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 Modelling for Organic Chemistry by Dr. Rzepa of Imperial College - 8 lectures/8 lecture-demos - super
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 into 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 Homepage  Tokyo 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 Medicine Chemical 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 Resources  collections of PDB files- excellent
Pharmaceuticals - 1000s  Tokyo Univ. ofPharmacy & 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 Biomolecules great 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 formats
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 - everythig 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 - 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 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.
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

Dr. Howard Black
Copyright ©2005

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