Searching the Chemical
Literature by Computer at Stony Brook
All these resources are
available for Stony Brook students to use for free because the Library pays
several hundred thousand dollars per year for their use.
The Library has subscriptions (i.e. purchases) to a large number of journals, the vast majority of them are available electronically as well. In particular, via the ACS archive, every paper ever published in an ACS journal is available on line. The web page of the main library has a complete list of electronic journals. For a shorter list of chemistry related electronic journals go to the chemistry library web page and for biochemical journals go to Biology Collection Page. For biological journals remember to also check the web page of the Health Sciences library as well.
The Cambridge Structural Database contains information on
the crystal structures of more than 325,000 small molecules (i.e not proteins
and not solid-state compounds). This Database can be accessed from the
computers in the Chemistry Library and in the
More complete help files are available:
Some short notes for Searching for Organometallic Pi System in the CSD and Crossfire Gmelin
Exporting Coordinates from Conquest to other Graphics
Programs.
Molecules can be viewed directly in Conquest or more completely in its
associated graphic program, Mercury. In Conquest, it is possible to save the 3D
Visualiser view of a molecule as a JPEG image. However it is better to export
the Coordinates of a molecule from Conquest into Professor Joe Lauher's
Molecular Graphics program, Chem-Ray: In Conquest export the coordinates
of a particular stucture (using the COORD:CSE coordinate file format) and open
them in Chem-Ray (using the *.cor). Similar procedures can be used to
export coordinates of molecules into other programs.
Professor Joe Lauher's Molecular Graphics program, Chem-Ray, is installed on the chemistry SINC center computers on the Fourth Floor and in the Chemistry Library. It is also installed on the computers in the Graduate Student SINC site. Some instructions on using Chem-Ray are given here. To get started open the basic.ctb file using the file (then open) pull down menus. Read the mouse commands for rotating the molecule and resizing the graphic windows. Explore the different dynamic styles. Use the arrow button on the top right to cycle through the different molecules. Probably, it you ask politely, Professor Lauher will let you install Chem-Ray on your own computer.
The PDB contains the information and coordinates for Proteins whose structures have been determined by X-ray crystallography or NMR techniques. There are currently more than 16,500 structures in the PDB. The structures can be visualized by a number of different graphics programs. A convenient (and free) methods uses Netscape (version 4.7 but not Version 6) and the Chime plug-in. (Microsoft's Internet Explorer with Chime is frequently problematic). Here are some simple instruction on using Chime to display a protein structure
Getting Started: Search for the protein you are interested in. Chose the particular protein by clicking on explore (on the right). Chose View Structure on the Left Menu. Chose option Protein Explorer.
You can read about Protein Explorer here (Protein Explorer now works with Internet Explorer).
There are many useful Biochemistry Tutorials on the structures of proteins and DNA at: World Index of Molecular Visualization Resources
MDL Crossfire Beilstein and Gmelin are powerful databases to
the properties of organic and inorganic compounds respectively. Access to these
databases are available on the computers in the Chemistry library and on the
fourth floor SINC center and in the Graduate SINC site on the third floor.
Access can also be obtained on any PC or Mac computer which has a sunysb.edu IP
address using client software that can be downloaded from http://minerva.library.wisc.edu (See
see Steve Koch
for the necessary password).
Instructions on using Crossfire can be obtained from a series of manuals which are on reserve in the Chemistry Library (the tutorials to Crossfire Beilstein and Crossfire Gmelin are recommended). There is a short manuals which can also be downloaded at http://www.beilstein.com/data/xfstrt2000.pdf
There are also a number of Web sites that are very useful
http://www.lib.uchicago.edu/e/su/chem/ucbeil.html
chemistry.library.wisc.edu/beilstein/home.htm
http://www.beilstein.com/beilst_2.shtml
SciFinder Scholar enables computer searching of Chemical Abstract including the ability to do substructure searching. Currently only five people in the university can use SciFinder at any one time; so be sure to log off from SciFinder when you are finished using it. SciFinder Scholar 2004 is available on all the SINC center computers. SciFinder Scholar requires a client software program to be installed on a PC or a Mac computer. SciFinder can be installed and used on any computer that has a Stony Brook IP address. The program is available for downloading by Stony Brook staff and students at SciFinder installation. There are some instructions for using SciFinder Scholar at http://www.cas.org/SCIFINDER/SCHOLAR/resources.html.
The Web of Science enables searching of the entire scientific literature via the WWW web. A key feature is the Science Citation Index by which the literature citation of a published paper can be obtained. You can also search by author and keywords. The Web of Science is available 24 hours a day by up to 15 Stony Brook users.