CDS News - Cambridge IsoStar Package   [updated 28 Mar 2013]

This section gives the latest information on the CDS implementation of the IsoStar Knowledge Base of Intermolecular Interactions which is part of the Cambridge Structural Database System (CSDS).

There is also a related CSDS Knowledge Base called Mogul which covers Molecular Geometry.

The new IsoStar client is available for download

See details below:

Item added 28/03/13

IsoStar 2.2 is now available

The new server and client (versions 2.2) was made available with the CSD software release 5.34. The older version of the client will cease to work on 31/3/13. You should download the new client immediately.

This release contains scatter plots for eight new contact groups. See the IsoStar documentation.

Click on the "Links..." menu bar at the head of this Newsfile for fuller information.

Item added 21/12/11

IsoStar 2.1.3 is now available

The new server and client (versions 2.1.3) was made available with the CSD software release 5.33. The older version of the client will cease to work on 31/3/12. You are advised to download the new client as soon as possible.

Item added 26/01/11

Some users may have experienced problems using the hyperlink option when using the IsoStar web client. These problems were restricted to entries which were new with latest knowledge base update. For CSD scatterplots some were simply not available for display. For PDB scatterplots various entries also crashed the client.

We hope to get a new version of the client, which we will make available for download. In the meantime we have implemented changes which we believe fix these issues. However, please get back to us if you experience continuing problems.

Item added 21/01/11

IsoStar 2.1.2 is available for the Server

Version 2.1.2 of the IsoStar Server has been made available with the new Cambridge Release (v5.32). This includes the latest version of the knowledge base.

Version 2.1.1 of the display client is available for download from the CDS website (follow the "Downloads" link in the top pulldown menu on all webpages). If you have recently downloaded this client it will continue to work. Note, however, that it has an expiry date of 31/3/11. A later version of the client awaits release. We will announce availability as soon we receive it from Cambridge.

Details of new features of all CSD components are available. Click on the "Links..." menu bar at the head of this Newsfile for fuller information.

Item added 12/12/08

IsoStar 2.1 information

IsoStar 2.1 was included with the recent major Release of the CSD system November 2008. This has now been installed and is available to CDS users.

Scatterplot data has been updated and now includes 22,161 scatterplots from CSD 5.30, 7,459 scatterplots from the PDB and 1550 potential energy minima. For further details follow the Cambridge Release Notes link above.

Registered users can download the IsoStar Client software from the CDS site. Client versions are available for Windows, Linux and Mac OS X.

Current users of Windows and Linux are advised to upgrade to the new version of the client which has been released with IsoStar 2.1. The old client will continue to work in the interim, but hyperlink access to structure files is likely to be blocked quite soon. The Mac client has been introduced for the first time with the new release. All versions of the client can be downloaded via the download link above

Item added 10/01/08

We have now made the Intel Linux IsoStar Client available for downloading. We have also updated the download and installation instructions for this and the PC Client.

Users should ensure they obtain the new Client which goes with Release 2.0.1. The Client for the previous release will cease to work quite soon.

Item added 10/12/07

IsoStar 2.0.1 was included with the recent major Release of the CSD
system (received 30/11/06). This has now been installed and is
available to CDS users. 

Scatterplot data has been updated and now includes 22,022 scatterplots
from CSD 5.29, 7,386 scatterplots from the PDB and 1550 potential
energy minima.

Please note that registered users should download the IsoStar Client
software from the CDS site. It is nolonger freely available from the
CCDC site.

Item added 12/12/05

IsoStar 2.0 was included with the recent major Release of the CSD
system (received 8/12/06). This has now been installed and is
available to CDS users.

With IsoStar 2.0 scatterplot data has been updated and now includes
21,850 plots from CSD 5.28, 7,129 from the Protein Database (PDB) and
1550 from potential energy minima calculations.

With the new release there is also a new integrated visualisation
client (use of the RasMol package is no longer required).

Users who use our X-Windows implementaion of IsoStar by logging onto
the CDS server (command isostar) will automatically access the new
client. 

Users who access IsoStar via the web browser mechanism from the CDS
web site should install the new version of the PC Client (we expect to
be able to make available versions of the client for other platforms
in the future). To download the client follow the links from the
"Downloads" heading in the top pulldown menu on the CDS homepage:

         http://cds.dl.ac.uk

We have added better links to the Cambridge User Guide & Tutorial
material (including that for IsoStar). These are now available under
the heading "Manual & Training Material" in the top pulldown menu on
the CDS Homepage

Item added 01/12/05

IsoStar 1.8 was included with the recent major Release of the CSD
system. There is also an associated new version of the PC Client
software. If you have Version 1.7 currently installed we advise you to
replace it with the new client as soon as is convenient. It is our
understanding that version 1.7 of the PC client has an expiry date at
the end of March 2006. Version 1.8 is due to expire a year latter.

Note that during the IsoStar installation process we have fixed a
problem in displaying individual entries from scatterplots. This
problem is not associated with the Version 1.8. It probably appeared
early October. This problem was associated with the PC Client
implementation only. It did not affect the X-Windows inplementation.

Item added 17/03/04

Please note that for those who do not have a Windows 2000 or XP
system, an access mechanism to the IsoStar knowledge base has been
reinstated on the main CDS server. The command "isostar" fires up a
CDS (Mozilla) web browser X-Window which is configured to connect to
the knowledge base. Graphics performance using the PC Client mechanism
(if you have this available) is likely to be much superior.
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Item added 18/1/01

Note that if you wish to generate your own custom IsoStar scatterplot
you must do so on a UNIX platform. You can perform a QUEST search of
the CSD for the required nonbonded contact on the CDS Server, and then
convert the results to a scatterplot with the program IsoGen. If you
then transfer the .istr file produced to your PC you can view the
results using the Client software described below.

Item added 17/1/01

Cambridge have developed a PC Client available for accessing IsoStar,
and we now make it available for downloading by registered CDS users
from our Web site. This is not a standalone product. The IsoStar
client software accesses the data on the CDS server, but it does the
manipulation and display on your local machine. It thus lowers network
traffic considerably, resulting in a much faster response.
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Item added 29/10/99

The IsoStar program has been developed and is maintained by the
Cambridge Crystallographic Database Centre. It provides access to a
library of information about the nonbonded interactions formed by a
wide variety of chemical groups. It is designed primarily for:

       Molecular modellers, especially those engaged in designing
       drugs and agrochemicals from protein 3D structures. 

       Medicinal chemists interested in identifying bioisosteric
       replacements. 

       Protein crystallographers. 

       Crystal engineers. 

IsoStar brings together data on nonbonded interactions from three
sources: 

     The Cambridge Structural Database (CSD), which contains
     small-molecule organic and metallo-organic crystal structures. 

     The Brookhaven Protein Data Bank (PDB), which contains, amongst
     other things, the crystal structures of protein-ligand complexes. 

     Ab-initio based molecular orbital calculations, using the
     Intermolecular Perturbation Theory (IMPT) method.

Using IsoStar, it is possible to select a particular chemical group,
the "central group" (e.g. ketone carbonyl), and investigate its
nonbonded interactions with a second group, the "contact group" (e.g.
N-H). This is done by displaying a 3D scatterplot. The plot shows the
experimental distribution of the contact group around the central
group, as observed in crystal structures taken from the CSD or PDB.
For example, the CSD ketone-carbonyl/N-H plot is produced by searching
the database for all contacts between these groups, and then
overlaying the contacts so that the ketone portions are exactly
superimposed.

Each scatterplot in ISoStar can be displayed in 3D by invoking the
molecular visualiser RasMol. Alternatively, each scatterplot can be
converted to a contoured density surface, which shows the spatial
distribution of contacts in a simple schematic form.

Each scatterplot in IsoStar is hyperlinked to the CSD or a subset of
the PDB, so that individual nonbonded contacts can be examined in
detail. Additionally, there may be theoretical (MO) data available
from IMPT calculations on a relevant model system. Both the
hyperlinked entries and contour plots are displayed using the RasMol
facility.

By using this information, insight can be gained into the energies and
preferred geometries of nonbonded interactions, and the likelihood
that they will occur in any given molecular environment. Browsing
through IsoStar is a useful way of finding novel interactions.
Comparing the scatterplots for two different central groups may
indicate whether one might be a bioisosteric replacement for the
other. Scatterplots can be loaded into molecular modelling programs as
an aid to protein-ligand docking, or used to help parameterise ligand
docking and crystal structure prediction programs.

The companion IsoGen program allows users to generate their own
acatterplots from the results of nonbonded searches of the CSD
performed with Quest.

The details above have been extracted, with slight modification, from
sections of the extensive help information available within the
IsoStar program. The help facility also includes example 2D snapshots
of various IsoStar 3D graphical displays. There are also a number of
interactive tutorials which cover all features of the program.

New features which were added in Release 1.3 include:

Three new central groups have been added.

   benzene fused to aliphatic ring 
   benzene fused to aromatic ring 
   benzene fused to partially reduced aromatic ring

New NH contact group definitions.

   The NH contact groups are now catagorised as uncharged or
   cationic allowing users to explore the effect
   of charge on N-H hydrogen bonding more easily.