From owner-chemistry@ccl.net Wed Jan 16 08:37:01 2008 From: "Enrico Purisima rico!A!bri.nrc.ca" To: CCL Subject: CCL: sietraj software release Message-Id: <-36040-080115221545-29151-dEZ8JbAsKzHKf6jXauTNHA**server.ccl.net> X-Original-From: Enrico Purisima Date: Tue, 15 Jan 2008 21:27:51 -0500 Sent to CCL by: Enrico Purisima [rico-*-bri.nrc.ca] === Software Release === sietraj is a collection of scripts for calculating binding free energies from molecular dynamics trajectories of protein-ligand or protein-protein complexes. The scripts make use of a Tcl runtime library (BRIMM) that provides Tcl-accessible functions for analyzing molecular structures and carrying out energy and solvation calculations. The library is a set of C++ classes and functions with a Tcl wrapper generated by Swig. sietraj is an alternative to the MM-PBSA software provided by the AMBER distribution. Solvated interaction energies (SIE) are calculated using parameters that have been fitted to reproduce binding free energies of a data set of 99 protein-ligand complexes. A boundary element solution of the Poisson equation is used for the solvent reaction field energy. The software is available from http://www.bri.nrc.ca/ccb/pub/sietraj_main.php --------- Enrico O. Purisima Biotechnology Research Institute National Research Council Canada From owner-chemistry@ccl.net Wed Jan 16 09:12:00 2008 From: "Renxiao Wang wangrx . mail.sioc.ac.cn" To: CCL Subject: CCL: Additional server of the PDBbind database is launched Message-Id: <-36041-080116030213-3568-GfsV69P2lpZpHQvNc3AtUg.@.server.ccl.net> X-Original-From: "Renxiao Wang" Date: Wed, 16 Jan 2008 03:02:09 -0500 Sent to CCL by: "Renxiao Wang" [wangrx-,-mail.sioc.ac.cn] Dear researchers, We announce the launch of an additional server of the PDBbind database. The PDBbind database is created to provide a comprehensive collection of experimentally measured binding affinity data for the protein-ligand complexes deposited in the Protein Data Bank. The current release is version 2007, which contains binding affinity data (Kd, Ki, & IC50) for over 3,100 protein-ligand complexes. The PDBbind database is now maintained and developed through collaborations between Prof. Shaomeng Wang's group at the University of Michigan in USA and Prof. Renxiao Wang's group at the Shanghai Institute of Organic Chemistry in China. The primary server of the PDBbind database (http://www.pdbbind.org) was officially launched in May 2004, which is hosted at the University of Michigan. This additional server, named as PDBbind-CN (http://www.pdbbind.org.cn), is hosted at the Shanghai Institute of Organic Chemistry. PDBbind-CN is created to better serve local users in China and other surrounding countries. On PDBbind-CN, the basic information of every protein-ligand complex is totally open to all users. External links to other relevant databases, such as PDB, PubChem, and BindingDB, are also provided. Registration is only required if users want to perform text/structure-based searching or to download data in bulk. Registration is free for academic as well as industrial users. The primary server of PDBbind is currently under reform towards this direction as well. Since synchronization between PDBbind and PDBbind-CN has not been fully established at this moment, the web interface of PDBbind-CN may be different from PDBbind, but their contents are identical. New versions of the PDBbind database will be released on both PDBbind and PDBbind-CN in the future. Best regards, Renxiao Wang, Ph.D. Professor Shanghai Insitiute of Organic Chemistry Shanghai, P. R. China From owner-chemistry@ccl.net Wed Jan 16 21:19:00 2008 From: "Sina T reli sinatureli,gmail.com" To: CCL Subject: CCL: Software for Electron Spin Density Message-Id: <-36042-080116211306-7663-kjJKlInnLsz39nQr1JHhWg(-)server.ccl.net> X-Original-From: "Sina T reli" Date: Wed, 16 Jan 2008 21:13:03 -0500 Sent to CCL by: "Sina T reli" [sinatureli*|*gmail.com] Hello, Do you know of any FREE and good tool for calculation of electron spin densities and visualization of molecular orbitals.. Thanks