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Is ditchwater dull? Naturalists with microscopes have told me that it teems with quiet fun.
G. K. CHESTERTON, The Spice of Life, 1936
Three-dimensional molecular structure is one of the foundations of structure-based drug design. Often, data are available for the shape of a protein and a drug separately, but not for the two together. Docking is the process by which two molecules fit together in 3D space.
The program AutoDock was originally written in FORTRAN-77 in 1990 by David S. Goodsell here in Arthur J. Olson's laboratory. It was designed to perform automated docking of ligands (small molecules like a candidate drug) to their macromolecular targets (usually proteins, sometimes DNA). In 1991, I took over the work on AutoDock. My work focuses on adding new science to AutoDock, including better search methods and parameters, better empirical free energy scoring functions, and on applying AutoDock to real-world problems in medicinal chemistry, in particular HIV-1 protease inhibitors. I have also applied AutoDock to the problem of protein-protein docking, notably to HIV neutralizing antibody b12 to HIV gp120. AutoDock is free to academics, and includes source code.
The AutoDock Home Page - software for automated docking and scoring of flexible ligands to receptors. I wrote the “Protein-Ligand Docking” chapter for a recent Wiley-VCH book in the series, “Methods and Principles in Medicinal Chemistry”. The title of the book is “Evolutionary Algorithms in Molecular Design”.
Our lab runs FightAIDS@Home - During the Autumn of 2005, we worked with IBM and their World Community Grid team to launch the World Community Grid FightAIDS@Home Project. FightAIDS@Home made history in September 2000 when it became the first biomedical Internet-based grid computing project. FightAIDS@Home was started with Scott Kurowski, founder of Entropia. People all around the World continue to donate their home computer's idle cycles to running our AutoDock software on HIV-1 protease inhibitor docking problems.
AutoDockScience's NetWatch (16 May, 2003)
The cover of Science News
Movies showing the results of AutoDock 2.4. The molecular surfaces seen in some of these animations were calculated using MSMS, Michel Sanner's molecular surface program. See how Ed Moret has used AutoDock in some interesting and animated dockings...
Structural Bioinformatics Meeting, 2002, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand.
(2 days on Docking, Homology Modelling, and 2 Days for an AutoDockTools Workshop.)
Molecular Structures ( Cells | Viruses & Molecular Assemblies | Nanotechnology | Proteins & Nucleic Acids | Small Molecules & Ligands | Molecules & Disease )
Cells Alive - drawings, micrographs and movies of microbes and cells. Cell and Molecular Biology Online - an emphasis on information for cell and molecular biologists Dictionary of Cell Biology - second edition. K i d ' s s i t e s : Microbes: Invisible Invaders, Amazing Allies - from Pfizer. | Science in Action: Microbes - from the BBC. | Microbe Zoo. | Infection Detection Protection - from the American Museum of Natural History. | Look Out For Germs - from Bristol-Myers Squibb. | Bugs in the News - from Prof. Jack Brown, Dept. Microbiology, Univ. Kansas.
^ Viruses and Molecular Assemblies
Viruses: From Structure to Biology - explores the historical developments that led to the determination of the structure and biological functions of viruses and their macromolecular components. Institute for Molecular Virology more computer visualizations of viruses, than downloadable structures. Includes: Bacteriophage MS2, Bacteriophage Phi X 174, Canine Parvovirus, Cowpea Chlorotic Mottle Virus, Flock House Virus,Foot and Mouth Disease Virus, Herpesvirus, Mengovirus, Poliovirus, Mammalian Reovirus, Rhinovirus, Southern Bean Mosaic Virus, and Tomato Bushy Stunt Virus. Simulations are also included. Human Immunodeficiency Virus: HIV HIVsdb: HIV Protease Data Base (Original version, HIVdb) . Search NIH (National Institutes of Health). Search BioMedNet for Reviews on HIV.
Nanotechnology and Richard P. Feynman's classic talk given on December 29th 1959 at the annual meeting of the American Physical Society at the California Institute of Technology Feynman Grand Prize - a press release from The Foresight Institute describing the $250,000 prize to motivate nanotechnology breakthrough. Computing with Molecules: a Scientific American article describing molecular switches, wires and even memory elements. Discusses some of the challenges in organizing these components.
^ Proteins and Nucleic Acids
The New PDB: Research Collaboratory for Structural Bioinformatics (RCSB)
- Protein Data Bank, or “PDB”, hosted at the RCSB. Answers to FAQ.
- PDB SearchLite - start your search for proteins here.
- PDB SearchFields - advanced search of the protein database.
- Some of my co-authored PDB entries (excuse the shameless self-promotion!):
- 1HZH = Human Immunoglobulin B12 (Intact) with broad & potent neutralizing activity against primary HIV-1 isolates. (Release Date: 15-Aug-2001).
- 2FIV = FIV Protease (D30N-mutant) Complexed with Inhibitor Ace-Nal-Val-Sta-Glu-Nam.
- 3FIV = FIV Protease (D30N-mutant) Complexed with Substrate Ace-Nal-Val-Sta-Glu-Nam.
- 3TLH = HIV-1 Protease (wild-type) Complexed with Inhibitor TL-3-093.
- 1B11 = FIV Protease (wild-type) Complexed with Inhibitor TL-3-093.
- 5FIV = FIV Protease (V59I-mutant) Complexed with Inhibitor TL-3-093.
- 6FIV = FIV Protease (Q99V-mutant) Complexed with Inhibitor TL-3-093.
- Protein and Nucleic Acid Databases.
- Archive of Obsolete PDB Structures.
- Protein Structural Homology.
- Protein Families
- Family Pairwise Search (FPS) - search a library of protein families with a protein sequence, GCG profile or BLAST checkpoint file that you provide.
- Protein Kinase Resource (PKR).
- The HET Group Dictionary. Lists the connectivity records of HET groups.
- PDB Format - a description of the atomic coordinate entry format.
- mmCIF: macromolecular Crystallographic Information File, and software tools.
- À La Mode - A Ligand and Monomer Object Data Environment.
- NDB: The Nucleic Acid Database - structural information about nucleic acids, and its Structure Finder.
- Proteins Plus from the NDB.
PDBSELECT provides a representative list of high-resolution structures. PDBFINDER is a database that is constructed using a PERL script from the PDB, DSSP and HSSP databases. Many of the fields contained in the PDBFINDER database are difficult to access from the original databases. Some information is retrieved from the original literature. OBSTRUCT - A service to obtain a largest non-redundant set of protein structures from PDB according to crystallographic resolution and sequence identity as specified by the user. Also NMR-elicited structures can be selected. PROCHECK - Checks the stereochemical quality of a known protein structure, producing a number of graphical plots analysing its overall and residue-by-residue geometry. Dali Domain Dictionary. SCOP - Structural Classification of Proteins in UK and USA. CATH - Protein Structure Classification. FSSP: Fold classification based on Structure-Structure alignment of Proteins HIV Protease Database originally from Alexander Wlodawer's Macromolecular Structure Laboratory at NCI-Frederick Cancer Research and Development Center. Atlas of Protein Side-Chain Interactions - based on the printed atlas of Singh & Thornton (1992) The Backbone Dependent Rotamer Library WebPage and the Protein Sidechain Webpage from Roland L. Dunbrack's group. Molecules R US - from the NIH. NCBI (National Center for Biotechnology Information) Structure Group.
- MMDB: The Molecular Modeling Database - this is a compilation of all the Brookhaven Protein DataBank 3-dimensional structures of biomolecules from crystallographic and NMR studies. (MMDB is a database of ASN.1 -formatted records, not PDB formatted records.)
- Structures in MMDB have been compared with one another using VAST (Vector Alignment Search Tool).
- Entrez (DNA/RNA + Protein + Structures + Medline subset).
The WWW Virtual Library: Biomolecules. RNA Secondary Structures. Image Library of Biological Macromolecules. Swiss-3DIMAGE -- protein structure images (many stereo) Antibody Resource Page - compilation of antibody sites and resources for locating antibodies. Protein Structure Prediction Center - hosts the CASP web sites. Molecular Information Agent (MIA) - a web server that searches biological databases to find the existing information about a macromolecule.
^ Small Molecules & Ligands
ReLiBase- “a database system for analysing receptor/ligand complexes deposited in the Protein Data Bank”. Search for complexes that contain a specific substructure, either by sketching a molecule or by typing a SMILES string. Alternatively, seach for a specific interaction, or in other ways. 2D and 3D Structural Information from the DTP (Developmental Therapeutics Program) at the National Cancer Institute 3D Database (NCI DIS 3D database. DIS = Drug Information System) contains some 400,000 drugs. Structures for some 200,000 compounds can be downloaded.Milne, G.W.A., Nicklaus, M.C., Driscoll, J.S., Wang, S. and Zaharevitz. D. ''The NCI Drug Information System 3D Database.'' J. Chem. Inf. Comput. Sci. 34:1219-1224 (1994). NCI Data and Online Services where you can search the NCI Database of compounds, convert file formats, and find public chemical data . 127,000 NCI open database compounds built by Corina (35MB file compressed, 200MB uncompressed). 140,000 plated compounds (75 MB file compressed, in MDL SD format). 1,980 diversity set compounds (in MDL SD format) representing the chemical diversity of the plated compounds. ZINC - a free dockable database project for virtual screening sponsored by the Shoichet Laboratory, Pharmaceutical Chemistry, UCSF, and hosted by docking.org. KEGG DRUG - a database of drugs approved in the USA and Japan, part of a bioinformatics resource named KEGG (Kyoto Encyclopedia of Genes and Genomes), produced by the Kanehisa Laboratories in the Bioinformatics Center of Kyoto University and the Human Genome Center of the University of Tokyo. ChemBank - a freely available collection of data about small molecules , from the Institute For Chemistry and Cell Biology, part of Harvard Medical School. The Three-Dimensional Drug Structure Databank - an NIH collection of experimental and approved therapeutic agents whose structures have been experimentally determined or built. There are not many structures right now (20 structures in March 1996). CCDC: Cambridge Crystallographic Data Centre and the Cambridge Structural Database, CSD, of organic and metal organic compounds. SMILECAS database from Syracuse Research contains more than 103 000 SMILES-Codes and CAS-numbers. CACTVS Online SMILES Translator and Structure File Generator, really useful if you want to convert from a SMILES string into a 3D structure; it works even with many molecules. Check out all the other goodies from the Erlangen/Bethesda Data and Online Services.
^ Molecules and Disease
- HotMolecBase - a database of information about 'hot molecules', i.e. related to common diseases, from the Weizmann Institute of Science.
Drug Design & Computational Chemistry ( Drug Design |Computational Chemistry |Languages/Algorithms |Molecular Mechanics & Dynamics |Molecular Modelling |Viewers|Miscellany )
Links on Drug Design, compilation of answers to a CCL question posed in February 2000. There is a good discussion of the generation and use of large 3D databases in drug discovery which is accessible on-line, from the September 1995 issue of NetSci. It covers pharmacophore-based 3D searches as well as searching in the context of the binding site of a given structural target. Thomas Wieland's summary of connections between topological indices, similarity, screening and drug design. Drug Discovery Online - “the first internet site devoted exclusively to drug discovery and early-stage drug development”. Methods for Structure Based Design - a review article describing docking methods. NCI Drug Information System 3D Database - a collection of 3D (built) structures of over 400,000 drugs. The AIDS 3D Database - a database of compounds active in the NCI AIDS Antiviral Screen. HIV Protease Database (HIVsdb) - 3D structures of HIV-PR inhibited complexes. World Wide Drugs - many links. Binding Database - data on noncovalent association, vital for the elucidation of the physical chemistry of molecular recognition and the discovery of new drugs .
HIV Drug Design
Search NIH for “HIV protease” - perform a search of the NIH for documents matching HIV protease.
- CCL - the Computational Chemistry List, provides software, an archive of list postings, data, documents, announcements about conferences and jobs, as well as links to other web sites.
- SDSC Computational Chemistry - combined program of computational prediction and experimental verification, to understand the design principles of molecular construction.
- SDSC Chemistry Software - for calculating chemical reactions, molecular modeling, and chemistry visualization.
- Journal of Computational Chemistry's Internet Resources - a very good collection of useful sites.
- Research Tools from Frontiers in Bioscience.
- Encyclopaedia of Computational Chemistry from Wiley.
- The Virtual Library:
- Network Science (NetSci) - a forum to explore and discuss current applications of science and technology. (Even though its mission sounds general, its focus seems highly molecular and biophysical). June and July's issues are on a fascinating topic: “Assessing Molecular Diversity”; there are articles on combinatorial chemistry, molecular diversity and mass screening. In the April,1996 issue Michael Connolly (“Molecular Surfaces: A Review”) and TJ O'Donnell (“Scientific and Artistic Uses of Molecular Surfaces”) looked at the evolution and use of molecular surfaces.
- Scientific Software Lists from Network Science.
- Netscape's helper applications page.
- In an attempt to bring standards to assist in the exchange of chemical information across the web, a number of types of data have been proposed. Here are the details on the various chemical MIME types.
^Languages and Algorithms
- SMILES Home Page - SMILES is a simple yet comprehensive chemical nomenclature; has pointers to tutorials, references, parsers, test suites, SMILES-compliant software, etc.
General Purpose Languages
- Python Home Page - an awesome, general-purpose, object-oriented, interpreted, portable (platforms include Linux, Unix, Macintosh, and Windows), high-level language, with several useful extensions for scientific computing.
- Check out the tutorials and the Python 2.3 Quick Reference page.
- The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology.
- Virtual Library's Computing page, with a page on Programming Languages.
- C Programming.com - covers C and C++.
- Programming By Example from MIT.
- Numerical Recipes Home Page - access the book online, or order the software.
- Artificial Intelligence - page from the Virtual Library.
- Web Pages that Perform Statistical Calculations.
^Molecular Mechanics (MM) and Molecular Dynamics (MD)
- AMBER - “all the bugs have not been removed”...; MM, MD
- PMD - scalar, scalable, parallel and free, and it can easily manage hundreds of thousands of atoms.
- Tinker - MM, MD; free software.
- NIH - Molecular Modeling.
- Molecular Modelling from BimCore, the Biomolecular Computing Resource. at Emory University.
- Rasmol - a popular and cross-platform molecular viewer.
- Chime - plug-in for web browsers, related to RasMol. It embeds 2D, and rotatable 3D chemical structures directly on web pages or in tables. It is free to academic and home users. Chime supports:- Brookhaven PDB files; MDL Information Systems; Inc.'s Molfile, RxnFiles, and Sketch files; concatenated XYZ files for animated structures; and Gaussian input files. (If you notice a resemblance to RasMol, it is because a portion of the 3D structural display code was originally written by Roger Sayle. Chime even supports RasMol scripting.) There are several examples on the web, but one of my favorites is the photosynthetic reaction centre from the purple bacterium. Supported OS's include: Mac OS (PowerPC and 680x0); Windows 95; Windows 3.1; and Silicon Graphics IRIX.
- VRML Browsers - why use VRML to view molecules? Because RCSB PDB offers this option.
- The VRML Repository - is an impartial, comprehensive, community resource for the dissemination of information relating to VRML.
- WorldView for Apple Macintosh PPC and Windows.
- Cosmo Player for SGI IRIX.
- X Swallow - a generic X-based plug-in for Netscape.
- Protein ScienceKinemages are viewable using MAGE, and can be created using PREKIN.
- WebLab(TM) Viewer - a molecular visualization from Molecular Simulation Standalone viewer and also an interface to Cerius2 SDK computational server software. Supported OS's include: v2.0 Windows 95, Windows NT, and Power Macintosh; v1.1 for Windows 3.1 and 680x0 Macintosh. SGI and IBM RS/6000 promised soon.Inc.
- Xmol from Network Computing Services, Inc. 3D molecular viewer for any X11 display. Supported OS's: UNIX (DEC, SGI, SPARCstation, Sun-3, IBM RS/6000).
- Moviemol is a program for visualization and animation of molecular structures for PC's, IBM RS/6000 and SGI workstations.
- VMD - Visual Molecular Dynamics from the Theoretical Biophysics Group at the University of Illinois at Urbana-Champaign.
- Links to Modelling/Theory Groups from Biophysics, Oxford.
- W. Graham Richards' Research Group.
- Janet Thornton's Structure and Modelling Group.
- Birkbeck College, UK, Department of Crystallography.
- Birkbeck College, UK, Simulation Group.
- Rik Belew's Research Group.
- Peter Kollman Group.
- David Case Group.
- Arthur J. Olson Group.
- David S. Goodsell Group.
- William E. Hart.
- Roland L. Dunbrack Group.
Bioinformatics ( General | Sequence Data | Useful Tables | Sequence Analysis | Homology Modelling )
Cytoscape is an open source bioinformatcs software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data. Objects in Bioinformatics '99 - focuses upon the role of object-oriented technology, reusable software components, design patterns, and distributed computing in bioinformatics and computational genomics. Bioinformatics @ La Jolla - serves the “San Diego bioinformatics community by providing information about local bioinformatics research, as well as news about upcoming seminars and events. The associated mailing list provides a forum for the open exchange of ideas and information between researchers.” Biological Data Representation and Query - research and software for analyzing structural biology data. CMS Molecular Biology Resource - a compendium of electronic and Internet-accessible tools and resources for Molecular Biology, Biotechnology, Molecular Evolution, Biochemistry, and Biomolecular Modeling, from the San Diego Supercomputer Center. OSC Bioinformatics SIG - the Oxford Supercomputing Centre Bioinformatics Special Interest Group. Biomolecules - from the Virtual Library. Bio-wURLd- a searchable, user-maintained collection of URL's related to bioinformatics, biochemistry, and molecular biology. Molecular Biology Computation Resource or MBCR - offers links to databases, homology searches, sequence analysis services and more. Biology Workbench provides a Web interface to major sequence databases and the tools to search those databases. Included is a Tutorial to assist in learning and using the workbench. BCM Search Launcher provides a single entry point for molecular biology searches - including protein sequence, nucleic acid sequence and protein secondary structure predictions, from the Human Genome Center, Baylor College of Medicine. Johns Hopkins University BioInformatics Web Server providess links to a collection of protein databas Bioinformatics Resources from the Brutlag group, Stanford University.
^ Sequence Data^Useful Tables
From National Center for Biotechnology Information (NCBI) : GenBank. Genome Database. Taxonomy Database. Protein Sequence Search Nucleotide Sequence Search Biomolecule 3D Structure Search BLAST Online Mendelian Inheritance in Man (OMIM) ExPASy Molecular Biology Server - resources for protein and nucleic acid sequence analysis, from the GenevSWISS-PROT, and PROSITE, a database of protein families and domains. OWL - Composite Protein Sequence Database. GeneCards - a database of over 6000 human genes describing gene function, gene produc EcoCyc: Encyclopedia of E. coli Genes and Metabolism. REBASE - The Restriction Enzyme Database, includes recognition sequences. Stanford Genomic Resources - genomic and biological information in the Saccharomyces Genome Database and the Arabidopsis thaliana Database (AtDB). The Institute for Genomic Research (TIGR) site contains the Microbial Database (MDB) and the TIGR Human Gene Index (HGI). Vector db - sequence information and annotations for vectors commonly used in molecular biology and links to other vector resources and GenBank. Table of Standard Genetic Code. Codon Usage Tables - for many organisms and microorganisms. Amino Acid Information - chemical, structural and genetic properties. Periodic Table of the Elements from Los Alamos National Laboratory.
^ Sequence Analysis
SeqAnalRef - bibliographic reference database covering sequence analysis. Protein Analysis Tools from Frontiers in Bioscience. Birkbeck College, UK, Crystallography Department Software Engineering Group and related projects. Sequence Analysis Tools includes tools for sequence similarity searches; analysis of primary sequences for physicochemical parameters, signal peptides, sequence repeats, glycosylation sites, etc.; secondary structure prediction; binary and multiple sequence alignments. BioSCAN Online is an interactive method to search for and match protein and nucleic acid sequences. The Biomolecular Structure and Modelling Group at University College, London, has made available a number of programs of use in homology modeling. Computational Analysis of DNA and Protein Sequences is a chapter from Genome Analysis: A Laboratory Manual. It provides basic Internet information as well as a summary of sequence analysis, multiple alignments, structure prediction and protein modeling, and many other related topics. A Guide to Sequence Searching provides a description of several biosequence comparison topics, including substitution matrices. Dali performs multiple structural alignments of proteins. Coordinates of protein structures are compared against those in the Protein Data Bank, and a multiple alignment of structural neighbors is returned. The Biocatalog contains a long listing of software programs for sequence search and analysis. Sequence Analysis Bibliographic Reference Database provides a comprehensive list of papers dealing with sequence analysis. johnsand Molecular Machines - all about sequence logos, and more, from the Laboratory of Computational and Experimental Biology at the National Institutes of Health in Frederick, MD
^ Homology Modelling
WHAT IF - a Web-based tool for generating homology models. SWISS-MODEL - a Web-based tool for generating homology models. HOMSTRAD - (HOMologous STRucture Alignment Database) for alignment of proteins. ModBase - a database of protein structures obtained by homology modeling. 3DCrunch - a project to create databases of protein structures by homology modeling.
Visualization ( Visualization Resources | Software | News )
^ Visualization Resources
OSC Visualisation SIG - the Oxford Supercomputing Centre Visualisation Special Interest Group
General Visualization Software
AVS (USA) and AVS (UK). OpenDX - Open Visualization Data Explorer from IBM. Iris Explorer. MATLAB - from Mathworks. Mathematica - from Wolfram Research.
Molecular Visualization Software
AutoDock's Useful Tools page. MDSCOPE and VMD - from Theoretical Biophysics Group, NIH Resource for Macromolecular Modeling and Bioinformatics , Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign.
^ NewsSIGGRAPH 2002 - the 29th international Conference on Computer Graphics and Interactive Techniques; from the Special Interest Group in Graphics, SIGGRAPH.
The Emerging Web
The Web Learns to Read - a nice introduction to the next generation of web technology, from Scientific American. What is XML, anyway? The XML 1.0 specs, from the W3C. Free XML software and XML software by platform. The Whirlwind Guide to SGML and XML Tools and Vendors. A comprehensive web site on XML and SGML by Robin Cover. Search the web for the latest on XML.
^ Python and XML
A mailing list and SIG on XML processing in Python. Also from the Python web site, a list of books on XML and SGML. Python/XML HOWTO from the firstname.lastname@example.org. Search the web for the latest on Python and XML.
^ XML + Chemistry -> CML
^ SOAP, XML-RPC, WSDL and UDDI
SOAP - Simple Object Access Protocol. From the W3C: “SOAP is a lightweight protocol for exchange of information in a decentralized, distributed environment. It is an XML based protocol.” Apache SOAP - an Apache implementation of SOAP. A Busy Developer's Guide to SOAP 1.1 - describes a subset of SOAP 1.1 that forms a basis for easy interoperation between different environments. XML-RPC Home Page - “Simple cross-platform distributed computing, based on the standards of the internet.” Also from the XMLRPC.com web site: “It's remote procedure calling using HTTP as the transport and XML as the encoding. XML-RPC is designed to be as simple as possible, while allowing complex data structures to be transmitted, processed and returned.” AppleScript XML-RPC - How to make XML-RPC and SOAP requests with AppleScript on Mac OS X 10.1 and later. X Methods - a list of publicly available web services that use emerging standards such as SOAP, WSDL and UDDI. WSDL - Web Services Description Language, from the W3C: “WSDL is an XML format for describing network services as a set of endpoints operating on messages containing either document-oriented or procedure-oriented information. The operations and messages are described abstractly, and then bound to a concrete network protocol and message format to define an endpoint.” UDDI - Universal Description, Discovery and Integration of Web Services, helps organizations to discover quickly and dynamically web services, both internally and externally.
XML stands for the eXtensible Markup Language, CML stands for Chemical Markup Language, and SGML is an abbreviation for the Standard Generalized Markup Language.
- Beginners Guide to Molecular Biology.
- BioMolecules in the Classroom: Educational Molecular Visualization with Chime & RasMol
- BioMolecular Structure Education Web Sites that use Rasmol and Chime.
- The Principles of Protein Structure organized by the Department of Crystallography, Birkbeck College and also available at the Brookhaven Mirror. This is part of the Virtual School of Natural Sciences (VSNS) of the Globewide Network Academy (GNA)
- The NIH Molecular Modeling Home Page
- Hypertextbook on Biology from MIT: go to the list of chapters. Has several awards.
- Course on Biotechnology and Enzyme Technology from Newcastle University, UK, which relies heavily on Rasmol and Kinemages.
- Secondary Structure Course from the Karolinska Institute, Stockholm, Sweden
- The Journal of Chemistry Education Online has a really nice set of QuickTime movies showing some spectacular, dangerous, and fascinating chemical phenomena, on their “Chemistry Comes Alive!” pages. There are just a few samples online, but the rest can be purchased on CD-ROM.
- Chemistry Online is a great set of resources from the Department of Chemistry, University of Oxford's Chemistry Information Technology Centre, including online courses, practicals, chemistry lectures, discussion groups, multimedia and more. See The Virtual Chemistry Laboratory and also Chemistry QuickTime TV.
- REVIEWS IN COMPUTATIONAL CHEMISTRY - Edited by Kenny B. Lipkowitz and Donald B. Boyd
- ''The Machinery of Life'' and ''Our Molecular Nature'' - two books from David S. Goodsell.
- Amazon.com - reputedly the Earth's biggest bookstore. Rumoured to have 40% off 500 titles; but watch those shipping charges, especially if you split your order based on delivery date.
- Barnes and Noble - a bookstore with the old-fashioned bricks-and-mortar approach, and a web site to rival amazon.com.
- Blackwells - a venerable bookstore on Broad Street, in the heart of Oxford, U.K., founded in 1879.
- Chambal - price-comparison web site for book shopping. founded in 1879.
Journals ( Search for Articles IJournals Online ) PubMed (NLM) to search Medline and Pre-Medline. Internet Grateful Med (NLM) - for review articles (phased out). HMS Beagle - science articles and journals. ChemWeb Library - access to many online journals. BioMedNet's Journal Collection - “The Internet Community for Biological and Medical Researchers”. ACM - publications from the Association for Computing Machinery. Carlo Nervi's list of journals, books, and others, related to chemistry. Frontiers in Bioscience - “a journal and virtual library”. Science - published by the AAAS. Nature - the “international weekly journal of science”. Network Science - the web journal of science and computers. embnet.news - European Molecular Biology Network Newsletter. JACS - Journal of the Americal Chemistry Society. JMB Online - Journal of Molecular Biology from Academic Press, London. JCAMD - Journal of Computer-Aided Molecular Design. Journal of Molecular Modelling - in cooperation with Springer. Protein Science - a publication of the Protein Society Structure - monthly international journal devoted exclusively to structural biology. Current Biology - dispatches from the front lines of biology. Journal of Computational Chemistry - from Wiley-Interscience. Journal of Physical Chemistry - free for a limited time. Journal of Computational Biology - computational molecular cell biology. Journal of Biological Chemistry - American Society for Biochemistry & Molecular Biology. TSRI network account holders now have free access to JBC OnlineThe Kresge Library holds an institutional subscription and no individual registration is required. Please contact Michaeleen Trimarchi at the Kresge Library, x8705 or email@example.com, if you have any questions. Chemistry & Biology - investigations at the interface of chemistry and biology. Biophysical Journal - edited by the Biophysical Society in cooperation with the APS. Foundations of Chemistry - Philosophical, Historical, Educational and Interdisciplinary Studies of Chemistry. CAOS/CAMM Center's copy of MMCC Results (MMCC = Molecular Modeling and Computational Chemistry). See also Bruce R. Gelin for information about subscription. Electronic Medicinal Chemistry Journal Chemical Physics - Preprint Database. Evolutionary Computation - developments in GAs, ESs, CSs, EPs and others, from MIT Press. Artificial Life - self-organizing systems, etc., from MIT Press.
Publishers and Periodicals
- Oxford University Press - UK and USA.
- Cambridge University Press - UK and North American branches.
- Wiley, WileyInterScience, and Wiley-VCH- books and journals.
- Springer-Verlag - scientific, medical and technical publishing company.
- SunSoft Press - definitive books written by Sun's experts.
- New Scientist - A popular weekly science magazine published in Britain.
- Popular Science - what's new in science and technology.
- Discover - yet another magazine of science and technology.
- Skeptic - magazine on rational skepticism, the scientific method, and critical thinking.
- BYTE - computer hardware and software.
- ZDNet - Ziff-Davis, publishers of popular Mac and PC magazines.
- HotWired - track the digital revolution with WIRED in cyberspace.
Science and Art
- Molecular Art, including a few of my own pictures.
- The Nanomedicine Art Gallery - from the Foresight Institute. Take a look at the thumbnails.
Dr. Garrett M. Morris
D.Phil. (Oxon.), M.A. (Oxon.)
The Scripps Research Institute,
Department of Molecular Biology, MB-5
10550 North Torrey Pines Road
La Jolla, CA 92037-1000, USA.
email: garrett (at) scripps (dot) edu
telephone: + (858) 784-2292
voicemail: + (858) 784-2292
fax: + (858) 784-2860
Last modified: Tuesday, 18 January, 2005