From jkl@ccl.net Thu Dec 12 01:44:21 1991 To: chemistry@ccl.net Subject: PDB file format description in PS Date: Thu, 12 Dec 91 01:44:15 EST From: jkl@ccl.net Status: R Yes, it is me again. Thanks to Torence P. Lo from U. British Columbia in Vancouver CAN we have fixed few typos in the LaTeX/Postscript version of Protein Data Bank Coordinate and Bibliographic Entry Format Description (see my posting on 91/12/10). The good news is that some of these typos were not ours but were diligently retyped from the original PDB document. Anyhow, I have put the new version in archives now. If you want it, read postings from 91/12/10 (you can get them by sending a message: send 91/12/10 from chemistry to OSCPOST@ccl.net or OSCPOST@OHSTPY.BITNET) and you will learn how to download them Jan Labanowski Ohio Supercomputer Center jkl@ccl.net From jkl@ccl.net Thu Dec 12 12:07:11 1991 To: chemistry@ccl.net Subject: Jan goes to Poland Date: Thu, 12 Dec 91 12:07:03 EST From: jkl@ccl.net Status: R Sorry for administrative business on the list. I. There will be major overhaul of ethernet in the OSC this weekend (starts Friday the 13th ! 5pm EST). Nothing will work till Monday (so they say). Do not sent anything to the chemistry@ccl.net or it will get lost. II. I (jkl@ccl.net = Jan Labanowski) am going for 1 month to Poland on the coming weekend and the chores of managing the list will be in Dave Heisterberg's hands (djh@ccl.net, DJH@OHSTPY.BITNET, chemistry-request.ccl.net). Please be considerate, for one month he will be doing a job of two people, his and mine, and believe me, there are some other small things which we do around here besides watching the list. He will be reading all my mail in my absence so the list business will be taken care of, though expect delays, he will be awfully busy. III. Please take the time and read the help file for the list. It will help you to keep Dave less busy during the time he is left with the list. To get the help file send a single line message: send help from chemistry to OSCPOST@ccl.net or OSCPOST@OHSTPY.BITNET Thanks. All the best wishes for all you folks over there. Have a nice Holiday and happy, fruitful and exciting New Year. Back after Jan. 20, 92 (assuming that the plane will land normally...) Jan Labanowski Ohio Supercomputer Center jkl@ccl.net From chemistry-request@ccl.net Thu Dec 12 12:08:02 1991 Date: Thu, 12 Dec 91 10:44:01 -0600 From: mcintosh@ccwf.cc.utexas.edu (aubrey mcintosh) To: chemistry@ccl.net Subject: Significant digits in calculations. Status: R As a chemist, I have always wanted my programs to recognize and manage significant digits. At this time, I have code that records significant digits on input, manages them correctly on add/subtract/multiply/divide, and correctly formats output. FORTRAN style input, e.g. 1.234567E+021 is accepted. On output, the exponent is changed to a SI suffix, e.g. (E-003, m), (E-006, u), (E-009, n), (E+006, M). These are recognized on input as well. A matrix algebra package is provided on top of these libraries. It is quite interesting to perform matrix calculations, especially eigenvector calculations, using significant digits. The library and matrix multiply source is available, and is described briefly in an upcoming article in Computers and Mathematics with Applications. I have been using this code now for over a year with minimal changes. I would now like some volunteers to "exercise" this code. System requirements are 1) A SPARC station. 2) A Mac II (68020 or higher) or 3) A vax running Ultrix and an X terminal. ftp access is recommended. Some setup is required. --Aubrey McIntosh From chemistry-request@ccl.net Thu Dec 12 15:32:48 1991 Date: Thu, 12 Dec 91 15:07:54 EST From: balbes@osiris.rti.org (Lisa Balbes) To: chemistry@ccl.net, sybyl@quant.chem.rpi.edu Subject: Rational Drug Design (better late than never) Status: R As promised, I have compiled a summary of references and information I gathered in reading all the responses to my (much) earlier request. All typos and mistakes are mine. A brief index/outline follows - for the entire 282 line file, email me at balbes@osiris.rti.org ____________________________ Introduction: Steps in rational drug design - 1. Determine receptor site of interest. 2. Build model of active site (receptor). a. Model entire protein - from xray of protein, homology modeling or b. build pharmacophore (geometric description of the minimal requirements of shape and charge complimentarity) 3. Develop inhibitor structures that fit active site model and dock. 4. Quantitate interaction, to predict activity of new compounds. 5. Synthesize compounds; evaluate their activity in the system of interest. 6. Refine (2), repeat (3) - (5). 7. Find effective, safe, synthesizable compound. Patent. Sell. $$$$$$$. Either a) start again at (1) or b) retire to Hawaii. ********** step 2 ******************************* GRID method of Peter J. Goodford ********** step 3 ******************************* Distance Geometry Devloped by Crippen and co-workers ********** step 3 (docking) ********************** DOCK Irwin D. Kuntz, Jr. ********** steps 3, 4 ****************************** GROW method of Moon and Howe (proprietary program, but methods useful). ************* step 4 ************************* Free Energy Perturbation ************* step 4 ************************* Min/MD cycling GENERAL APPROACHES ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Quantitative Structure Activity Relationship (QSAR) Active Analog Approach Simulated Annealing Molecular Dynamics (MD) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ General Reviews %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% standard disclaimer %%%% Lisa M. Balbes, Ph.D. phone: 919-541-6563 Research Triangle Institute, PO Box 12194 vmail: 919-541-6767, xt 6563 Research Triangle Park, NC 27709-2194 email: balbes@osiris.rti.org - This came directly from a computer and should not be doubted or disbelieved.- From chemistry-request@ccl.net Thu Dec 12 21:32:20 1991 Date: Thu, 12 Dec 1991 18:17:56 PST From: "W. Todd Wipke" To: chemistry@ccl.net Subject: Large (100,000 lines of code) programs Status: R John Rupley asked to hear from someone involved in large fortran programs. I have been involved in several, e.g., our SECS synthesis planning program that involved more than 60 person-years of programming, MACCS, REACCS, are other examples. The SECS program has its own virtual memory system, dynamically allocated arrays, lists, sets, a compiler and interpreter, i.e., many complex data structures for AI applications. Now we are writing much code in C, mainly because of ease of interface with X-windows. I have found that the fortran code is more readable and much easier to debug. C provides automatically many features we had to program in Fortran, but we built into our Fortran implementations checks to catch wild pointers. Once we made an interface layer in C to catch wild pointers, debugging became easy, and the code looked more like our Fortran code with function references rather than direct pointer access. Readability is a key for long term projects. I worked on TACOS-II in 1965 and the program is still being used today, it simulated the Patriot missles we saw in action not long ago. Thats pretty good longevity and transportability. C is like a double-edged razor blade, it takes skill to avoid hurting yourself!