From chemistry-request@server.ccl.net Sat Dec 5 01:21:30 1998 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA01321 for ; Sat, 5 Dec 1998 01:21:29 -0500 Received: from csb0.IPC.PKU.EDU.CN (csb0.ipc.pku.edu.cn [162.105.177.12]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id BAA28782 Sat, 5 Dec 1998 01:16:57 -0500 (EST) Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for chemistry@www.ccl.net id AA25752; Sat, 5 Dec 98 14:15:31 -0800 Date: Sat, 5 Dec 1998 14:15:31 -0800 (PST) From: Arthur Wang To: CCL Subject: Free program release: predict the binding affinity Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII (Please forward this email to whom may concern) Free program release: SCORE: Predict the Binding Affinity of a Protein-Ligand Complex --------------------------------------------------------------- SCORE is an empirical method developed for estimating the binding affinity of a protein-ligand complex with known three-dimensional structure. It uses a linear scoring function to describe the binding free energy, which includes terms to account for van der Waals contact, metal-ligand bonding, hydrogen bonding, hydrophobic effect, and deformational change upon the binding process. The coefficients of each term are obtained by multivariate regressional analysis of 170 protein-ligand complexes. The scoring function reproduces the binding free energies of the whole training set with a cross-validated deviation of only 6.3 kJ/mol. Although SCORE follows the pioneering idea of H.J.Bohm, it gives considerably better result. It may be applied to screening the hits given by database searching or ranking the results of de novo design programs. An innovation of this method is the introduction of atomic binding score, which allows the researcher to inspect and optimize the lead compound rationally in a structure-based drug design procedure. For more details, you can come to: Renxiao Wang, Liang Liu, Luhua Lai, and Youqi Tang, "SCORE: A New Empirical Method for Estimating the Binding Affinity of a Protein-Ligand Complex", Journal of Molecular Modeling, 1998, 4, 379-394. The program, SCORE, is now released to the public. You can get it via WWW or anonymous FTP to ftp.ipc.pku.edu.cn (162.105.177.12) /pub/software/score/. The electronic reprint of the paper is available by contacting the following address. Best wishes, Arthur _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ Renxiao Wang Doctoral Candidate _/ _/ Molecular Design Laboratory _/ _/ Institute of Physical Chemistry, Peking University _/ _/ Beijing 100871, P.R.China _/ _/ _/ _/ E-mail: arthur@ipc.pku.edu.cn _/ _/ Tel: 86-10-62751490 Fax: 86-10-62751725 _/ _/ WWW: http://www.ipc.pku.edu.cn/~arthur/arthur.html _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From chemistry-request@server.ccl.net Sat Dec 5 14:23:31 1998 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA01564 for ; Sat, 5 Dec 1998 14:23:31 -0500 Received: from ex1.ncsa.uiuc.edu (ex1.ncsa.uiuc.edu [141.142.3.16]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id OAA00672 Sat, 5 Dec 1998 14:18:53 -0500 (EST) Received: from mx1.ncsa.uiuc.edu (mx1.ncsa.uiuc.edu [141.142.3.15]) by ex1.ncsa.uiuc.edu (8.9.1a/8.8.8) with ESMTP id NAA18258 for ; Sat, 5 Dec 1998 13:18:55 -0600 (CST) Received: from mckelvey (mckelvey.ncsa.uiuc.edu [141.142.41.30]) by mx1.ncsa.uiuc.edu (8.9.1a/8.8.8) with SMTP id NAA19840 for ; Sat, 5 Dec 1998 13:18:54 -0600 (CST) Message-Id: <3.0.5.32.19981205131933.00bf9620@pop.ncsa.uiuc.edu> X-Sender: mckelvey@pop.ncsa.uiuc.edu X-Mailer: QUALCOMM Windows Eudora Pro Version 3.0.5 (32) Date: Sat, 05 Dec 1998 13:19:33 -0600 To: chemistry@www.ccl.net From: John McKelvey Subject: Disks Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-md5sum: 387961784027d0966e3c6e3299493d28 X-md5sum-Origin: mx1.ncsa.uiuc.edu I have a question concerning disks for ab initio calculations [serial mode only] on an existing NT/Linux dual bootable, dual processor 180MHZ PPro PC with 96MB memory for G98W and Jaguar. I currently have a type "N" [i.i. the old ones, not "fast", or "fast-wide", etc] Seagate SCSI drive. I want to add more disk. I am thinking about adding 9.1GB, 7200 rpm DMA/ATA drive [burst rate 33MBS] with PCI controler ($275.) Is this ill advised? If it is reasonable for 180MHZ, how about 333 MHZ PII, or even 450MHZ PII ? Many thanks! Will post summary. thanks, John McKelvey NCSA