dbases.html

Data Bases

General * Molecular Structures

General:

BioMedNet

http://biomednet.com/db

A collection of databases including Medline and a Macromolecular dbase plus links to important

biological-chemical data resources. Password protected but a free subscription is available. 7/98

Searchable: Biomedlink http://biomednet.com/db/biomedlink

Spectral Data Base System for Organic Compounds
http://www.aist.go.jp/RIODB/SDBS/menu-e.html
SDBS: Integrated Spectral Data Base System for Organic Compounds, a searchable database that contains: MS (ca 18,000 spectra), ¹³C NMR (ca 9,700 spectra), Compound Dictionary, ¹H NMR (ca 10,100 spectra, 29,000 compounds) with plans to add ESR, IR and Raman. 3/98

"Exclusive Chemistry"
http://www.exchemistry.com/orgsyntheses.html
Links to Organic Syntheses 12/04

Various Databases for Organic Chemistry
http://131.96.145.20/post_docs/koen/wbojoar.html
Extensive list of commercial and free data bases for organic chemists. Dr. Koen Van Aken,
Georgia State University

Drug Database
http://pharminfo.com/cgi-bin/print_hit_bold.pl/drugdb/db_mnu.html
Pharminfo Net Searchable Drug Database by generic or tradename.

U.S. Patent Bibliographic and AIDS Database Search Site
http://patents.uspto.gov/

IBM Patent Server
http://patent.womplex.ibm.com
IBM lets you access over 26 years of U.S. Patent & Trademark Office (USPTO) patent descriptions as well as the last 23 years of images. The first entries date back to January 5, 1971. You can search, retrieve and study over two million patents. 1/98

List of Over 100 Searchable Databases (Physical, Environmental, Health and Safety Data)
Search with ChemFinder
http://chemfinder.camsoft.com/
A Service of CambridgeSoft Corporation. An outstanding search engine for a wide variety of chemical and chemically related information.

Bio-Molecular Chemical Data Base
http://ep.llnl.gov/msds/mc2dbase.html
A collection of links, informational resources and structures.
Dr. Ron Rusay, Diablo Valley College, ModularCHEM Consortium

NIST Chemistry Webbook
http://webbook.nist.gov/chemistry
Free government database that includes numerous compounds. Provides a variety of data: physical, thermodynamic and spectroscopic. IR and MS spectra available for a portion of the compounds in the data base. An excellent resource. 4/97

NDB-Nucleic Acid Database

http://ndbserver.rutgers.edu

Relational crystal structure data base: DNA, RNA, Drug Complexes, Protein-Nucleic Acid Structures (gif files)

Martindale's: The Virtual Chemistry Center

An extensive collection of Web Resources.

Structural Data Bases: (Also see WEB-sters' Molecular Modeling and Viewing)

TheWWW Chemical Structures Database

http://schiele.organik.uni-erlangen.de/services/webmol.html

Searchable database of over 2250 compounds: search operations can include full-structure and substructure search, formula search, name search, and more. Dr. W.D. Ihlenfeldt, University of Erlangen-Nurnberg

Protein Data Bank

http://www.pdb.bnl.gov

Brookhaven National Laboratory's extensive, comprehensive protein, nucleic acid / bio-molecular collection

See also: What is the PDB and Molecules R Us

Molecular Library

http://www.nyu.edu/pages/mathmol/library/library.html

New York University, Collection of small molecules in .pdb format

Okanagan University College's PDB Collection

http://www.sci.ouc.bc.ca/chem/molecule/molecule.html

Dr. Dave Woodcock's extensive, searchable collection in .pdb format

The Three-dimensional Drug Structure Databank

http://cmm.info.nih.gov/modeling/drugbank.html

NIH database of .pdb formatted files of anti- : ulcer, viral, TB, AIDS and cancer drugs

Virtual Molecular Model Kit

http://lightning.chem.wwu.edu/dept/molecule.html

Collection of a large number of structures in .pdb format, excellentassortment of hydrocarbons with rotamers and stereoisomers plus natural products. Prof. Donald Pavia, Western Washington University.

Klotho List

http://www.ibc.wustl.edu/moirai/klotho/compound_list.html

A searchable collection of over 400 compounds in .pdb format. Washington University,

St. Louis, MO

National Toxicology Program: Structures Page

http://ntp-support.niehs.nih.gov/Main_Pages/pub-Structures.html

NTP searchable database of .gif and .pdb formatted structures from all of

NTP's technical reports. Large number of compounds.

Malathion Teaching Module Structures

http://ep.llnl.gov/msds/pdb/pdb-structures.html

A collection of over 100 bio-molecular structures: small molecules (drugs, pesticides and

others) and proteins

Drs. Ron Rusay and Leverett Smith, ModularCHEM Consortium

Corina 3-D Coordinates

http://schiele.organik.uni-erlangen.de/services/3d.html

A description of Corina 3-D. Files are readable with Chime. Drs. Christof Schwab and W.D.

Ihlenfeldt, University of Erlangen-Nurnberg

National Cancer Institute's (NCI) Developmental Therapeutics Program

http://epnws1.ncifcrf.gov:2345/dis3d/3ddatabase/pubstruc.html

Over 125,000 structures, Downloadable (200 Mb, expanded), Cancer and AIDs screened

compounds.Public Sector Compounds only. Convertable to Corina 3-D coordinates then Chime readable.

RasMol / Chime Home Page

http://klaatu.oit.umass.edu:80/microbio/rasmol/

A resource that includes Gallery of Images and Molecules Galore with information on image resources and RasMol Chime background information. Prof. Eric Martz, University of Massachusettes

The Twenty Common Amino Acids

http://www.curtin.edu.au/curtin/dept/biomed/teach/biochem/tutorials/chemAA.html

Chime viewable images from Curtin University, Australia

Smell Data Base

http://mc2.cchem.berkeley.edu/Smells/index.html

Approximately 50 olfactory molecules in pdb format. UC Berkeley

IMB Jena Image Library of Biological Macromolecules

http://www.imb-jena.de/IMAGE.html

Three-dimensional structures of biopolymers.. It provides access to all structure entries deposited at the Protein Data Bank (PDB) including nucleic acid-containing X-ray entries also available at the Nucleic Acid Database (NDB). In addition, general information on the architecture of biopolymer structures is available. Images generated with Molscript in PDF (mono, stereo) and VRML format and RasMol and WebMol interfaces.

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"Entrez" Molecular Modeling Data Base

http://www.ncbi.nlm.nih.gov/Structure/struchelp.html

National Center for Biotechnology Information (NCBI): Molecular Modeling Data Base and

others. RasMol, Kinemage and/or ASN.1 viewer required.

MMDB: Molecular Modelling Database

The complete, updated Brookhaven Protein Database in ASN.1 format. Over 3,000 bio-molecules. Searchable. Requires Cn3D viewer.

GenBank:

Other NCBI Resources: