CAVEAT: A Program to Facilitate the Design of Organic Molecules

Developed by Georges Lauri, Gary Shea, Scott Waterman, Steve Telfer, and Paul A. Bartlett

Department of Chemistry, University of California, Berkeley, California 94720

(see: Lauri, G.; Bartlett, P.A., "CAVEAT: A Program to Facilitate the Design of Organic Molecules" J. Comp. Aided Mol. Design 1994, 8, 51-66)

For current CAVEAT users...

A script named fixcsd is provided so that CAVEAT can read the latest version of the Cambridge Structural Database (CSD 5.099). Click here to load the script into your viewer. Save the text as 'fixcsd' and make sure permissions are set to executable (i.e. type 'chmod ugo+x fixcsd').

Some of the more common questions about CAVEAT are the following:

What kinds of problems can CAVEAT be used for?

Designing mimics of known ligands, designing linking units to constrain acyclic molecules, de novo design of active site ligands, identifying 3-dimensional homology among proteins, etc.; in essence, any problem for which the solution requires a specific 3-dimensional relationship between bonds.

How have other people used CAVEAT?

Reported applications of CAVEAT in structure-based design

What databases does it search?

Originally developed for the Cambridge Structural Database, CAVEAT can search 3D databases in essentially all of the common formats. In addition, our own TRIAD and ILIAD databases of 411,000 and 110,000 structures, respectively, can be provided in CAVEAT-vector format directly.

How fast is it?

Fast! A typical CAVEAT search on the TRIAD database on our old Indigo R3000 can yield 200-2000 hits in 1-2 minutes; the auxiliary progams TWIST and CLASS will align, screen, and cluster these hits in another 1-2 minutes to provide the user with 10-30 "interesting" molecules to look at. This is "real time design"!

What platforms are supported?

Silicon Graphics Iris and Indigo workstations for executable code; source code is readily compiled on IBM RISC/6000 and other Unix-based workstations with ANSI-C compiler.

What is the user interface?

CAVEAT is a stand-alone program that can be used in conjunction with any modeling system; it is controlled by a relatively small number of commands entered from a text window.

What else comes with it?

CAVEAT comes with a number of auxiliary programs, including TWIST, which transforms the coordinate systems of retrieved hit structures so that they match the search target, and CLASS, which carries out a rapid post-search screening and clustering of the hits. CLASS not only allows the hits to be screened for steric interference (with a surface, for example), or on the basis of structural type or bond hybridization, but it also groups them according to structural or geometric similarity. Because hit lists of hundreds or even thousands of molecules can be rid of clearly "useless" structures and partitioned into a relatively small number of groups, search tolerances can be opened up to realistic values, and a diverse range of hits evaluated easily.

How can the program be obtained?

Licenses for CAVEAT and the TRIAD and ILIAD databases are available from the University of California Office of Technology Licensing

Please contact Rowena Prelock for information on licensing arrangements.

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