From chemistry-request@ccl.net Fri Jul 12 05:35:07 1991 Date: Thu, 11 Jul 1991 21:40:58 PDT From: "W. Todd Wipke" To: chemistry@ccl.net Subject: re: Chemical Taxonomy Status: R >David States >National Center for Biotechnology Information / National Library of Medicine writes: >Which raises the question: do you really want a taxonomy, or would you >in fact want an efficient subgraph matching and lookup algorithm? A >taxonomy implies a statitic, hierarchical classification of the data, but >different users of a chemical database almost certainly have different >applications and different views in mind. Indeed, the question in my mind is for what do you want the taxonomy? Typically, taxonomy requires a hierarchy of decision criteria, and for multipurpose use, one wants different orderings. To take an extreme position, I would say that taxonomy was for manual systems because the human mind was limited to a few principles of organization. Taxonomy has been most successful in chemistry in the Beilstein classification system. The principle of neighborhood is better for many purposes. What is the primary goal you have in mind? -Todd Wipke Wipke@secs.ucsc.edu From chemistry-request@ccl.net Fri Jul 12 10:58:58 1991 Date: Fri, 12 Jul 91 14:42:47 GMT From: jpj@lotus.medicine.rochester.edu (Jeffrey P. Jones) To: Chemistry@ccl.net Subject: Self Consistent Reaction Field Program? Status: R Hello, Does anyone have a self consistent reaction field program that can be used with G90 or GAMESS? ############################################################################## Jeffrey P. Jones U. of Rochester Department of Pharmacology 601 Elmwood Ave. Rochester, NY 14642 internet jpj@lotus.medicine.rochester.edu %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% From chemistry-request@ccl.net Fri Jul 12 15:17:01 1991 Date: Fri, 12 Jul 91 14:01:51 CDT From: liberte@ncsa.uiuc.edu (Daniel LaLiberte) To: chemistry@ccl.net, wipke@SECS.UCSC.EDU Subject: re: Chemical Taxonomy Status: R Todd Wipke writes: > Indeed, the question in my mind is for what do you want the taxonomy? > Typically, taxonomy requires a hierarchy of decision criteria, and for > multipurpose use, one wants different orderings. I asked about taxonomies to learn more about different classification schemes. I hadn't heard about the "neighborhood" concept which sounds like a valuable alternative. What I really need is a way to describe the properties of chemical structures and the relationships between those properties. Strictly hierarchical taxonomies would be rather limited I expect, but that's all I guessed would be out there. I will be adapting whatever classification schemes I come across to an object-oriented framework. The OO language I am using includes multiple inheritance, which appears to be a necessary feature for chemistry applications. The chemistry tool we are building will support runtime extensions of the builtin chemistry class library so that specialists will not be limited by whatever we decide should be in the builtin library. Knowledge encoded in each class will tell how to check whether a certain property exists (if it is a property class) or how to calculate additional attributes if a given property exists. Related properties may be in a subclass-superclass relationship, or sibling subclasses of another superclass, or other possible relationships. One of the limitations of object-oriented frameworks is that higher-order kinds of relationships are often difficult or impossible to express in the language. So figuring out what kinds of relationships are appropriate for chemistry is a way for me to explore language concepts that will be required to express these relationships. I am also interested in classifications of other aspects of chemistry besides chemical structures (molecules and complexes) - such as reaction types, types of reaction sequences, and more mundane, though highly complex things like visualization of simulations and experimental and theoretical research projects, plans, and results. liberte@ncsa.uiuc.edu (217) 244-0785 Daniel LaLiberte National Center for Supercomputing Applications 152 Computing Appliations Building 605 East Springfield Avenue Champaign, IL 61820 From chemistry-request@ccl.net Fri Jul 12 19:21:22 1991 Date: Fri, 12 Jul 1991 18:12 EST From: LONCHARICH_RICHARD_J@LILLY.COM Subject: dynamics of proteins To: chemistry@ccl.net Status: R I am interested in recent references for molecular dynamics studies of protein dynamics as a function of temperature and/or solvent. For example, a series of classical experimental papers by Frauenfelder et al (Nature 1979, 280,558-563; PNAS 1982,79,4967-4971). study the metmyoglobin protein by x-ray diffraction at several different temperatures. Also Wong, Zheng, and McCammon (Chem Phys Lett 1989,154,151-154) have used molecular dynamics to study the atomic motion of tuna ferrocyctochrome C in SPC/E water from low temperatures to room temperature. I would appreciate receiving any references or preprints of molecular dynamics simulations or any experimental work of proteins studied at several different temperatures and/or in several different solvents (ie, CCL4, methanol, water). Thanks for your help! ================================================ Richard J. Loncharich = Eli Lilly and Company = Lilly Corporate Center = Indianapolis, IN 46285-0403 = = Internet: loncharich_richard_j@lilly.com = ================================================ From: LONCHARICH RICHARD J (MCVAX0::RX82788) To: FOREIGN TRANSPORT ADDRESSEE (MCDEV1::IN%"chemistry@ccl.net")