From owner-chemistry@ccl.net Mon May 5 02:56:01 2014 From: "Josh BERRYMAN Josh.Berryman- -uni.lu" To: CCL Subject: CCL: binding sites comparison for homologous proteins Message-Id: <-50024-140505020701-26496-bHKOgb5KkySlL43BIev/Cw###server.ccl.net> X-Original-From: Josh BERRYMAN Content-Language: en-JM Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 5 May 2014 06:06:54 +0000 MIME-Version: 1.0 Sent to CCL by: Josh BERRYMAN [Josh.Berryman-x-uni.lu] You could try FEW ("free energy workflow"), I haven't used it myself yet but it seems to be aimed approximately in the direction of what you need, and it is one of the FOSS components of AMBER. Let me (or the list) know how you get on Josh ________________________________________ > From: owner-chemistry+josh.berryman==uni.lu===ccl.net [owner-chemistry+josh.berryman==uni.lu===ccl.net] on behalf of Andrew Voronkov drugdesign[*]yandex.ru [owner-chemistry===ccl.net] Sent: Sunday, May 04, 2014 11:11 AM To: Josh BERRYMAN Subject: CCL: binding sites comparison for homologous proteins Sent to CCL by: Andrew Voronkov [drugdesign=yandex.ru] Dear CCL users, I need to make comparison and selectivity analysis for the small ligands binding sites among multiple proteins from the same family. One way it to make pairwise superposition and manual analysis of all the interactions and amino acids. But is there a way or to automatize it? For example to write a script, which will analyze superimposed structures at ome distance from small molecule and make a list of different amino acids or maybe even which will make superposition of the structures and then analyze non-identical amino acids around small molecule? Is anything like that available? Best regards, Andreyhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt