needs to upload coordinates rather than input a PDB code, but it still works as of today! I'm not sure how the tool treated ligands, however.
http://capture.caltech.edu/ Emily. Emilia ("Emily") C. Arturo Postdoctoral research associate Laboratory of Dr. Erica Ollmann Saphire Center for Infectious Disease and Vaccine Research La Jolla Institute for Immunology, California USA Twitter @moonlighterturo @ljiresearch @EOSpahire On Tue, Apr 20, 2021 at 1:21 PM Soisson, Stephen M < [email protected]> wrote: > Might anyone be aware of a similar database tracking small molecule > ligands making cation-pi or pi-cation interactions with proteins? > > Cheers, > > Steve > > > On Apr 20, 2021, at 3:41 PM, Christine Gee <[email protected]> wrote: > > > > *EXTERNAL EMAIL* – Use caution with any links or file attachments. > Hi Stephan, > > It seems to be online at the following > > http://cmm.osdd.net/gnsmmg/databases/cad/ > > Regards > Christine > > > On Tue, Apr 20, 2021 at 12:27 PM [email protected] < > [email protected]> wrote: > >> Dear BB, >> >> Does anyone know if the cation-aromatic database (Reddy, 2007, Prot Sci) >> is still available? The link listed in the manuscript ( >> http://203.199.182.73/gnsmmg/databases/cad/) no longer appears to work. >> >> Thanks, >> Steve >> >> Dr Stephen Carr >> Research Complex at Harwell (RCaH) >> Rutherford Appleton Laboratory >> Harwell Oxford >> Didcot >> Oxon OX11 0FA >> United Kingdom >> Email [email protected] >> tel 01235 567717 >> >> This email and any attachments may contain confidential, copyrightand or >> privileged material, and are for the use of the intended addressee only. If >> you are not the intended addressee or an authorized recipient of the >> addressee, please notify us of receipt by returning the e-mail and do not >> use, copy, retain, distribute or disclose the information in or attached to >> this email. >> >> >> >> Any views or opinions presented are solely those of the author and do not >> necessarily represent those of the Research Complex at Harwell. >> >> >> >> There is no guarantee that this email or any attachments are free from >> viruses and we cannot accept liability for any damage which you may sustain >> as a result of software viruses which may be transmitted in or with the >> message. >> >> >> >> We use an electronic filing system. Please send electronic versions of >> documents, unless paper is specifically requested. >> >> >> >> This email may have a protective marking, for an explanation, please see: >> >> >> http://www.mrc.ac.uk/About/informationandstandards/documentmarking/index.htm >> . >> >> ------------------------------ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > Notice: This e-mail message, together with any attachments, contains > information of Merck & Co., Inc. (2000 Galloping Hill Road, Kenilworth, > New Jersey, USA 07033), and/or its affiliates Direct contact information > for affiliates is available at > http://www.merck.com/contact/contacts.html) that may be confidential, > proprietary copyrighted and/or legally privileged. It is intended solely > for the use of the individual or entity named on this message. If you are > not the intended recipient, and have received this message in error, > please notify us immediately by reply e-mail and then delete it from > your system. > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
