From cmartin@london.ks.uiuc.edu Tue May 16 01:36:59 1995 Received: from london.ks.uiuc.edu for cmartin@london.ks.uiuc.edu by www.ccl.net (8.6.10/930601.1506) id BAA28870; Tue, 16 May 1995 01:30:19 -0400 From: Received: from caliban.ks.uiuc.edu by london.ks.uiuc.edu with ESMTP (1.37.109.16/16.2) id AA207032217; Tue, 16 May 1995 00:30:18 -0500 Received: by caliban.ks.uiuc.edu (1.37.109.16/16.2) id AA164552217; Tue, 16 May 1995 00:30:17 -0500 Message-Id: <199505160530.AA164552217@caliban.ks.uiuc.edu> Subject: The ab initio basis of DFT and semi-emp methods To: chemistry@ccl.net Date: Tue, 16 May 95 0:30:16 CDT Mailer: Elm [revision: 70.85] On the subject of DFT, semi-empirical methods, and ab initio theory: At first sight it may appear that DFT methods have a stronger "ab initio" basis than semi-empirical methods, in fact I will argue that the reverse is actually true because the ab initio basis of semi-empirical methods are more highly developed and has been more extensively researched than DFT. In order to say that there exists an ab initio basis for either DFT and/or semi-empirical methods, I argue that there must exist (1) a formal mathematical theory linking the exact molecular electronic Schr\"odinger equation and the approximate method (DFT or Semi-Emp) (2) an ab initio method which can compute all of the mathematical parameters (be them matirx elements, functionals, densities, etc) in the approximate method (3) tests of the assumptions of the approximate method using the ab initio techniques described in (2) (4) [the hardest and most challenging requirement] actual and meaningful improvements must have been sugested and incoproated into the approximate methods based on the ab initio tests. For both Semi-Emp methods and DFT I do not believe that all 4 requirements have been met, however, I beleive that the ab initio theory of Semi-Emp methods has been more highly developed than the DFT. It can be argued that the Hohenberg-Kohn (HK) theorem and the Kohn-Sham equations provide (1) for DFT, however, I must point out that niether of these provide an exact presecription for computing the density function for an arbitrary molecular system the state of DFT theory lies somewhere between requirements (1) and (2). I know of of only one paper which describes an ab initio algorithm for computing the universal density functional using ab initio techniques for a general molecular system (Karl F. Freed and Mel Levy, JCP vol 77, page 396 1 July 1982). Some recent work by Parr describes ab initio techniques for (3), however; Parr provides some diagnostic tools for testing the assumptions of DFT with out actually computing the functionals themselves (I saw this in a recent talk Parr and I do not know how well this is described in his book on DFT). Likewise, other work in the literature exists which describes how to express the exact functional for some model systems (I can not recall all of the work. I recall that Bob Harris at U.C. Berkeley has some intersting work in the area.) If there is other important work in the area plase bring the attention of the CCL forum. In contrast, the theory of semi-empirical methods is more highly developed as requirements (1)-(3) have been met with the use of the effective valence shell effective Hamiltonian (Hv) ab initio method (see, for instance, Charles H. Martin and Karl F. Freed, JPC, Vol 99, page 2701, 1995, and Karl F. Freed, In Conceptual Trends In Computational Chemistry; VCH: New York, 1991; Vol II) I do not beleive that condition (4) has been fully borne out by the Hv theory, however, some suggestions have been discussed by Walter Thiel (Tetrahedron vol 44, page 7393, 1988), and other semi-empirical methods have been based on related ab initio theories (Malieru's work, the PCLIO of Peter Fulde) Neither DFT nor Semi-empirical methods desrve full ab initio status at this time, however, because neither method may be systematically corrected with higher levels of theory. It is this feature that distinguishes ab initio theory from other approximate methods as it is always possible, although not always practical, to systematically extend the methods as close as possible to the exact solution of the Schr\"odinger equation (or to extend the Schr\"odinger equation, for that matter) to any desired accuracy obtainable with current experimental techniques. I find it most unfortuneate that the ab initio basis of both Semi-empirical methods and DFT has not been more rigorously explored; there is tremendous room for advancement in these areas of research, especially in the area of semi-empirical methods. Indeed, the ultimate goal of such research would be to obtain ab initio accuarcies with semi-empirical speeds, a most formidable challenge. From teck.lim@pembroke.oxford.ac.uk Tue May 16 05:06:58 1995 Received: from oxmail2.ox.ac.uk for teck.lim@pembroke.oxford.ac.uk by www.ccl.net (8.6.10/930601.1506) id FAA01402; Tue, 16 May 1995 05:00:15 -0400 Received: from sable.ox.ac.uk by oxmail2.ox.ac.uk. with SMTP (PP) id <05781-0@oxmail2.ox.ac.uk.>; Tue, 16 May 1995 10:00:16 +0100 Received: (from pemb0035@localhost) by sable.ox.ac.uk (1.4/8.6.12) id JAA05436; Tue, 16 May 1995 09:59:48 +0100 Date: Tue, 16 May 1995 09:59:47 +0100 (BST) From: Teck Lim To: ccl Subject: xdbx source Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Recently, I posed a query on location of xdbx source for SGI machines. Here are the extracts from the replies I received. Special thanks to Andy, David, Walter, Lawrence and Michael. -------------------------------------------------------------------------- From: "David L. Freeman" / Walter Koppensteiner / Michael Bass / "Lawrence S. Norris" ftp site...ftp.sgi.com cd sgi cd xdbx There is a tar file there. I have used this for fortran. I assume it will work for C. ------------------------------------------------------------------------- From: Mr Andrew D Allen We do have xdbx!!! though, I've tar'ed and compressed it and put it onto our ftp server. ftp 131.227.110.69 -> /pub/INCOMING/xdbx.tar.Z --------------------------------------------------------------------------- best regards - tecksin From HRUSAK@jh-inst.cas.cz Tue May 16 05:22:01 1995 Received: from uivt1.uivt.cas.cz for HRUSAK@jh-inst.cas.cz by www.ccl.net (8.6.10/930601.1506) id EAA01351; Tue, 16 May 1995 04:55:06 -0400 Received: from bob223.jh-inst.cas.cz ([147.231.28.65]) by uivt1.uivt.cas.cz (4.0/SONY-4.0MX) id AA01909; Tue, 16 May 95 10:53:16 +0200 Received: from BOB/MAILQUEUE by bob223.jh-inst.cas.cz (Mercury 1.20); 16 May 95 10:54:25 GMT+1 Received: from MAILQUEUE by BOB (Mercury 1.20); 16 May 95 10:54:17 GMT+1 From: "Dr. Jan Hrusak" Organization: Institute of Physical Chemistry To: chemistry@ccl.net Date: Tue, 16 May 1995 10:54:11 +0100 Subject: Is ab initio semiempirical ? Return-Receipt-To: "Dr. Jan Hrusak" Priority: normal X-Mailer: Pegasus Mail/Windows (v1.22) Message-Id: In general I do not like such philosophical discussions, but on the other hand I would like to stress my opinion to this particular problem. I think there is no reason for DFT to enter a claim to be called ab initio. Since in my wiev just very few ab initio calculations are realy "first principle" calculations. First of all, ab initio is just an approximation to solution of the Schroedinger equation. There is usually an (arbitrary or not) chosen a basis set (parameter set?) for a given atom. Further, in many of the ab initio codes not all the integrals are evaluated in course of the calculation. (neglecting small int., cuttoff criteria are set etc.) Thus "ab initio" in a strong sense is just an terminus technicus describing a given technique, which is more or less non empirical. Jan ---------------------------------------------------------------------------- Dr. Jan Hrusak ############################### J. Heyrovsky Institute of Physical Chemistry ## MEMOR ESTO CONGREGATIONIS ## Academy of Sciences of the Czech Republic ## TVAE QVAM POSSEDISTI ## Dolejskova 3, CZ-182 23 Prague 8 ## AB INITIO ## Czech Republic ############################### ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Phone: (0042 2) 66 05 3436 FAX: (0042 2) 858 2307 E-Mail: hrusak@jh-inst.cas.cz ---------------------------------------------------------------------------- From hs@helix.mdy.univie.ac.at Tue May 16 08:37:03 1995 Received: from helix.mdy.univie.ac.at for hs@helix.mdy.univie.ac.at by www.ccl.net (8.6.10/930601.1506) id IAA03917; Tue, 16 May 1995 08:25:03 -0400 Received: by helix.mdy.univie.ac.at (940816.SGI.8.6.9/940406.SGI) for chemistry@ccl.net id OAA28389; Tue, 16 May 1995 14:23:53 +0200 From: "Hellfried Schreiber" Message-Id: <9505161423.ZM28387@helix.mdy.univie.ac.at> Date: Tue, 16 May 1995 14:23:51 -0600 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@ccl.net Subject: CONFERENCE ANNOUNCEMENT Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii >> INTERNATIONAL CONFERENCE ON MOLECULAR STRUCTURAL BIOLOGY << Organized by the Austrian Chemical Society Vienna (Austria), September 17-20, 1995 TOPICS: 1) The Impact of Molecular Biology on Structural Biology 2) Biomolecular Structure Determination a) X-Ray Diffraction b) NMR Spectroscopy 3) Dynamics and Function of Biomolecules 4) Computational Methods 5) Protein Engineering and Design The scientific programme is designed to cover a broad range of disciplines in molecular structural biology. Topics will be presented in the form of plenary lectures, posters, discussions and exhibitions. Sunday, (17.9) ----------------------------------------------------------------------------- Registration Welcome Cocktail Honory Lecture by H.Neurath Monday, (18.9) ----------------------------------------------------------------------------- 1. The impact of Molecular Biology on Structural Biology C.Cantor (USA) "Application of Streptavidin and Genetically Engineered Variants" T.Blundell (GB) "Protein Super Families: Genome Analyses and Drug Discovery" 2. Biomolecular Structure Determination a) X-Ray Crystallography R.Huber (D) "Proteolytic Enzymes and Their Natural Inhibitors - New Functions and New Structures and No End in Sight" M.Walkinshaw (CH) "Structures and Biological Implications of Series of Cyclophilin-Cyclosporin Crystal Complexes" I.Schlichting (D) "Ligand Binding in Heme Proteins Studied by Kinetic X-Ray Crystallography" Tuesday (19.9.) ----------------------------------------------------------------------------- b) NMR Spectroscopy O.Jardetzky (USA) "Flexibility and Function in a DNA Binding Protein - the Trp-Repressor of E.Coli" P.Roesch (D) "The Structure of Iron-Sulfur Proteins in Solution" C.Dobson (GB) "The Structural Basis of Protein Folding" 3. Dynamics and Function of Biomolecules J.Lakowicz (USA) "Fluorescence Spectroscopic Studies of the Structure and Dynamics of Biomolecules" W.Kuehlbrandt (D) "Structure Determination of Membrane Proteins by High-Resolution Electron Microscopy" H.Frauenfelder (USA) "Dynamics and Function of Biomolecules" Wednesday (20.9.) ----------------------------------------------------------------------------- 4. Computational Methods M.Karplus (USA) "Simulations of Protein Folding From the Native to the Denatured State and Back Again" J.Skolnick (USA) "A Hierarchial Approach to the Prediction of Protein Structures" H.-J.Boehm (D) "New Computational Tools for Structure Based Drug Design" 5. Protein Engineering and Design A.Fersht (GB) "Pathways of Protein Folding" L.Presta (USA) "Protein Engineering of Immunoglobulins and Immunoglobulin-Like Domains" M.Mutter (CH) "De Novo Protein Design" CALL FOR POSTERS ----------------- All those intending to participate in the conference are invited to submit posters presenting original work. Abstracts prepared according to the instructions given below should arrive NOT LATER THAN JUNE 30th, 1995. The authors will be informed about the provisional acceptance in July, 1995. The presentation of the posters will be finally approved and thus the contribution included in the Book of Abstracts when at least one of the registers before August 1st, 1995. Contributors of outstanding posters will be chosen by the scientific committee to give a 20 minute lecture. Head of Scientific Committee: P.Schuster EXHIBITON: --------- An exhibition of instruments, accessories, software, literature and other items is planned. Companies interested in displaying their products are kindly requested to contact the conference secretariat. INDUSTRIAL SATELLITE MEETING: ----------------------------- A half day industrial symposium is planned. Those companies who are interested in presenting up-to-date results obtained on their products in the form of 20 minute lectures are kindly requested to contact the conference secretariat. Registration Fees (before August 1): Regular Participant 4000 ATS GOeCH Member 3500 ATS Student 2000 ATS The registration fee includes the Book of Abstracts, the welcome cocktail and buffet, the invitation to the Viennese Rathaus, a ticket for the piano concert, coffee breaks and tram tickets. If your are interested in a folder of the second announcement including a registration form and the social program, please contact: A.Kungl Gesellschaft Oesterreichischer Chemiker AG Biophysikalische Chemie Nibelungengasse 11 A-1010 Wien, Austria Tel.: (43) 1 587249 FAX.: (43) 1 587966 e-mail: msb95@helix.mdy.univie.ac.at -- +-----------------------------------------------------------------------------+ | | | Hellfried Schreiber, Ph.D. | | | +---------------------------------------+-------------------------------------+ | | | | Institute for Theoretical Chemistry | | | Theoretical Biochemistry Group | Mail: hs@helix.mdy.univie.ac.at | | Waehrigerstrasse 17 | Voice: +43 1 40480 - 618 | | A-1090 Wien, Austria, Europe | FAX: +43 1 4028525 | | | | +-----------------------------------------------------------------------------+ From ivarm@boc.ic.ee Tue May 16 09:22:10 1995 Received: from argus.chemnet.ee for ivarm@boc.ic.ee by www.ccl.net (8.6.10/930601.1506) id JAA04828; Tue, 16 May 1995 09:08:34 -0400 Received: from boc.ic.ee (boc.ic.ee [193.40.63.200]) by argus.chemnet.ee (8.6.9/8.6.9) with SMTP id PAA26972 for ; Tue, 16 May 1995 15:54:00 +0300 Received: from argus.chemnet.ee by boc.ic.ee id aa12400; Tue, 16 May 95 16:12:39 estonia From: "Ivar Martin" Date: Tue, 16 May 95 16:00:56 EST Message-Id: <5667.ivarm@boc.ic.ee_POPMail/PC_3.2.2> Reply-To: X-POPmail-Charset: English To: chemistry@ccl.net Subject: Imaginary frequency and rate constant? Hello! As it is expected, MOPAC calculates one and only one negative vibrational frequency at TS. The value lies (-300 - -150 cm-1). Now, is it correct to use this frequency as pre-exponent factor (frequency factor) in Arrhenius rate constant equation? The reaction I study is C-C single bond forming (or splitting) reaction. If there will be interest, I'll give the summary to list. Thanks, _______________________________ Dr. Ivar Martin Department of Bioorganic Chemistry tel: +372 2 526510 Institute of Chemistry fax: +372 2 536371 Akadeemia tee 15 EE0026 e-mail: ivarm@boc.ic.ee Tallinn, ESTONIA From dimitris@3dp.com Tue May 16 10:37:05 1995 Received: from boris.3dp.com for dimitris@3dp.com by www.ccl.net (8.6.10/930601.1506) id KAA06776; Tue, 16 May 1995 10:27:41 -0400 Received: from europa.3dp.com by boris.3dp.com via SMTP (931110.SGI/930416.SGI) for chemistry@ccl.net id AA24466; Tue, 16 May 95 10:29:13 -0400 Received: by europa.3dp.com (931110.SGI) id AA26478; Tue, 16 May 95 10:27:26 -0400 From: "Dimitris Agrafiotis" Message-Id: <9505161027.ZM26476@europa.3dp.com> Date: Tue, 16 May 1995 10:27:25 -0400 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: dvm@extreme.chem.rpi.edu Subject: Delaware Valley Modeling Club Meeting Cc: chemistry@ccl.net, krystek@bms.com Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Dear DVM'ers, The next meeting of the Delaware Valley Molecular Modeling Club will be held on May 31, 1995, at 6.30 pm. The subject will be diversity profiling for combinatorial libraries, and the meeting will be hosted by 3-Dimensional Pharmaceuticals in Exton, PA. PLEASE let me know if you are going to attend, to help us make the necessary catering arrangements. See you all in a couple of weeks. ----------- DIRECTTIONS: ----------- 3-Dimensional Pharmaceuticals, Inc. Eagleview Corporate Center 665 Stockton Drive, Suite 104 Exton, PA 19341 1) From Philadelphia: Take the Schuykill Expressway (I-76) to Rt. 202 South. Continue South on Rt. 202 to Rt. 30 West. Continue on Rt. 30 West to Rt. 100 North. You will make a right onto 100 North. Continue North on 100 until you see the exit for the Pennsylvania Turnpike and continue with directions below. 2) From the Pennsylvania Turnpike (Exit 23), and Rt. 100 North: Go 1/2 mile to traffic light. Just north of the light, take jughandle to the right for entrance to Eagleview Boulevard West. You will cross Rt. 100. Follow Eagleview Blvd. 1/4 mile to second right (Pennsylvania Drive). Go Right on Pennsylvania Drive for 3/10 mile to Rice Blvd. on left. Go left on Rice Blvd. for 1/10 mile to Stockton Drive (firth right). Go right on Stockton Drive to second building on right (3rd lot entrance). -- Dimitris K. Agrafiotis, PhD | e-mail: dimitris@3dp.com 3-Dimensional Pharmaceuticals, Inc. | tel: (610) 458-6045 665 Stockton Drive, Suite 104 | fax: (610) 458-8249 Exton, PA 19341 From jkl@ccl.net Tue May 16 11:37:08 1995 Received: for jkl@ccl.net by www.ccl.net (8.6.10/930601.1506) id LAA09101; Tue, 16 May 1995 11:36:46 -0400 Date: Tue, 16 May 1995 11:36:46 -0400 From: Jan Labanowski Message-Id: <199505161536.LAA09101@www.ccl.net> To: chemistry@ccl.net Subject: Re: Molecular Graphics and Animation Workshop - Please Post Forwarding: Mail from 'jeanne@tc.cornell.edu (Jeanne C. Butler)' dated: Tue, 16 May 1995 09:44:43 -0400 MOLECULAR GRAPHICS AND ANIMATION WORKSHOP The Cornell Theory Center will hold a workshop June 29-July 1, 1995, focusing on the use of computer graphics in molecular and biological sciences. The workshop will cover the principles of molecular graphics using the IBM Visualization Data Explorer (DX) software in combination with a publicly available chemistry module suite (CM) that was written at CTC. In cooperation with the Division of Biological Sciences, participants will have access to a state-of-the-art interactive graphics workstation facility, complete with stereo-viewing equipment and hardware rendering. Although some previous UNIX and DX experience is desirable, the workshop will include an introduction to both. Participants are encouraged to bring their own data sets. Consulting staff will be available to assist researchers in their visualization projects. The first morning of the workshop will be held on the seventh floor (rm 708) of the Engineering and Theory Center Building on Hoy Road on the Cornell University campus in Ithaca, New York. The reception desk can be reached at (607) 254-8686 from 8:00 a.m. to 5:00 p.m. The remainder of the workshop will be held at Stimson Hall in the Laboratory of Computer Graphics (rm G04) and in the CTC Visualization facility (rm 653). Saturday morning will be open lab time for final video productions and virtual reality experiments. COVERED IN THE WORKSHOP: -theory and use of the basic molecular graphics constructs (CPK, stick models, ribbon representations, and molecular surfaces) -visualization of electrostatic fields, quantum mechanics, and dynamics -three-dimensional reconstructions from microscopy -advanced rendering (volumetric rendering, constructive solid geometry, and texture maps) -animation techniques using DX -virtual reality using the DX-to-CAVE module So that each participant will have access to a workstation, class size will be limited to ten. Short lectures and video presentations will be interspersed with generous periods of lab time. Participants will be provided with examples from a wide variety of research projects, which they can copy and modify to fit their own research problems. Also available will be CTC computing and data facilities, including a high-quality color printer and a growing virtual reality environment. HOTEL ACCOMMODATIONS: Attendees are responsible for their own hotel reservations and meals. Paid parking is available on campus, but walking or public transportation are recommended. -Best Western University Inn (<1 mile) East Hill Plaza Ithaca 607/272-6100 FAX: 607/272-1518 -Collegetown Motor Lodge (walking distance) 312 College Avenue Ithaca 607/273-3542 800/745-3542 -Sheraton Inn (<3miles) One Sheraton Drive Ithaca 607/257-2000 FAX: 607/257-3998 -Statler Hotel (1 block from Theory Center) Cornell University campus 607/257-2500 FAX: 607/257-6432 TO APPLY: Due to restricted space, registration for this workshop is limited. The completed application form, along with payment, must be received by Friday, June 9, 1995. Applications will be accepted after this date only if openings still remain. The workshop fee includes all workshop materials. Local researchers may charge the registration fee to the appropriate Cornell University account number. Applications that do not include payment cannot be accepted. Payment checks will be returned promptly to applicants not accepted due to over-enrollment. Notification will be mailed on June 12, 1995. PAYMENT SCALE, PAYABLE TO CORNELL UNIVERSITY: Academic participants: $70 Corporate Research Institute members: $250 Other corporate participants: $350 ------------REGISTRATION FORM------------------ This registration form and payment must be received by June 9, 1995. SEND TO: Jeanne Butler Cornell Theory Center 427 Engineering and Theory Center Building Ithaca, NY 14853-3801 (607) 254-8813 jeanne@tc.cornell.edu REGISTRATION FORM Name__ Institution__ Address__ City, State, Zip__ Telephone__ Fax__ Preferred electronic mail address__ Do you have a current CTC account: __no __yes; my userid is__ Do you have a pending allocation request: __no __yes Social Security #:____-_____-_____ to set up new supercomputer accounts. (Submission of social security numbers is voluntary and will not affect eligibility for access to CTC facilities. However, SSNs are an integral part of the National Science Foundation's information system and assist in managing the Supercomputer Centers program. SSN solicited under NSF Act of 1950, as amended.) Special needs (e.g., mobility impaired)__ Account number to charge (Cornell applicants only)__ Academic discipline (e.g., biological sciences, geosciences, chemical eng.)__ Status (check all that apply) Academic __Undergraduate __Graduate __Postdoctoral __Faculty __Smart Node Consultant/Advisor __Other: Corporate/Commercial __Research __Other: ETHNIC ORIGIN (OPTIONAL) __African American __Caucasian __Asian American __Hispanic American __Native American __Alaskan Native __Other: If possible, please list the various types and formats of data you are likely to bring to the workshop (optional). This will help ensure that we can read your data into the graphics programs. (e.g., molecular structures in Brookhaven Protein Databank format, or electron densities from Gaussian, or confocal microscope images from our own lab [can send sample] ). ___ If nonstandard format, please contact richard@tc.cornell.edu. *All trade names referred to are trademarks or registered trademarks of their respective companies. ----------- End Forwarded Message ----------- From shep@appsdiv.cray.com Tue May 16 15:07:06 1995 Received: from timbuk.cray.com for shep@appsdiv.cray.com by www.ccl.net (8.6.10/930601.1506) id PAA13960; Tue, 16 May 1995 15:05:01 -0400 Received: from ss1.cray.com (ss1.cray.com [128.162.171.15]) by timbuk.cray.com (8.6.11/CRI-fence-1.4) with SMTP id OAA15020 for ; Tue, 16 May 1995 14:04:59 -0500 Received: by ss1.cray.com (4.1/CRI-5.14) id AA04563; Tue, 16 May 95 14:04:58 CDT Date: Tue, 16 May 95 14:04:58 CDT From: shep@appsdiv.cray.com (Shepard Smithline) Message-Id: <9505161904.AA04563@ss1.cray.com> To: chemistry@ccl.net Subject: similarity Dear Netters, A while back I posted some questions regarding similarity. Below is the original question and the responses I received. Thanks to all who responded. Shep Smithline __________________________________________________ Original Posting: Dear Netters, I have some questions for the similarity gurus out there. (i) What are the commonly used (public or commercial) similarity programs? (ii) What are their major features? For example: Do they allow a test structure to rotate or translate relative to a reference structure or can the internal geometry change? Do they perform any additional analyis once the indexes are computed? (iii) What sort of data do they use to compute the similarity? For example: Do they compute indexes based only on volume or shape? Do they use charges or other quantum mechanically derived data to compute an index? Please foward responses directly to me. I will summarize to the net. Thanks, Shep Smithline _______________________________________________________________________ Responses: Dear Shep I have a method of similarity searching based on the method of "icosahedral matching". The algorithm is described in reference (1). It was taken up by workers at Organon Oss (reference 2) who developed a 3D database seaching program called SPERM. Subsequently and independently I amplified the original method into a series of programs all of which use the library of subroutines but the different programs do different things:- THREEDOM 3D-database searching COMPARISONS Compares a single structures with many structures CORRELATE Compares structures in one series with those in another series (the two series may be the same) The feature of icosahedral matching is that it makes use of the symmetry of the icosahedral group to increase the efficiency of the matching process (over brute-force methods) by the factor of 60 (120 if mirror image searching is included). The programs use the ideas of Dean (reference 3) on gnomonic projections to handle the properties being compared. These properties can either be shape (e.g. distances from points on an encompasing sphere to the nearest atoms) or electronic (potentials at points on the encompasing sphere), and in principal other properties could be used (e.g. hydrophobicity). The icosahedral matching algorithm takes care of the business of rotating one of the pair of structures being matched with respect to the other. It does not incorporate any translational operation. Because the icosahedral matching process does not take into account the overall size of structures being compared, it is necessary in database searching to apply some prefiltering, to avoid comparing grossly disimilar structures. Accordingly there are two other programs:- PREFILTERS and QUICKSCAN. The first of these will produce an index file for the database for the parameters:- volume, size of largest axis, and ellipticities (i.e. ratios of three principal axes), for all structures in the database. The second program will extract just those structures from the database which meet criteria of similarity (+/- percentages of volume, axis size, ellipticity) to the target structure). These extracted structures are then submitted to the program THREEDOM. All of these programs are available from QCPE as part of the INTERCHEM package for quite modest fees. References: (1) P. Bladon J. Mol. Graphics, 1989,7,130-137. (2) V. J. van Geerestein, N. C. Perry, P. D. J. Grotenhuis, and C. A. G. Haasnoot, Tetrahedron Computer Methodology, 1990, 3, 595-613; N. C. Perry and V. J. van Geerestein, J. Chem. Inf. Comput. Sci., 1992, 32, 607-616. (3) P.-L. Chau and P. M. Dean, J. Mol. Graphics, 1987,5,97; P. M. Dean and P.-L. Chau, J. Mol. Graphics, 1987,5,152; P. M. Dean and P. Callow, J. Mol. Graphics, 1987,5,159; P. M. Dean, P. Callow, and P.-L. Chau, J Mol. Graphics, 1988,6,28. Yours sincerely Peter Bladon Phone/Fax +44-(0)141-776-1718 email cbas25@vaxa.strath.ac.uk _________________________________________________________ Shep, You should be aware of the Oxford Molecular package Asp, this is an implementation of the Carbo method of similarity calculation as developed by Dr. Graham Richards et al in Oxford University. The method relies on the calculation of property overlap integrals and uses either a grid-based method, or a gaussian approximation. The latter is significantly faster, and yields indices which are comparable with the grid calculations. The 'property' is either shape, charge, lipophilicity or any other user-supplied potential that may be calculated from atom-centred values. Similarity indices may be calculated either for; 1) fixed orientations, 2) rigid rotation/translation 3) flexible (bonds). In all cases the 'lead' molecule is fixed and the comparison is optimised. The software runs on SGI, IBM and HP workstations, and presents the user with a spreadsheet-based GUI. Alternatively, Asp may be run via the OM product Tsar, which is an integrated package (molecular spreadsheet) for QSAR analysis. Further details may be obtained from any OM office, or via the OM WWW pages at; http://www.oxmol.co.uk/ Hope this helps, Rob Scoffin =========== Dr. Robert Scoffin ________________ Group IT Manager | #### | & Product Manager | ## ## ## | Oxford Molecular Ltd | ## ## ## | The Magdalen Centre | ## ## ## | Oxford Science Park | ###### | Oxford OX4 4GA | ## | Tel: (0865)784600 | ## | Fax: (0865)784601 | #### | Mobile: (0378) 210813 ---------------- ___________________________________________________________________ Dear Shepard, What kind of similarity are you referring to? Similarity can be structurally based, such as an RMSD. Or, similarity can refer to an aggregate representation of a molecule comprising the number and types of functional groups, presence absence of rings, etc. As I am mopre familiar with the latter, Daylight which develops and markets the MedChem suite of programs is indeed the best for the latter. Hope this helps... -mark ****************************************************** * * * * * Mark A. Zottola * * markz@dna.chem.duke.edu * * Department of Chemistry * * Duke University * * Durham, NC 27704 * * * * * * The fault, dear Brutus, lies not with ourselves, * * but rather within our CPUs. * * (with apologies to Shakespeare * * * * * ****************************************************** ________________________________________________________________ Hello, I read your request for similarity methods and I would like to 'submit' the following information about a superposition method developed in the group of Prof. J. Kroon at Utrecht. The method is to be published soon. ------------------------------------------------------------------------------- * QUASIMODI * Molecular superposition by means of simulated diffraction patterns. * Patterson (electron) density superposition. QUASIMODI is a superposition program using similarity index calculation by means of simulated crystallographical data. Optimization of overlap is performed in Fourier space; the constraint of overlap is Patterson (electron) density (which automatically includes steric and electronic factors). As for now, the input requires atomic coordinate data for two molecules (.mol, .res files). Internal rotations are not incorporated, so a fixed conformation is to be supplied. A job file specifies the optimizations to be performed. Resolution of the Patterson (electron) density description is defined by the user. Further use is made of quantum-chemical data which are incorporated in the program (taken from SHELX). Automated optimization is performed starting from 12 starting geometries which are generated by the program. The output contains a list of optimized rotation and translation parameters for a number of overlays which give rise to maxima in the similarity parameter space. Optimized parameters are given with respect to the input geometry. Root Mean Squared deviations with respect to the input coordinate data (or a user-supplied molecule) can be determined. Output of the optimized geometries is possible. Calculation times are rather fast: Twelve optimizations are performed in 5-10 minutes at intermediate resolution (twelve low resolution calculations are performed within two minutes). The twelve starting optimizations cover the parameter space to be searched well (in practice it is seen that the number of optimal overlays, i.e. the number of -local- maxima in similarity index parameter space is less than 12). Submission of the program to QCPE will follow. --- I hope this is of any use to you. Kind regards, Willem Nissink ________________________________________________________________ J.W.M. Nissink | Utrecht University | E-Mail: Department of Analytical | W.Nissink@ams.chem.ruu.nl Molecular Spectrometry | P.O. Box 80.083 | S-mail: 3508 TB Utrecht | Poortstraat 14 bis The Netherlands | 3572 HJ Utrecht Tel. +31.30.536817 / 537500 | Holland Fax. +31.30.518219 | ________________________________________________________________ Shep, Thought I'd take the opportunity to describe some new stuff I've done (we're shipping it with Spartan V4.0)... (i) What are the commonly used (public or commercial) similarity programs? (ii) What are their major features? Spartan now has a similarity/superposition tool - it aligns a series of molecules against a user-specified template by maximizing the similarity of 3D grid-based functions surrounding each molecule. These can be classical "functions" like volume or electrostatic potential from formal charge or quantum-based functions like density, electrostatic potential, etc. In addition, the user can import functions calculated outside of Spartan. It's a simplex-based optimizer, since that seems to be pretty successful in spanning problem space (and is less dependent on initial guesses for alignment). Naturally, the code can be used as a similarity measure as well. It does not allow for internal motion (although it can be mated with conformational analysis to "emulate" flexible fitting). We also have a form of Hopfinger's molecular shape analysis - it will report the volumes, pairwise volumes and volume similarities for a series of molecules. Hope this helps! Joe (iii) What sort of data do they use to compute the similarity? The MSA code uses a MC/numerical integration scheme to calculate volume/shared volume. The similarity/superposition module uses 3D grid-based functions - as simple as y/n values for VdW-sphere volume to as complex as the user can calculate. It uses Spartan's graphics module to calculate the grids (which permits difference grids, etc) and can import grids from outside Spartan. There are a range of error functions (RMS, correlation, Carbo, etc). -- ------------------------------------------------------------------------ Joe Leonard Wavefunction Inc. 18401 Von Karman, Suite 370 Irvine, CA 92715 I am a professional... 714-955-2120 do not attempt this at home. 714-955-2118 fax jle@wavefun.com _____________________________________________________________ Shep, The topic of structural similarity is fairly old and diverse now. Here is an ever so quick low down: 1. 2D methods The earliest are topological, and the following are some of the approaches: - Fragment keys for substructure search (Pfizer, Willett) - Atom-pair enumeration (Lederle) - 'Torsional descriptors' (Lederle) - Maximal common subgraph (Willett) - Topological indices (?) The best summary is Willett, "Similarity and Clustering in Chemical Information systems," RSP, 1987. 2. 3D methods - Grid or field overlay (Richards), w/ or w/o conformational flexibility - Projection ('Sperm') - Atom-triplet enumeration (Lederle, CAS) - Atom-triplet enumeration, with fancy indexing (IBM's "FLASH") - Distance matrix comparison (Willett) - 3D Maximal Common Subgraph (Willett) - ... And lots more than that... Enjoy -- Tom Moock, MDLI ______________________________________________________________________ Dear Dr. Smithline Here is an answer to your query about 'similarity'. I hope you will summarize and post the answers you get. >i) What are the commonly used (public or commercial) similarity > programs? ---- I don't know how many of the programs themselves are available, but do you realize how many different methods are available ? There are indeeed very many, ranging >from topological indices ( Randic, Balaban, Keir & Hall and many others ), surface topology and homology groups of algebraic topology ( Mezey ), graph theoretical methods ( Randic, Bayada ), quantum mechanical methods ( Carbo, Richards et al., Cioslowoski, Allen & Cooper and others ) and surface shape descriptors ( Bywater et al.,and various researchers at Scripps: Duncan, Olson, Getzoff, Max). You will find all the references to these methods in a forthcoming book : "~Quantitative Measurement of Molecular Similarity using Shape Descriptors~" in R. Carb\'{o} (~Ed.~), "~Molecular Similarity and Reactivity~: from Quantum Chemistry to Phenomenological Approaches~", Kluwer Verlag, 1994. As to programs that are available, you should ask Oxford Molecular about the program ASP. The shape descriptor programs developed by myself and colleagues will be available one day, but don't expect that to happen too soon, ask me again in about 6 months from now. But in the meanwhile, you might want to read these papers : S. Leicester, J. Finney & R. Bywater J. Mol. Graph. (1988) 6 104-108 S. Leicester, J. Finney & R. Bywater J. Mathematical Chemistry (1994) 16 315-341 S. Leicester, J. Finney & R. Bywater J. Mathematical Chemistry (1994) 16 343-365 Good luck ! Robert Bywater Novo Nordisk A/S DK-2880 Bagsvaerd Denmark ----------- End Forwarded Message ----------- From matt@metis.tripos.com Tue May 16 18:22:08 1995 Received: from gatekeeper.tripos.com for matt@metis.tripos.com by www.ccl.net (8.6.10/930601.1506) id SAA16956; Tue, 16 May 1995 18:08:14 -0400 Received: (from news@localhost) by gatekeeper.tripos.com (8.6.12/8.6.12) id RAA08816 for ; Tue, 16 May 1995 17:06:58 -0500 Received: from tripos.tripos.com(192.160.145.1) by gatekeeper.tripos.com via smap (V1.3) id sma008814; Tue May 16 17:06:55 1995 Received: from metis.UUCP (metis.tripos.com [192.160.145.41]) by tripos.tripos.com (8.6.12/8.6.12) with SMTP id RAA07451 for ; Tue, 16 May 1995 17:02:33 -0500 Received: by metis.UUCP (4.0/4.7) id AA17980; Tue, 16 May 95 17:02:26 CDT From: matt@metis.tripos.com (Matt Clark) Message-Id: <9505162202.AA17980@metis.UUCP> To: chemistry@ccl.net Subject: Modeling on the Ebola virus Date: Tue, 16 May 95 17:02:26 EDT Do any of you know of groups modeling drugs to inhibit the Ebola virus? From Matthew.Harbowy@tjlus.sprint.com Tue May 16 18:52:08 1995 Received: from sprintf.merit.edu for Matthew.Harbowy@tjlus.sprint.com by www.ccl.net (8.6.10/930601.1506) id SAA17210; Tue, 16 May 1995 18:41:28 -0400 X400-Received: by mta merit in /PRMD=internet/ADMD=telemail/C=us/; Relayed; Tue, 16 May 1995 18:40:05 -0400 X400-Received: by /ADMD=TELEMAIL/C=US/; Relayed; Tue, 16 May 1995 18:30:58 -0400 X400-Received: by /PRMD=SMXFL2/ADMD=TELEMAIL/C=US/; Relayed; Tue, 16 May 1995 16:12:30 -0400 X400-Received: by /PRMD=LANGATE/ADMD=TELEMAIL/C=GB/; Relayed; Tue, 16 May 1995 16:12:00 -0400 Date: Tue, 16 May 1995 16:12:00 -0400 X400-Originator: Matthew.Harbowy@tjlus.sprint.com X400-Recipients: non-disclosure:; X400-MTS-Identifier: [/PRMD=LANGATE/ADMD=TELEMAIL/C=GB/;Tue May 16 16:12:27 199500] X400-Content-Type: P2-1984 (2) Content-Identifier: Re: CCL:Are meth From: Matthew.Harbowy@tjlus.sprint.com Message-ID: <"Tue May 16 16:12:27 199500*/G=Matthew/S=Harbowy/OU=2812NJLP/O=TMUS.TJL/PRMD=LANGATE/ADMD=TELEMAIL/C=GB/"@MHS> To: chemistry@ccl.net Subject: Re: CCL:Are methods based on DFT ab initio? MIME-version: 1.0 Content-type: multipart/mixed; boundary="ZHdk1HQrlrn4CD3rIE5eZASMviZ9sm6l" --ZHdk1HQrlrn4CD3rIE5eZASMviZ9sm6l Content-type: text/plain; charset="us-ascii" ---------------------------------- Forwarded ---------------------------------- From: Matthew Harbowy at 2812NJLP Date: 5/16/95 8:37AM To: chemistry-request@ccl.net at INTERNET Subject: Re: CCL:Are methods based on DFT ab initio? ------------------------------------------------------------------------------- --ZHdk1HQrlrn4CD3rIE5eZASMviZ9sm6l Content-type: text/plain; charset="us-ascii" RFC-822-Headers: Errors-To: ccl@ccl.net Precedence: bulk --ZHdk1HQrlrn4CD3rIE5eZASMviZ9sm6l Content-type: text/plain; charset="us-ascii" I believe that it was one of Prof. Dewar's remarks that practically all HF was 'semi-empirical' in a number of senses: ultimately that it had to pe compared to reality at some point, which meant for STO-nG calculations one would fudge around explaining why the computations were so bad. I'm not one to say whether such comments are truth or propaganda, nor can I say whether DFT has forms which are 'ab-initio enough' to be ab-initio. However, one can parameterize mm2 methods to reproduce HF or MP energies, and no-one would believe that those methods are 'ab-initio', even though from a black-box view they might be. Likewise, from a black-box view the fact that DFT spews out HF or MP quality results does not mean that the calculations are ab-initio. Personally, I don't care much for the need to distinguish the two in any other way than to say that semi-empirical methods are fudged to make them look better. Given a 'good' ab-initio method, it would seem foolish to not fudge the parameterization a little to 'represent nature' better, either subsequent to the calculation with pages and pages of text to explain what the difference between theory and experiment is, or before the calcualtion with pages and pages of text to explain why this parameter or that functional makes the calculation mirror reality better. Matthew Harbowy 'my views have nothing to do with lipton' ______________________________ Reply Separator _________________________________ Subject: CCL:Are methods based on DFT ab initio? Author: chemistry-request@ccl.net at INTERNET Date: 05/15/95 9:25 PM Does this make HFS a semi-empirical theory? I think not: There is one and only one adjustable parameter, and the functional should be equally applicable in any part of any molecule. If you insisted on calling such a scheme semi-empirical, then you'd have to call Hartree- Fock frequencies adjusted by the famous 10% factor semi-empirical as well. (If you already do, that's fine with me. You're a purer man than I am, Gunga Din.) In a semi-empirical method, parameters are chosen for *each atom*, and if you don't have parameters for cesium, you simply cannot do semi-empirical calculations on cesium chloride. But once you have this one DFT parameter -- or even two or three -- you can do calculations anywhere on the periodic table (modulo relativity). Now there have been calculations carried out in which this HFS alpha parameter *was* different for each atomic environment (the so-called muffin-tin method), and those I *would* call semi-empirical. But that does not represent the main body of present-day density functional theory. There are certainly more recent examples of density functionals containing one or more fitted parameters; my former boss Axel Becke frequently ends up with one unknown left over when he's inventing a new functional. Nevertheless, in every case I know of the result after the fitting has been a density functional intended to be universally applicable. What we are pursuing, after all, is Hohenberg's and Kohn's universal functional of the density -- you only need, in principle, one functional and you can then calculate all nondegenerate ground states. If we try to derive this functional from physics, we are working "from first principles" -- or "ab initio". The other sense in which I can imagine DFT being characterized as "semi-empirical" is the manner in which the recent proliferation of functionals has been greeted by the user community. I've seen more papers and talks and posters than I can count that had the nature of "try six different density functionals and see which one gives the best results for my systems." If some thought then goes into the relationship between the underlying physics of the functionals and their performance, this is quite reasonable. But if the lowest average deviation from experiment -- sometimes by a vanishingly small margin -- is then taken as the only reason for choosing functional X over functional Y for further studies on analogs of these systems, then we are at some risk of passing straight through semi-empirical methods into pure empiricism, and neither DFT nor semi-empirical specialists might care to claim such work as characteristic of their field. (Although I should confess I'm prone to this disease myself. Mea culpa.) In conclusion, I don't really care what DFT is called except inasmuch as naming affects understanding. I myself try not to use language which classes DFT as either ab initio or semi-empirical, because those terms have accreted fairly specialized meanings over the last twenty years and DFT really doesn't fit comfortably into either. Cheers, Ross M. Dickson, Ph.D. (dickson@zinc.chem.ucalgary.ca) Chemistry Dept., The University of Calgary, Alberta, Canada. -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: dickson@zinc.chem.ucalgary.ca -- Original Sender From: Address: dickson@zinc.chem.ucalgary.ca CHEMISTRY@ccl.net -- everyone | CHEMISTRY-REQUEST@ccl.net -- coordinator MAILSERV@ccl.net: HELP CHEMISTRY | Gopher: www.ccl.net 73 Anon. ftp www.ccl.net | CHEMISTRY-SEARCH@ccl.net -- archive search http://www.ccl.net/chemistry.html | for info send: HELP SEARCH to MAILSERV --ZHdk1HQrlrn4CD3rIE5eZASMviZ9sm6l--