From owner-chemistry@ccl.net Mon May 26 05:50:01 2014 From: "Bin Sun sunbinxod*gmail.com" To: CCL Subject: CCL: Free docking software with exhaustive search of conformational space Message-Id: <-50117-140526054829-30122-0zVRC7s7OZUi+F5zxCSkxw===server.ccl.net> X-Original-From: Bin Sun Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 26 May 2014 17:46:33 +0800 MIME-Version: 1.0 Sent to CCL by: Bin Sun [sunbinxod- -gmail.com] Dear all, Could anyone recommend me a free docking software that can perform exhaustive docking? In my experiment, I only need the ligand poses generated by the conformational search method of the docking software, the scores of these poses given by the scoring function are not necessary since we plan to use an in-house scoring function to rank the poses. So I need to ensure that the sampling of the ligand conformational space is sufficient ( exhaustive docking ). Thanks in advance ! -Sun From owner-chemistry@ccl.net Mon May 26 10:32:01 2014 From: "janl[a]speakeasy.net" To: CCL Subject: CCL: Changes to CCL spam filters Message-Id: <-50118-140526102644-23371-Rr4o5aWi4ZjsqLT0dVNTgw#,#server.ccl.net> X-Original-From: janl.#,#.speakeasy.net Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Mon, 26 May 2014 10:26:36 -0400 MIME-Version: 1.0 Sent to CCL by: janl/a\speakeasy.net Dear CCL Subscribers, The sad fact of my life is that I am getting more and more busy rather than enjoying the retireent and reading the books that I always wanted to read again. I simply cannot give the CCL as much time as I would like to. At the same time, the income that CCL generates would not cover the cost of external services or help. Since CCL runs from my basement, there is no "free stuff" from the "parent organization". Either I pay for it, or I will not have it. I am also deeply emotional about enlisting volunteers. You can blame it only on myself. With the avalanche of spam that the CCL is getting (over 10k spam attempts a day), I decided to change the way I do blacklisting. My /etc/mail/access file was about 20 MBytes long and it contained over 300k spamming addresses. This was getting hard to maintain. So I decided to change most of the individual IP rejected addresses to Class C blocks. This may impact people who are in smaller organizations or in countries without a legal and/or technical infrastructure where most of spambots and botnets ( http://en.wikipedia.org/wiki/Botnet ) are located. If your IP address is among "bad guys", you will get rejected. If your email message to CCL gets rejected (with a 5.7.1 Access Denied code) please let me know through the Web interface:and I will restore your email access. The Web form above does not refer to /etc/mail/access file. It also allows you to send mail to the CCL subscribers [PLEASE SELECT THE RIGHT OPTION] in the meantime. Now... I could convert the CCL into a blog and wash my hands... However, I still believe that CCL is a community and while you are bothered with a stream of CCL messages and frantically click on [Delete] when you are busy, you still see at least the Subject lines and participate. Since I am a manager of CCL, I need to include a plug: 1) Please send good messages to CCL and answer questions when you can. Read the damned http://www.ccl.net/instructions and rules. 2) Contribute/upload good stuff to the archives 3) Please use CCL services:    http://www.ccl.net/chemistry/aboutccl/supporting/index.shtml Note: for the paid services I did not change the price since 2000. Believe it or not, the inflation since that time took almost 40% of the value of the US Dollar. At the same time, I am not asking for charity (Oh, well, I am asking...) The job announcement page really brings good candidates, and the banners are really placing your organizational site link in the Google and they do generate traffic. So talk to your boss or use your development account. Thank you for your patience and have a great rest of the Memorial Day if you are in the US. Jan __ Jan Labanowski CCL Manager jkl^ccl.net From owner-chemistry@ccl.net Mon May 26 16:25:00 2014 From: "David A Case case]-[biomaps.rutgers.edu" To: CCL Subject: CCL: Free docking software with exhaustive search of conformational space Message-Id: <-50119-140526094503-21639-/AnAKzdO8VHpqf0Ptd8jIw() server.ccl.net> X-Original-From: David A Case Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Mon, 26 May 2014 09:44:53 -0400 MIME-Version: 1.0 Sent to CCL by: David A Case [case,biomaps.rutgers.edu] On Mon, May 26, 2014, Bin Sun sunbinxod*gmail.com wrote: > > Could anyone recommend me a free docking software that can perform > exhaustive docking? Take a look at DOT2: http://www.sdsc.edu/CCMS/DOT/ ...dave case From owner-chemistry@ccl.net Mon May 26 21:08:00 2014 From: "Greg Warren greg__eyesopen.com" To: CCL Subject: CCL: Free docking software with exhaustive search of conformational space Message-Id: <-50120-140526210421-12741-+Cd4xDuZE8wHYfPPmfrvAA::server.ccl.net> X-Original-From: Greg Warren Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 27 May 2014 01:04:15 +0000 MIME-Version: 1.0 Sent to CCL by: Greg Warren [greg-,-eyesopen.com] Dear Sun, OpenEye's docking program FRED is a very fast exhaustive docker. If you are only developing a scoring function it is free for academic research in North America and Europe. Please use the attached link to apply. http://www.eyesopen.com/academic-request Regards, Greg -----Original Message----- > From: owner-chemistry+greg==eyesopen.com++ccl.net [mailto:owner-chemistry+greg==eyesopen.com++ccl.net] On Behalf Of Bin Sun sunbinxod*gmail.com Sent: Monday, May 26, 2014 3:47 AM To: Greg Warren Subject: CCL: Free docking software with exhaustive search of conformational space Sent to CCL by: Bin Sun [sunbinxod- -gmail.com] Dear all, Could anyone recommend me a free docking software that can perform exhaustive docking? In my experiment, I only need the ligand poses generated by the conformational search method of the docking software, the scores of these poses given by the scoring function are not necessary since we plan to use an in-house scoring function to rank the poses. So I need to ensure that the sampling of the ligand conformational space is sufficient ( exhaustive docking ). Thanks in advance ! -Sunhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt