- Chemicals with Pharmaceutical Activity - A 3D Structural Database
- Department of Chemistry, University of Oxford.
- The compounds are listed alphabetically.
See also: Molecules of the Month
- Chemistry Molecular Models
- Tom Zamis, Ph.D., Chemistry Department,
University of Wisconsin - Stevens Point.
- A nicely organized list of links to the hundreds of structures available at the
Protein Databank of the
Research Collaboratory for Structural Bioinformatics,
the single international repository for
the processing and distribution of 3D macromolecular
structure data primarily determined experimentally by X-ray
crystallography and NMR. There are now over 10,000 structures available.
- Hetero Compound Information Centre (HIC-Up)
- Gerard J. Kleywegt, Departments of Structural Biology,
- Structures of almost 2,000 heterocyclic compounds are available.
The site allows compounds to be located by
Non-H atoms and
- Hyperactive Molecules
- A smorgasbord of 3D animated renderings of biological molecules. The collection
is small but interesting.
- IMB Jena Image Library of Biological Macromolecules
- Instut für Molekulare Biotechnologie.
- "The IMB Jena Image Library of Biological Macromolecules is aimed at a better dissemination of information on
three-dimensional biopolymer structures with an emphasis on visualization and analysis. It provides access to all structure entries
deposited at the Protein Data Bank (PDB) or at the Nucleic Acid Database (NDB). In addition, basic information on the architecture
of biopolymer structures is available. The IMB Jena Image Library intends to fulfill both scientific and educational needs."
- Includes: Basic Information on Biological Macromolecules and an Atlas of Macromolecule
Structures with 3D animated structures of proteins and nucleic acids.
- Klotho: Biochemical Compounds Declarative Database
- "Klotho is part of our attempt to model biological processes, beginning with
. . . .
I call the whole project Moirai, after the three Fates of antiquity, since fundamentally these
are questions about the fates of molecules and cells."
See: Klotho: Alphabetical Compound List.
- Molecular Expressions: Images from the Microscope.
- Michael W. Davidson, Florida State University.
- "Welcome to the Molecular Expressions Website featuring our acclaimed photo galleries that
explore the fascinating world of optical microscopy. We are going where no microscope has gone
before by offering one of the Web's largest collections of color photographs taken through an
optical microscope (commonly referred to as "photo-micro-graphs"). Visit our Photo Gallery for an
introductory selection of images covering just about everything from beer and ice cream to
integrated circuits and ceramic superconductors."
- The site includes photomicrographs of what appear to be crystalline forms of many
biochemicals and organic compounds. Included are Amino-Acids, Vitamins, Pesticides
- Molecular Models for Biochemistry at CMU
- "The linked pages described here have tutorials and quizzes that are based
on Chime and RasMol images of the molecules and macromolecules found
in biochemistry. They are intended to complement standard biochemistry
texts where more explanation is provided, but where interactive 3-D images
of the molecules are not available."
- This is a large collection of links to 3D molecular images.
- Multimedia Chemistry Resources
- Ghislain Deslongchamps, Department of Chemistry, University of New Brunswick.
- This is a HUGE collection of links to 3D molecular image resources. It includes
links to most of the 3D imaging software such as Chime and RasMol.
- Nick's Molecular Art Gallery
- Nicholas C. DeMello Ph.D.
- "Welcome to my gallery. These are images of molecular art that I have
created to illustrate various chemical discoveries. I think molecular
illustration can be both an intriguing topic for artistic expression,
and--more importantly--an extremely effective way to communicate the
nuances of chemical reactivity. I hope you enjoy exploring these
These images were created with some combination of POV-Ray,
Photoshop, LightWave, Chem3D, BBEdit and my own proprietary
software. For the best effect, you are strongly recommended to view
these images with your monitor set to 16 bit or higher color depth."
- Online Macromolecular Museum
- David Marcey - California Lutheran University.
- "The Online Macromolecular Museum (OMM) is a site for the display and study of macromolecules.
Macromolecular structures, as discovered by crystallographic or NMR methods, are scientific objects
in much the same sense as fossil bones or dried specimens: they can be archived, studied, and
displayed in aesthetically pleasing, educational exhibits. Hence, a museum seems an appropriate
designation for the collection of displays that we are assembling. The OMM's exhibits are interactive
tutorials on individual molecules in which hypertextual explanations of important biochemical features
are linked to illustrative renderings of the molecule at hand."
- Includes: Hall of Introductory Exhibits,
Hall of DNA polymerization,
Hall of DNA recombination,
Hall of DNA modification,
Hall of oxidoreductases,
Hall of cell adhesion and
Hall of porins and channels.
- RasMol Gallery
- University of Massachusetts Amherst
- RasMol Images by Roger Sayle. Four high-resolution images illustrating RasMol's best by
the creator of RasMol.
- RasMol Images by Eric Martz. Images from "movie" scripts on DNA, antibody:antigen, major
histocompatibility proteins presenting peptide antigens, SH2 domain with phosphotyrosine.
Also non-script images of ATP, tRNA, and lipid bilayers.
Gallery of Non-RasMol Images in the Other Software section.
Common and Interesting Compounds
- Indiana University.
- Categories include:
Medicines, Drugs and
Plants and Stuff,
Weird and Neat Stuff,
Organic Compounds and
Structures from the
research laboratories of
- Small Molecules for Modern/Cell Biology
- Department of Biological Sciences, Carnegie Mellon University.
- Available structures are:
ATP (Adenosine Triphosphate),
Glucose (cyclic form),
cAMP (cyclic AMP),
Three H2O molecules,
MgATP (hydrogens not shown),
Glucose (open chain form),
Oleic Acid (a fatty acid),
Palmitic Acid (a fatty acid),
- Smell Database
ModularCHEM Consortium, UC Berkeley.
- A large collection of 3D molecular models for smelly compounds. The
compounds are listed in alphabetical order.
- Structure Data Base
Tokyo University of Pharmacy and Life Science
- "Here you will find a comprehensive listing of the 3D
pharmaceutical structures compiled according to the
Japanese Pharmacopeia, 13th edition. The Japanese
ethical, or nonprescription drugs are noted with an * (cf.
the Physicians' Desk Reference (PDR), and the U.S.
Parmacopeia, National Formulary)."
- Compounds are arranged alphabetically by name and there is a search tool.