From owner-chemistry@ccl.net Fri May 30 19:41:00 2014
From: "Matt Challacombe matt.challacombe#,#gmail.com" <owner-chemistry * server.ccl.net>
To: CCL
Subject: CCL: software for docking waters?
Message-Id: <-50125-140530130518-27293-uafE97op/TVUn4U1s3BiuA * server.ccl.net>
X-Original-From: Matt Challacombe <matt.challacombe~!~gmail.com>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Date: Fri, 30 May 2014 11:05:10 -0600
MIME-Version: 1.0


Sent to CCL by: Matt Challacombe [matt.challacombe|gmail.com]
Hi CCL,

 From the posts of Bin Sun & Prof. Case, I see there are great softwares 
for molecular docking.  I'm wondering about a related problem I haven't 
seen much about, namely the docking of large water nets, eg. in active 
sites, binding pockets etc.  Beyond just "do MD" is there an exhaustive 
approach?  Maybe some experimental code?

Cheers, Matt Challacombe


From owner-chemistry@ccl.net Fri May 30 20:51:00 2014
From: "Mezei, Mihaly mihaly.mezei()mssm.edu" <owner-chemistry%%server.ccl.net>
To: CCL
Subject: CCL: software for docking waters?
Message-Id: <-50126-140530204829-1911-xWYC+K4Jj3yW7JW3WRfmHQ%%server.ccl.net>
X-Original-From: "Mezei, Mihaly" <mihaly.mezei.:.mssm.edu>
Content-Language: en-US
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset="us-ascii"
Date: Sat, 31 May 2014 00:48:21 +0000
MIME-Version: 1.0


Sent to CCL by: "Mezei, Mihaly" [mihaly.mezei*o*mssm.edu]

> From the posts of Bin Sun & Prof. Case, I see there are great softwares
> for molecular docking.  I'm wondering about a related problem I haven't
> seen much about, namely the docking of large water nets, eg. in active
> sites, binding pockets etc.  Beyond just "do MD" is there an exhaustive
> approach?  Maybe some experimental code?

Monte Carlo simulations in the grand-canonical ensemble would solvate your target molecule inside and around.  If you need a program have a look at MMC: http://inka.mssm.edu/~mezei/mmc

Mihaly Mezei

Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai
Voice:  (212) 659-5475   Fax: (212) 849-2456
WWW (MSSM home): http://www.mountsinai.org/Find%20A%20Faculty/profile.do?id=0000072500001497192632
WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei
WWW (Department): http://www.mssm.edu/departments-and-institutes/structural-and-chemical-biology