From owner-chemistry@ccl.net Sat Oct 25 00:49:00 2014 From: "Amiram Goldblum amiramg!A!ekmd.huji.ac.il" To: CCL Subject: CCL: diversity set for virtual screening Message-Id: <-50645-141025004716-29978-xOhILuT4mDVbU8zQKD0/gA]|[server.ccl.net> X-Original-From: Amiram Goldblum Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Sat, 25 Oct 2014 04:47:07 +0000 MIME-Version: 1.0 Sent to CCL by: Amiram Goldblum [amiramg _ ekmd.huji.ac.il] Dear Mannan: A bit of a long response.. If you have a protein structure and there has a Chembl set of active molecules, you Should always start with screening of known molecules, most important is that Your screening process (What is it ? docking ? pharmacophore ?) can detect A large part of the knowns and reject those that are known not to interact. Only in that case you may continue to screen "diversity sets", which you Could determine on the basis of the known molecules, rejecting the similar Ones and leaving those that have Tanimoto indexes of 0.7 or so with all others. You use a set of their properties (MW, H-bond donors/acceptors, ClogP and more) To create and "applicability domain" and pick molecules from a huge dataset (for which you must calculate properties) that are within that applicability Domain, then check their similarities and remain with a smaller set of diverse Molecules that may be useful for your screening. Kind regards, Amiram ********************************* Prof. Amiram Goldblum Molecular Modeling and Drug Design Institute for Drug Research The Hebrew University of Jerusalem, Israel Tel. +972-544-653292 Fax: +972-2-679658 amiramg---ekmd.huji.ac.il http://medchem-models.ekmd.huji.ac.il ********************************* -----Original Message----- > From: owner-chemistry+amiram==vms.huji.ac.il---ccl.net [mailto:owner-chemistry+amiram==vms.huji.ac.il---ccl.net] On Behalf Of Mannan K malie_03###yahoo.co.in Sent: 24 June, 2014 09:47 To: fw-amiramg Subject: CCL: diversity set for virtual screening Sent to CCL by: "Mannan K" [malie_03*_*yahoo.co.in] Hi CCLers, I want to do a virtual screening against a protein of my interest. To begin, I would like to start with relatively small diversity set to save some computational time. Where do I get a diverse chemical set. or Do i need to prepare a library of my own diverse set? or Is there any other way to begin? Many Thanks for your time, Mannanhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Sat Oct 25 03:05:00 2014 From: "Chris Swain swain=-=mac.com" To: CCL Subject: CCL: Scientific Applications under Yosemite Message-Id: <-50646-141025030432-961-4uGTzZ3Gjx/ydLVHW9OUzA#server.ccl.net> X-Original-From: Chris Swain Content-type: multipart/alternative; boundary="Apple-Mail=_7F837417-5AB6-40C0-A45F-6F7853167490" Date: Sat, 25 Oct 2014 08:04:25 +0100 MIME-version: 1.0 (Mac OS X Mail 8.0 \(1990.1\)) Sent to CCL by: Chris Swain [swain .. mac.com] --Apple-Mail=_7F837417-5AB6-40C0-A45F-6F7853167490 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 For Mac users. I=E2=80=99ve been compiling a compatibility list of scientific = applications under Yosemite. = http://www.macinchem.org/blog/files/0f5cfea643bdf4d2dfcae3991300b886-1611.= php = I try to update it daily, so feel free to send any additional = information Cheers, Chris= --Apple-Mail=_7F837417-5AB6-40C0-A45F-6F7853167490 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8 For Mac users.

I=E2=80=99ve been = compiling a compatibility list of scientific applications under = Yosemite.

http://www.macinchem.org/blog/files/0f5cfea643bdf4d2dfcae399130= 0b886-1611.php

I try to update it daily, so feel free to send any additional = information

Cheers,

Chris
= --Apple-Mail=_7F837417-5AB6-40C0-A45F-6F7853167490--