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Comprehensive Sites - Collections of Useful Links
Pericyclic and other Orbital Symmetry-Controlled Reactions orbital symmetry, Woodward-Hoffman Rules, a variety of pericyclic processes, incl. electrocyclic and sigmatropic reactions, theoretical chemistry, many others.
World Index of Molecular Visualization Resources huge - links to tutorials, DeepView, PDB resources, software, etc.
Molecular Modeling for Organic Chemistry by Dr. Henry Rzepa of Imperial College - an excellent treatment of modeling with both molecular mechanics and M.O. theory
Network Science - ChemInformatic 3-D Database searching for drugs, pharmacophores, lead cmpds., etc.
Molecular Visualization Tools and Sites Indiana U. - primarily software links, along with many galleries
MathMol (Math & Molecules) great intro for beginners to molecular modeling
TORVS - Chemical Internet Services Prof. J. Gasteiger's excellent site with free services, incl visualizations, spectral simulators, animations, etc.
Centre for Molecular and Biomolecular Informatics Univ. of Nijmegen - Dutch center for computational molecular sciences
ACCVIP (Australian Computational Chemistry via the Internet Project): teaching modules, compchem web resources and course materials, e-papers, more
ORNL Resources of Protein Modeling Oak Ridge Nat'l. Labs - includes databases
3D Molecular Modeling HomepageTokyo Univ. of Pharmacy - huge gallery of Chime images, with detailed instructions on how it's done
Molecular Modeling, Viewing and Drawing from Web-Sters Organic Chemistry, a large, complete link collection

WWW Chemistry Resources  UCLA's great collection of chemistry resources
Chemical Drawing and Visualization from Organic Chemistry Resources Worldwide, very complete
National Library of MedicineChemical Information Web Links
ExPASy Molecular Biology Server proteomics server; multitude of links to databases, educational resources, software packages, etc.
World Index of BioMolecular Visualization Resources excellent collection of Deep View/Swiss-PDBViewer Resources



Structure Libraries
MolVis Resources NCBI VAST Home Page - huge - links to tutorials, DeepView, PDB resources, software, etc.
The Online Macromolecular Museum a site for the display and study of macromolecules from Cal. Lutheran Univ.
World Index of BioMolecular Visualization Resourcescollections of PDB files- excellent
Pharmaceuticals - 1000s Tokyo Univ. of Pharmacy & Life Science - Chime images of huge no. of every drug in Japanese Pharmacopeia
Brookhaven Protein Database single worldwide repository for the processing and distribution of 3-D biological macromolecular structure data
National Library of Medicine - Chem. Info. the homepage for NLM various databases, including the following:

  • ChemIDplus Chemical Search Input Page for main database, incl. over 360,000 records
  • NCI-3D  Chemical Search Input Page for Nat'l. Cancer Inst. database, incl. over 210,000 records
  • AIDSDrugs the AIDSDRUGS database; provides Chime structure images

3-D Virtual Chemistry Library 150 mols. from Imperial College
Chemicals with Pharmaceutical Activity a 3D Structural Database - provides rotating PDB images of 400 molecules
Molecular Models from Okanagan St. Coll.1500+ molecules in PDB format; uses Chime plugin
The Web3D VRML Repository  everything you need to understand the Virtual Reality Modeling Language and its applications
Common Molecules  includes biochemical, medicinal, environmental, highly reactive, taste molecules; minerals/gems, macromolecules
Chemist's Art Gallery Finnish IT Center; many great images, along with the definitive dir. of visualization and animation sites
Swiss-PdbViewer Art Gallery  the ExPASy gallery; not very large, but great images
Structure of Biomoleculesgreat link collection from univ. in Belgium
Organic Reaction Animations a CD from Norton; $35, but accompanies certain texts
Chemistry Molecular Model UW Stevens Pt. - lots of mols., plus links to other collections

Molecular Modeling Home Pag a super, comprehensive site from Lebanon Valley College
The Protein Data Bank
  "the single worldwide repository for processing/distributing 3D biological macromolecular structure data"
The MathMol Library of 3-D Molecular Structures several molecular groups, avail. in GIF, VRML, or PDB format
Molecular database without transition elements
great teaching site; mostly simple molecular types
Colby OChem Visual Demos some of the best teaching animations around!


DeepView (formerly Swiss-PDB Viewer)
DeepView - Swiss PDV Viewer Homepage enables simultaneous analysis of several proteins, so durg-receptor studies are easy
DeepView Tutorial complete, easy to follow guide
Creating Simple animations of DeepView files in POV-Ray create beautiful rotating images
Advanced POV Animation for Beginners source of the new ClockMod software (free), along with simple instructions
Constructing and Exploring Crystal Contacts 35 step guide to exploring the contact between asymmetric crystals
MolGraph DeepView/POVRay images and discussion board - FANTASTIC images!
Learning Biochemistry with DeepView great tutorial, using DeepView images



RasMol
RasMol Home Page actually goes to Protein Explorer, but it's still designated as the RasMol homepage.
RasMol Quick Start just what it says - everything you need to be up and running in one page!
CMU RasMol Tutorial an extremely nice tutorial; only six web pages long.
RasMol Tutorial Files essentially an interactive tutorial
RasMol Manual: Table of Contents for RasMol v. 2.6
RasMol Manual: Frames same as the page above, except that the TOC is in a left frame - a major improvement.
RasMol V2.6-beta-2 Reference Manual an incredibly detailed user's manual. If you can't find it in here, it's not important!
RasMol V2.6-beta-2/Chime 0.99 Manual same as above, except that Chime has been added in (seamlessly, btw).
Preparing RasMol-Saved Scripts for Teaching a guide on embedding Chime structures in web pages.  It's easy.
Gasteiger Research - the CORINA Site for converting 2D into 3D structures

Chime
3D Molecular Graphics on the World Wide Web  excellent , concise primer on using 3D images on the web.
The MDL Chime Site the home site.
An Introduction to Chime Scripting a very clever twoframe technique makes learning Chime a pleasure!
Chime 2.6 Tutorial great, highly detailed site, again with two vertical columns.
Chime Tutorial from Cabrillo College Part of large "Computers in Chemistry" site; similar in feel to above.
Chime Toolbox a truly excellent addition to other Chime docs; has many tricks I've not seen anywhere else.
MoveTo Function for Chime how to make a rotating structure stop at a predetermined place or time.
Constructing OMM Exhibits just a slightly altered Chime method


VRML
VRML sites:

Mark B. Fischer's Virtual Reality Links a huge, impressive link collection with subtitles such as Virtual Reality and VRML, Virtual Reality Sites, Virtual Reality Hardware, and VRML in Chemistry and other Molecular Modeling Software
VRML for the communication with 3D scenarios of biomolecules  several programs for making and manipulating VRML files.
ORC, Inc. the great site with the weird name!  A source of docs on VRML, Java, and VRML.
Creating VRML Pages  a great, succinct, well-hyperlinked primer on generating VRML structures and embedding them in web pages.
ParallelGraphics (a 3D VRML company)  home site for the Cortona VRML plugin.
PDB to VRML Converter a very easy program to convert the common PDB files into VRML files.
Cosmo Homepage  home site of the CosmoPlayer VRML plugin.
Virtual Chemistry Experiments nice visualization of general chem. topics like coordination chemistry, equilibria, kinetics, etc.
Virtual Chemistry at Oxford a series of chemical applications of VRML, being developed by a series of undergraduates; includes:

VRML in Chemistry an old, but still very useful, paper by Prof. Henry Rzepa of Imperial College
VR Chemical Bonding:

VRML Models a gallery of images in all kinds of areas outside of chemistry.
VRML Worlds you've got to have some fun with it occasionally!  This is probably what you envision when you think of virtual reality.


Model Construction
Free Molecular Modelling Programs - great comparative review of 15 popular programs
Gasteiger Research - the CORINA Site creates PDB files from SMILES or JME editor - easy and quick
VRML File Creator for Chemical Structures  creates PDB files as the above site, but many variables can be specified - more control, more time
PDB to MultiGif Page creates animated gifs (rotating) from PDB files - very fast
Mol4D Web Organic Chemistry University of Nijmegen - create models, animations, does M.O. calculations on-line which are visualized.
Java-Based SMILES Generator  draw a molecule and it generates the SMILES string necessary for many visualization programs
CARP: Calculate and Animate a Reaction Path  - from the Mol4D site
Spinwave - Graphics File Compression incredible gif compression - >90% reduction!  (GIF files are already compressed, which makes this quite amazing)
Submit a molecule or reaction for calculation (MOPAC)  - from the Mol4D site: easy, fast site that's an ideal introduction to visualizing orbitals
CHEMINT98: Chemistry and the Internet ACD/I-Lab "Web Librarian" database interface


Additional Resources
WebMO - Computational Chemistry on the WWW  interface to computational packages; unix/Linux-based
Visual Molecular Dynamics visualization program for displaying, animating, and analyzing large biomolecular systems
Amber Home Page Assisted Model Building with Energy Refinement, from UCSF; comes only on CD, acad. price is $400
ACD/Free Stuff great software, incl. ChemSketch, ISIS/Draw, IUPAC naming add-on, 3D viewers, more...and it's all free!
Catalog of Free Compilers and Interpreters   free software for language tools, primarily aimed at developers rather than researchers
Drug Design Laboratory Medicinal Chem. Institute, Milan - source of VEGA, a great mol. dynamics package (free)
TMMeC - The Molecular Modeling Electronic Conference


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