From owner-chemistry@ccl.net Fri Jul 2 06:06:00 2010 From: "Andreas Klamt klamt%a%cosmologic.de" To: CCL Subject: CCL: solubility in DMF and THF Message-Id: <-42234-100702055544-22251-Vj2MaYDSxCq7XZsOMHmBxg!A!server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Fri, 02 Jul 2010 11:55:40 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt-$-cosmologic.de] In addition to my previous entry: We just calculated the solubilities of PEG400 in DMF and THF with COSMOtherm. According to these calculations, PEG400 should be completely miscile (even with a negative excess free energy) in both solvents. This may be the reason why you do not find experimental data for solubility, because a finite solubility does not exist. Hope I am right Andreas Am 01.07.2010 13:33, schrieb Rafael Gozalbes rgozalbes(0)cipf.es: > Sent to CCL by: "Rafael Gozalbes" [rgozalbes()cipf.es] > Dear all, > > A colleague of mine would like to know the solubility of PEG400 in DMF and in THF. > > We would greatly appreciaty if anyone can point us to a database containing this kind of information, or if there is someone that has developped a predictive model for this property and could help us. > > Thank you very much in advance, > > Rafael> > > > -- PD. Dr. Andreas Klamt CEO / Geschäftsführer COSMOlogic GmbH& Co. KG Burscheider Strasse 515 D-51381 Leverkusen, Germany phone +49-2171-731681 fax +49-2171-731689 e-mail klamt+*+cosmologic.de web www.cosmologic.de HRA 20653 Amtsgericht Koeln, GF: Dr. Andreas Klamt Komplementaer: COSMOlogic Verwaltungs GmbH HRB 49501 Amtsgericht Koeln, GF: Dr. Andreas Klamt From owner-chemistry@ccl.net Fri Jul 2 13:19:01 2010 From: "Jason Cole cole*o*ccdc.cam.ac.uk" To: CCL Subject: CCL: has anyone made implementation fo scroing and consensus scoring functions to GoldSuite? Message-Id: <-42235-100702113953-31736-Bo0WGNTcbXRsiKleWVikWA**server.ccl.net> X-Original-From: Jason Cole Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 2 Jul 2010 16:39:40 +0100 MIME-Version: 1.0 Sent to CCL by: Jason Cole [cole---ccdc.cam.ac.uk] Hi Andrew, This is probably the longest anyone will have ever had to wait for a reply on CCL but I only rarely check the list; I don't know if the answer will still be relevant to you, but for the record: GOLD does indeed have a programming API for writing your own scoring functions or augmenting the pre-existing ones. You will need to be a C-coding hound to use it. I'm unaware of many third party publications that have made use of this, but I am aware of some users who have taken advantage of the functionality (I actually wrote the very original API code years ago now but it has changed a lot since I was involved). The main use of the API has been internal to CCDC or by close collaborators: by having it, we have managed to implement several different scoring functions for GOLD. GOLD now supports the original score (GoldScore) and several other scores (ChemScore, Astex Statistical Potential and ChemPLP) as well as score modulators (Receptor Density Scaling, which is a way of rewarding tight pocket binding). All these scores were implemented using the API code. That said, given my history, I am probably biased towards it ... Best Wishes Jason Cole CCDC > -----Original Message----- > From: owner-chemistry+cole==ccdc.cam.ac.uk%ccl.net [mailto:owner- > chemistry+cole==ccdc.cam.ac.uk%ccl.net] On Behalf Of Andrew Voronkov > drugdesign-*-yandex.ru > Sent: 13 April 2010 09:49 > To: Jason Cole > Subject: CCL: has anyone made implementation fo scroing and consensus > scoring functions to GoldSuite? > > > Sent to CCL by: Andrew Voronkov [drugdesign(0)yandex.ru] > > Dear CCL users, > the GoldSuite software allows user-defined scoring functions > implementation. However I haven't found references on CCDC web site on > groups\publications where additional scoring functions will be > implemented. Has anyone here tried to do it or maybe to design own > consensus scoring function? > > > Best regards, > Andrew> To recover the email address of the author of the message, please > change> LEGAL NOTICE Unless expressly stated otherwise, information contained in this message is confidential. If this message is not intended for you, please inform postmaster%ccdc.cam.ac.uk and delete the message. The Cambridge Crystallographic Data Centre is a company Limited by Guarantee and a Registered Charity. Registered in England No. 2155347 Registered Charity No. 800579 Registered office 12 Union Road, Cambridge CB2 1EZ. From owner-chemistry@ccl.net Fri Jul 2 18:44:01 2010 From: "Carlos Ortega caoz96]^[yahoo.es" To: CCL Subject: CCL: Inhibition or Activation Message-Id: <-42236-100702183952-22885-TJjCMeq95SrxTDE3rSAUpg#server.ccl.net> X-Original-From: "Carlos Ortega" Date: Fri, 2 Jul 2010 18:39:27 -0400 Sent to CCL by: "Carlos Ortega" [caoz96*o*yahoo.es] Dear CCL users The reason for this question is about the doubt when realice a molecular docking in proteins. How i know if a ligand docked have power of inhibition or activation in the protein target? From owner-chemistry@ccl.net Fri Jul 2 19:18:00 2010 From: "jacqueline cawthray jcawth01*|*gmail.com" To: CCL Subject: CCL: Energy minimization of protein units Message-Id: <-42237-100702190655-21321-lFz5rIvY5Yc2UhtpVY6OjQ^server.ccl.net> X-Original-From: "jacqueline cawthray" Date: Fri, 2 Jul 2010 19:06:54 -0400 Sent to CCL by: "jacqueline cawthray" [jcawth01|,|gmail.com] We are investigating the rational design of ligands for specific protein-ligand interactions. We are quite new to theoretical work on large molecules and are not sure how to minimize the protein structures prior to docking investigations. Is this something Amber or Gromacs is useful for? We were then going to use Autodock to investigate various ligand interactions with the protein. Thanks