summary of pdb motif searching....
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.
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# Jon Erickson e-mail: jaeric ( ( at ) ) mtcamm.monsanto.com #
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From: Max <wk01189 ( ( at ) ) worldlink.com>
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,
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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
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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
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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
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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
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From: Johan Postma <POSTMA ( ( at ) ) EMBL-Heidelberg.DE>
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
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