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Foresight Update 35

page 5

A publication of the Foresight Institute

Foresight Update 35 - Table of Contents | Page1 | Page2 | Page3 | Page4 | Page5


Web Watch.35

The following four Web sites were recommended by Peter McCluskey and Eugene Leitl as excellent sources of information on Open Source molecular modeling software.

This page lists tools (web sites for both commercial and freeware tools) for computational chemists. The tools are grouped in the following categories:

  • Charge Fitting Programs
  • Crystallography Programs
  • Force Fields
  • Genetic Algorithms
  • Manuals and Guides
  • Miscellaneous
  • Modeling, Docking, Molecular Design, Drug Design
  • Molecular Databases
  • Molecular Dynamics & Brownian Dynamics Programs
  • Molecular File Format Documentation
  • Molecular Mechanics Programs
  • Molecular Surface and Volume Computation Programs
  • QSAR
  • Quantum Chemistry Software
  • Quantum Molecular Dynamics, Car-Parrinello Methods
  • Simulated Annealing
  • VRML
  • Visualization, Animation, and Rendering tools; Molecular editors and Converters

"The Molecular Modelling Toolkit (MMTK) is a program library for molecular modelling applications. Its aim is to provide researchers, especially those working on the development of new simulation and modelling methods, with a code basis that can be easily extended and modified to deal with standard and non-standard problems in molecular modelling. ... MMTK is based on an object-oriented model of molecular systems... developed in and around Python, a high-level object-oriented general-purpose programming language." This Web site contains in addition to MMTK links to the necessary Python software as well as manuals and papers with applications of MMTK.

This is the Web page for NanoCAD, a freeware nanotech design system based in JavaTM, including source code. An earlier version of this page was listed in Web Watch.26.

This page lists Linux software of use in chemistry and biology, including commercial, freeware, and GNU General Public License software.

Those who would like to bone up on basic chemistry and physics before tackling computational chemistry and its application to nanotechnology, as provided by the above four sites, will be interested in the following Web sites.

The above two links are to the CHEMystery Web site, "a virtual chemistry textbook, to provide an interactive guide for high school chemistry students. In addition, CHEMystery allows you to further expand your chemistry knowledge by letting you interact with other Internet resources on the World Wide Web." The first link is to the original version of the site; the second to a version with a new interface for which updated content is being prepared.

One of the authors of the CHEMystery Web site has produced the Fizzics Fizzle Web site as an interactive guide to physics. There are separate sections for beginning, introductory, and advanced students, with the latter corresponding to introductory college physics.

Moving from the basics to advanced topics, this Web site on metalloprotein structure and design is a project from The Scripps Research Institute meant to be a first step toward developing a distributed environment for interactive metalloprotein design. Since metal ions confer catalytic activity on many natural enzymes, the inclusion of metal ions is a major goal in protein design efforts.

Moving from software tools to physical tools for nanotechnology, Angstrom Tools, Limited is a firm that has been nurtured by Molecular Manufacturing Enterprises to develop a scanning probe microscope (SPM) aimed "fairly specifically at nanotechnology research and development needs." ATL is "gathering input from anyone that may be interested in such a device, to further tune it's R&D efforts and to further flesh out its marketing plan." Interested parties are invited to participate in a survey on their Web site. In addition, their site provides articles on the history, design and theory of scanning tunneling microscopes, and other resources for further information.

Foresight Update 35 - Table of Contents


Thank You

Foresight Credits and Kudos

Tracking all those who make a difference to our organizations has become impossible. Here is a sample of those deserving mention this quarter:

Immense amounts of great volunteer work went into the technical conference covered in this issue; thanks go to Al Globus and Deepak Srivastava (co-chairs), Jan Hoh (tutorial chair), Ralph Merkle (past chair), Neil Jacobstein (Prize session chair).

Great conference staff work as always from conference planner Marcia Seidler, webmaster James Lewis, Elaine Tschorn, Harriet Hillyer, and Tanya Jones. Great appreciation goes to the staff volunteers: Robert Armas, Emanuel Barros, Tihamer Toth-Fejel, Paul Melnyk, Chip Morningstar, Norma Peterson, Max Sims, and Chris Sapyta. Immense thanks to Carol Shaw who continues to be a tremendous help to Foresight fine tuning the data base and bringing the computer systems up to speed.

Many thanks to Jim Lewis and Jeff Soreff for the endless hours of note taking at the conference and the excellent job of reporting in this issue of the Update.

Ongoing vigorous thanks go to Ka-Ping Yee (known as Ping), for putting so much of his free time -- after working long hours at Industrial Light & Magic all week -- into the Foresight Web Enhancement Project, CritSuite,

Special thanks this quarter go to Joe Seidler, whose pro bono management consulting is enabling Foresight to attain new heights of budgeting competence.

Thanks to Philippe Van Nedervelde, Executive Director of Foresight Center (Europe), for creating a multimedia presentation on nanotechnology and presenting it at the "Micromechanics and Molecular Nanotechnology" symposium at the University of Groningen in The Netherlands.

Thanks to Paul Saffo of Institute for the Future for leading the "Engelbart's Unfinished Revolution" conference and enabling us to announce CritSuite and demo at lunch in our blue CritSuite baseball hats. Thanks to Doug Engelbart for starting and continuing his wonderful, unfinished revolution.

Thanks to Senior Associate Jeff Thompson for his work on the Project Proposal process web forms for the new Senior Associate website, and thanks to staffer Tanya Jones for building this new website.

Thanks to the Foresight staff for helping me clean out twelve years of oxidizing Foresight files. We can now fit new papers into the files.

For sending information, thanks go to: Chris Campbell, Doug Denholm, Richard Fannon, Donald Fears, John Faith, Jones Hamilton, Stan Hutchings, Thomas Mazanec, Tom McKendree, Vic Olliver, Anthony Napier, Ed Reifman, Chris Walker, Brian Wang.

--Chris Peterson
  Executive Director, Foresight Institute

Foresight Update 35 - Table of Contents


Upcoming Events

Combinatorial Approaches for New Materials Discovery: Polymers, Catalysis, Electronic Materials, January 21-22, 1999. San Jose, California. "Combinatorial approaches have been highly successful in pharmaceutical applications and are just emerging within the materials industries. Though the approach has, for the most part, been applied to industrially interesting materials only within the last few years, already, scientific papers indicate impressive results and successful utilization of the approach." Sponsored by The Knowledge Foundation, Inc., 101 Merrimac, Boston, MA 02114, USA. Phone: (617) 367-7979; Fax: (617) 367-7912. E-mail: Web:

Reason's 1st Annual Dynamic Visions Conference: "Exploring creativity, enterprise, and progress" February 12-15, 1999 (President's Day Weekend) Santa Clara Marriott, Silicon Valley. "Come hear a lineup of cutting-edge thinkers explore the new vision that is transforming how we understand nature and culture, law and custom, politics and economics, art and technology. In each of these areas, independent but parallel developments have overturned the ideal of a carefully balanced static equilibrium, replacing it with a vision of dynamic, open-ended evolution. At the First Annual Reason Dynamic Visions Conference, speakers and attendees will examine what this new perspective means for our ideas about creativity, enterprise, and the human future." Speakers include Christine Peterson, executive director, Foresight Institute, co-author, Unbounding the Future and Leaping the Abyss, and Eric Raymond, open-source software pioneer, author of The Cathedral and the Bazaar. For more information, contact Erica Mannard, 310-391-2245,

The Second International Conference on Integrated Micro/Nanotechnology for Space Applications: "Enabling Technologies for New Space Systems" April 11-15, 1999. The DoubleTree Hotel, Pasadena, California. Sponsored by The Aerospace Corporation, The Jet Propulsion Laboratory (JPL), and The USAF Research Laboratory. Papers will be presented that highlight the development of micro/nano technologies for space systems, and the novel mission architectures enabled by the application of these new capabilities. Space systems based on microelectromechanical systems (MEMS), nanoscale design and materials, low power quantum electronics, and high bandwidth photonics are of special interest, as are the demonstrations of space subsystems based on these technologies. Contacts: Dr. Timothy Krabach, phone 818.354.9654; Dr. Seymour Feuerstein, phone: 310.336.6000; Dr. Christine Anderson, phone 505.846.6243.

First ELBA-Foresight Conference on Molecular Nanotechnology, 14 to 16 April 1999, Rome, Italy. Conference registration will take place in the evening of 14 April. It is a multidisciplinary meeting on nanotechnology and nanoscale science, with particular interest on the new experimental results, theoretical and modeling. Contact EL.B.A. Foundation, tel +39-6-35420728, fax +39-6-35451637, email On the Web:

Commercialization Advances in Large-Scale Production of Carbon Nanotubes, April 22-23, 1999. The Loews l'Enfant Plaza ~ Washington, D.C. A Forum Designed to Examine Cost-Effective Approaches to Large-Scale Manufacturing of Carbon Nanotubes. The Knowledge Foundation, Inc., 101 Merrimac, Boston, MA 02114, USA Phone: (617) 367-7979, Fax: (617) 367-7912, E-mail:; Web:

euspen: 1st Conference and General Meeting of the European Society for Precision Engineering and Nanotechnology, 31 May to 4 June, 1999, Congress Centre, Bremen, Germany. Topics include: mechanical and chemo-mechanical processes, nano fabrication processes and assembly, modelling and simulation in micro- and nanotechnology. Deadline for abstracts: October 16, 1998. euspen Conference Headquarters, Universität Bremen FB04/FB06, Badgasteiner Strasse 1, 28359 Bremen, Germany. tel ++49 (0) 421 218 74 81, fax ++49 (0) 421 218 44 55, email:

Universal Applications of Molecular Modelling, 7-10 June, 1999, Marseilles, France. The aim of this meeting is to gather scientists from various domains, such as polymer science, reactivity, catalysis, biology and many more in order to demonstrate that applications of molecular modelling are universal, from chemistry to biology. Contact: Dr. Véronique Lazzeri, Faculté des Sciences de Saint-Jerôme Université d'Aix-Marseille, Av. Escadrille Normandie-Niemen - case 532, 13013 Marseille, France. Phone : 33(0) 491 288 005, Fax : 33(0) 491 581 977. Email: Web:

Peptides for the New Millennium, June 26-July 1, 1999, Minneapolis, Minnesota. Topics include: solid-phase organic synthesis and combinatorial methods, design and folding. The 16th American Peptide Symposium, c/o University of Minnesota, P.O. Box 64780, St. Paul, MN 55164-0780. Symposium hotline: (612) 624-7505, fax: (612) 625-2207, e-mail:, Web:

Foresight Update 35 - Table of Contents | Page1 | Page2 | Page3 | Page4 | Page5

From Foresight Update 35, originally published 30 January 1999.


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