From chemistry-request@server.ccl.net Sat Jun 15 06:07:36 2002 Received: from bjapp9.163.net ([202.108.255.198]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5FA7Y500958 for ; Sat, 15 Jun 2002 06:07:35 -0400 Received: by bjapp9.163.net (Postfix, from userid 1005) id B86671D30621B; Sat, 15 Jun 2002 18:07:27 +0800 (CST) MIME-Version: 1.0 Message-ID: <3D0B11DF.000016.29002@bjapp9> Date: Sat, 15 Jun 2002 18:07:27 +0800 (CST) From: "songyunlong" To: chemistry@ccl.net Subject: =?gb2312?B?U2NvcmluZyBmdW5jdGlvbiBmb3IgRE5BIA==?= X-Priority: 3 X-Originating-IP: [61.171.42.43] X-Mailer: Coremail2.0 Copyright Tebie Ltd., 2001 Content-Type: Multipart/Alternative; boundary="Boundary-=_EcgLBvEWZEQBkcrHJRratHmAHjfd" --Boundary-=_EcgLBvEWZEQBkcrHJRratHmAHjfd Content-Type: text/plain; charset="gb2312" Content-Transfer-Encoding: 8bit Dear sir, I want to evaluate some compounds which interact with protein-DNA complex, ie, they have a skeleton which interact with DNA, and some substituents can make further interaction with the protein residues. I know there are several scoring functions, such as Cscore of Tripos, DrugScore, Chemscore, and etc. GOLD and FLEXX have their own scoring functions too. Many scoring functions are developed from the protein-ligand complex crystals. I wonder if anyone of them have been successfully used to such compounds, such as DNA intercalators, and can give a quite accurate estimation of the binding affinity with protein-DNA complex. Any suggestions are wellcome! The other question is how I can develop parameters for the DNA in order to score the compoundsacting on the DNA. Could you give me any suggestions? Thank you in advance! Song Yunlong, Ph.D _______________________________~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dept of Med Chem Sec Mil Med Univ Guohe Road,325 Shanghai 200433 China E-mail:songyunlong@hotmail.com ________________________________ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ --Boundary-=_EcgLBvEWZEQBkcrHJRratHmAHjfd Content-Type: text/html; charset="gb2312" Content-Transfer-Encoding: 8bit Dear sir,

I want to evaluate some compounds which interact with protein-DNA complex, ie, they have a skeleton which interact with DNA, and some substituents can make further interaction with the protein residues. I know there are several scoring functions, such as Cscore of Tripos, DrugScore, Chemscore, and etc. GOLD and FLEXX have their own scoring functions too. Many scoring functions are developed from the protein-ligand complex crystals. I wonder if anyone of them have been successfully used to such compounds, such as DNA intercalators, and can give a quite accurate estimation of the binding affinity with protein-DNA complex. Any suggestions are wellcome!

The other question is how I can develop parameters for the DNA in order to score the compoundsacting on the DNA. Could you give me any suggestions?

Thank you in advance!

Song Yunlong, Ph.D

_______________________________~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Dept of Med Chem
Sec Mil Med Univ
Guohe Road,325
Shanghai 200433
China
E-mail:songyunlong@hotmail.com
________________________________
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


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--Boundary-=_EcgLBvEWZEQBkcrHJRratHmAHjfd-- From chemistry-request@server.ccl.net Sun Jun 16 17:58:48 2002 Received: from ivory.trentu.ca ([192.75.12.103]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5GLwiC00913 for ; Sun, 16 Jun 2002 17:58:48 -0400 Received: from trentu.ca ([206.248.117.30]) by trentu.ca (PMDF V5.2-32 #37862) with ESMTP id <01KJ09X8TIP40008MH@trentu.ca> for chemistry@ccl.net; Sun, 16 Jun 2002 17:58:24 EST Date: Sun, 16 Jun 2002 18:00:07 -0400 From: elewars Subject: Hartree-Fock, Coulomb, Fermi To: chemistry@ccl.net Message-id: <3D0D0A67.F124BA7A@trentu.ca> MIME-version: 1.0 X-Mailer: Mozilla 4.79 [en] (WinNT; U) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en 2002 June 16 Hello, The HF method gives "absolute" energies that are too high, because it overestimates electron-electron repulsion. However, there are two kinds of electron-electron repulsion: classical Coulomb (-->Coulomb hole), arising from electric charge, and quantum mechanical or Fermi repulsion (--> Fermi hole), which exists between electrons of like spin. The HF approximate treatment of electron correlation arises from the use of just one determinant, and from the "smeared electron cloud" integration used to get the J and K integrals. Questions: (1) Is it now well-recognized which effect, Coulomb or Fermi, causes the main problem with HF energies? (2) Is there general agreement on which approximation is worse, single-determinant or average electron cloud (or maybe the two can't be disentangled)? Thanks E. Lewars =====