From jaeric -A_T- mtcamm.monsanto.com Thu Jun 3 10:46:21 1993 From: Jon A. Erickson Message-Id: <9306032046.AA05201- at -mtcamm.monsanto.com> Subject: summary of pdb motif searching.... To: chemistry#* at *#ccl.net (OSU Comp. Chem. List) Date: Thu, 3 Jun 93 15:46:21 CDT Here is a summary of responses to the following posting: I am looking for tools/references/methods/any thoughts for finding all occurrences of an arbitrary structural specification (eg. a certain loop in relation to a particular helix) in a protein. Many thanks for all the responses. ################################################################ # Jon Erickson e-mail: jaeric ":at:" mtcamm.monsanto.com # # Monsanto Company, U3E phone: (314) 694-1511 # # 800 N. Lindbergh Blvd. # # St. Louis MO, 63167 # # # # What is a magician but a practising theorist? # # -- Obi-Wan Kenobi # ################################################################ ------------------------------------------------------------------- From: Max Hello, I know of at two commercial packages that probably do what you want. One is IDITIS, sold by Oxford Molecular and originally developed at Janet Thornton's lab. The other is PROTE, sold by your TRIPOS neighbors, and origi- nally developed by Peter Willet (a recent, 1992 or 1993, paper in J. Mol. Biol. describes this program). Also, I have seen descriptions of a program called WHATIF by Vriend (I believe at the EMBL in Heidelberg) that may include this type of functionality. I also think Vriend makes this program available (for a fee). I saw a demo of IDITIS by the graduate student who worked on it (and who is now with Oxford Molecular); it looks good. I also worked a little bit with an "alpha" version of PROTE: it is much faster for what it does, although the range of applications is not as wide as that of IDITIS. The bottom line: I think there are a few options out there to do what you want (if you are willing to spend a non-trivial amount of money). I would be interested to find out of any cheaper alternatives your query to the net may produce. Best wishes, ======================================== Max Vasquez Protein Design Labs, Inc. 2375 Garcia Ave. Mountain View CA 94043 Phone (415) 903 3744 FAX (415) 903 3730 e-Mail wk01189 |-at-| worldlink.com ======================================== ------------------------------------------------------------------- From: stoutepf $#at#$ lldmpc.dnet.dupont.com (Pieter Stouten, +1-302-695-3515) >In response to Jon Erickson's enquiry, I would like to suggest the >program "IDITIS". IDITIS is a relational database for searching >protein structures from the Brookhaven Protein Databank. > I am not sure that a strictly relational approach is very effective when searching protein sequence and structure databases since one often is interested in properties of stretches of residues rather than individual residues. In a purely relational system this requires a large number of operations or columns. Permit me to suggest an alternative program. The multi-purpose modelling program WHAT IF incorporates a very fast and flexible database system (SCAN3D), which uses the relational paradigm whenever possible, but also allows for matching of a stretch of residues with a single comparison. For more information, please contact WHATIF's author Gert Vriend directly. He can be reached at vriend # - at - # embl-heidelberg.de. Relevant references are: * G. Vriend, "WHAT IF: a molecular modeling and drug design program", J. Mol. Graph., 8, 5255 (1990). * P.F.W. Stouten & G. Vriend, "How to Extract Non-Trivial Information from Protein Structure and Sequence Data: The SCAN3D Retrieval System," Chem. Design Autom. News 7(5) (1992) 18-23. * G. Vriend, C. Sander & P.F.W. Stouten, "A Property-Profile-Oriented Protein Sequence-Structure Database." Submitted for publication. Hope this helps. Cheers, Pieter Stouten The Du Pont Merck Pharmaceutical Company P.O. Box 80353 Wilmington, DE 19880-0353 Phone + 1 - 302 - 695 - 3515 Fax + 1 - 302 - 695 - 2813 E-mail stoutepf- at -lldmpc.dnet.dupont.com ------------------------------------------------------------------- From: tripos!david-: at :-uunet.UU.NET (David Mosenkis) Jon Erickson, The PROTEP product from Tripos will find all occurences of a specified structural relationship between alpha helices and beta strands in the Brookhaven PDB, or alternatively, occurences of a subset of the pattern of these secondary structural elements. However, it currently does not know about anything except helices and strands. Sybyl also has facilities for doing fast queries for a restricted set of structural criteria from the Brookhaven PDB, including finding fragments of a given length with a given end-to-end distance, and wild-card patterns of sequences (using Unix regular expressions). I would be interested to hear what other responses you get. David Mosenkis (david[ AT ]tripos.com) Tripos Associates 215-844-3479 ------------------------------------------------------------------- From: rwoods: at :biop.ox.ac.uk Dear Netters, In response to Jon Erickson's enquiry, I would like to suggest the program "IDITIS". IDITIS is a relational database for searching protein structures from the Brookhaven Protein Databank. I have not used the program yet myself, but others in the group use it with apparent success. Iditis is distributed by Oxford Molecular Ltd. Their number is (from the U.S.) 011-44-865-784600. Good searching, Rob Woods Robert J. Woods, Ph.D. Glycobiology Institute University of Oxford South Parks Road Oxford, OX1 3QU ------------------------------------------------------------------- From: Johan Postma Dear Jon Erickson, For your information: we are working on a long-term project to design "simple" tools to process PDB - data and a "general" query program. Enclodes is a sample program (VMS-FORTRAN/PASCAL/C), showing the functionality of the PDB-access-functions. Additionaly the same "hard-wired" query can be done using a "query-description" file, which is then processed by QUE (general query program). The programs are still in a stage of development. These data-access-functions do not "act" upon the PDB-ASCII files but a "binary" representation of them (produced by a program call YABP). Once this "data-file" has been created any item can be access with high speed and efficient use of memory-resources etc.. The timings of the example programs were done on several VAX's (PDB-binary-file contains (test-case) 334 PDB-Files) VAX 900-420 1 CPU second Micro-VAX 3100.80 2 CPU seconds VAX-station 7 CPU seconds regards. Johan P.M. Postma EMBL Heidelberg Germany -------------------------------------------------------------------