From owner-chemistry@ccl.net Thu Oct 30 02:19:01 2008
From: "Renxiao Wang wangrx(~)mail.sioc.ac.cn" <owner-chemistry,,server.ccl.net>
To: CCL
Subject: CCL: All small-molecule ligands in PDB are in the PDBbind-CN database now
Message-Id: <-37993-081030021543-19313-qyZaunM+//1Cjl062C2xTA,,server.ccl.net>
X-Original-From: "Renxiao  Wang" <wangrx!=!mail.sioc.ac.cn>
Date: Thu, 30 Oct 2008 02:15:39 -0400


Sent to CCL by: "Renxiao  Wang" [wangrx(~)mail.sioc.ac.cn]
Dear researchers,

This message is to announce a new function implemented on the PDBbind-CN server. The PDBbind database aims at providing a comprehensive collection of the experimentally measured binding affinity data for all types of biomolecular complexes deposited in the Protein Data Bank (PDB). The latest release of PDBbind (version 2008) is currently available on the PDBbind-CN server at http://www.pdbbind.org.cn/. This release consists of binding affinity data of a total of 4,300 protein-ligand, nucleic acid-ligand, protein-nucleic acid, and protein-protein complexes.

On the PDBbind-CN server, substructure/similarity search of the chemical structures of small-molecule ligands used to be limited to the ones with known binding data. Now it has been expanded to all small-molecule ligands in PDB (>8700 non-redundant molecules), a much larger body of information to explore. You may use this new function on the "STRUCTURE" page by selecting the "All small-molecule ligands in PDB" or the "Non-redundant ligands in PDB" set for conducting search. Registration is needed to access this page, but it is totally free to all users.

Thank you for your interests in our work! We also love to know your feedbacks.

The PDBbind-CN team
Shanghai Institute of Organic Chemistry
Chinese Academy of Sciences
Shanghai, P. R. China


From owner-chemistry@ccl.net Thu Oct 30 15:38:00 2008
From: "sabri alkis alkis{}ufl.edu" <owner-chemistry]-[server.ccl.net>
To: CCL
Subject: CCL: DLPOLY
Message-Id: <-37994-081030153714-18570-AneSJK6lo+Tu27W4mdsDmw]-[server.ccl.net>
X-Original-From: "sabri  alkis" <alkis**ufl.edu>
Date: Thu, 30 Oct 2008 15:37:10 -0400


Sent to CCL by: "sabri  alkis" [alkis(a)ufl.edu]
Dear DLPOLY users,

We have Co atoms coming inside the organic molecules and we want to fix the z-coordinates of these Co atoms and let the x-y coordinates free to move. Which subroutine should I go to? what should I change in that routine? Which subroutine handles this? We just want to fix the z-coordinates of these atoms in the system. Then calculate the force on these atoms then integrate the force with respect to z value to get the free energy.


Thanks, for your help.


Sabri...