21. Molecular Modeling Home Page molecular modeling was introduced at Lebanon Valley College through support by the College and a $49,188 grant titled molecular modeling Throughout the http://www.molecules.org/index_noframes.html

Frames version Molecular Modeling for Chemical Education Chemical Structures Workshops Record of ... Other Sites Summary of Activities at Lebanon Valley College Molecular modeling was introduced at Lebanon Valley College through support by the College and a $49,188 grant titled "Molecular Modeling Throughout the Chemistry Curriculum" from the National Science Foundation. The Chemistry Department built a Molecular Modeling Laboratory housing 10 Power Macintosh computers (233-MHz G3, 64 MB Ram, 4 GB hard drive, internal ZIP drive, 24X CD-ROM) which run CAChe Scientific software and a Silicon Graphics Indigo II Workstation running Tripos software. Another grant from the National Science Foundation "A Consortium for Molecular Modeling Using Workshops and the World Wide Web" supports workshops for undergraduate faculty . This web site has grown from the activities under these grants. Please browse the site using the links given toward the top of the page. We would like to have your comments and suggestions, so please let us know you were here and give us feedback A Slide Show describes uses for molecular modeling.

22. EBioinformatics BioNavigator eBioinformatics offers BioNavigator a webbased service incorporating tools and databases from many sources; enabling you to perform sequence analysis, database searching, PCR primer design, and molecular modeling. http://www.BioNavigator.com/

23. Linux4Chemistry - Linux Software For Chemistry: Molecular Modeling, Visualizatio An upto-date website with the links to Linux software for chemistry including computational, visualization, graphic, molecular modeling, both free and commercial software useful in different fields of chemistry. http://zeus.polsl.gliwice.pl/~nikodem/linux4chemistry.html

Links for Chemists Chemistry section of the WWW Virtual Library Virtual Library Science Chemistry : Software: Linux4Chemistry This page is maintained by Nikodem Kuznik. All comments, suggestions, updates and new urls should be e-mailed to Nikodem Kuznik Not sure about the availability 2 Dimensional Finite Difference Hartree-Fock Program a numerical Hartree-Fock program for diatomic molecules. ABINIT ABINIT is a package for First-Principles calculations of the electronic structure of solids and molecules. It uses a plane-wave basis set and several different types of norm-conserving pseudopotentials, and will soon be functional with PAW pseudopotentials as well. ABINIT can calculate total energies and band structures, relax geometries, but also do linear-response calculations of phonons, perturbations with respect to strains, and electric fields. (GNU/GPL) [added 2/4/2004] achemso Package which formats the Bibliography according to the standards of the American Chemical Society (LaTeX/BibTeX). [added 2/17/2001] ADF the Amsterdam Density Functional program system for high-quality computational chemistry research. The two main programs are ADF, for molecules, and BAND for periodic structures: polymers, slabs, and crystals. Several smaller utility and property programs are available for pre- and post-processing data of the main calculations.

24. Molecular Modeling Photosynthesis. molecular modeling. Instrumentation. Analysis/Modeling. Website Map. Index. Online Protein Viewers. Software Used in molecular modeling and Molecular Dynamics. Cool molecular modeling http://www.arc.unm.edu/~aroberts/main/molmod.htm

This Site The Web Get your own free Search Engine Home Up Photosynthesis Molecular Modeling Instrumentation Analysis/Modeling Website Map For Bugs or adding links,Please email me! Index Online Protein Viewers Software Used in Molecular Modeling and Molecular Dynamics Cool Molecular Modeling Sites Click here for books on Molecular Structures Cool Molecular Modeling Sites Chemical Computing Group Inc. is a leading world-wide supplier of high-end scientific software and services for High Throughput Screening, Bioinformatics and Computer Aided Molecular Design applied to Drug Discovery and Life Sciences. CCG has been operating in Montreal since 1994 (Updated 3/25/01). CCL-Computational Chemistry List Home was established on January 11, 1991, as an independent electronic discussion forum for chemistry researchers and educators from around the world. It is located at Ohio Supercomputer Center (Updated 6/16/99). Chemistry Software List at NIU Cheminformatics Site provides a list of software for the small molecule molecular modeling scientist at the NIU CHemistry Cheminformatics (Updated 5/22/99).

25. CMS Molecular Biology Resource A compendium of tools for molecular biology, biotechnology, molecular evolution, biochemistry and biomolecular modeling. http://restools.sdsc.edu/

Sequence Databases Physico-Chemical Features Analyses Enzyme Info and Structure Databases Organism-Specific Genome Databases Sequence Databases Physico-Chemical Features Analyses Enzyme Info and Structure Databases Organism-Specific Genome Databases ... Protein Seq/Syn Services

26. SpringerLink - Publication Journal of molecular modelingMolecular, protein, peptide and drug design, computational modeling, molecular mechanics/dynamics http://link.springer.de/link/service/journals/00894/

Articles Publications Publishers Home Publication Journal of Molecular Modeling Publisher: Springer-Verlag Heidelberg ISSN: 1610-2940 (Paper) 0948-5023 (Online) Subject: Chemical Sciences Life Sciences Medicine Physics and Astronomy Issues in bold contain article full text that you are entitled to view. Online First Volume 10 Number 3 Number 2 Number 1 Request a sample Volume 9 Number 6 Number 5 Number 4 Number 3 ... Number 1 Volume 8 Number 12 Number 11 Number 10 Number 9 ... Number 1 Volume 7 Number 12 Number 11 Number 10 Number 9 ... Numbers 1-3 Volume 6 Number 12 Numbers 10-11 Number 9 Numbers 7-8 ... Number 1 Volume 5 Number 12 Number 11 Number 10 Number 9 ... Number 1 Volume 4 Number 12 Number 11 Number 10 Number 9 ... Number 1 Volume 3 Number 12 Number 11 Number 10 Number 9 ... Number 1 Volume 2 Number 12 Number 11 Number 10 Number 9 ... Numbers 1-2 Volume 1 Number 4 Number 3 Number 2 Number 1 Publication 1 of 1 Previous Publication Next Publication Linking Options About This Journal Editorial Board Manuscript Submission Quick Search Search within this publication...

27. MoluCAD Educational software for chemistry students, for the creation and visualization of complex molecular structures in 3D. Demo and online purchasing available. http://www.molucad.com/molucad/index.htm

MoluCAD ...a molecular modeling and visualization tool MoluCAD is a full-featured molecular modeling and visualization tool designed for Windows. Originally conceived as an aid for students of organic chemistry, MoluCAD has quickly evolved into much more. The latest version incorporates many advanced features only found in expensive workstation-based modeling packages. Ease of use, premium graphical quality, and computational robustness are the trademarks of MoluCAD. Novice users are able to quickly generate models, view them form any perspective, create reaction animations, and save all data to disk. MoluCAD is distributed by download from this website. [Download MoluCAD Demo] Easily Model Structures in True 3D Build Reaction Animations Easily Examples: EAS Diels-Alder Cyclohexane-Flip Interactive Periodic Table HTML-Based Help Built-In MM2 Energy Minimization MoluCAD is the result of a 3-year National Institutes of Health biomedical technology research project aimed at producing low-cost educational software for chemistry students. See the December 1997 NCRR Reporter article, "

28. Computational Chemistry And Molecular Modeling Service for chemical pictures, animations, 3D files and molecular properties (HOMO, LUMO, charges, dipole, spin). http://www.molecular-modelling-service.de/

Home deutsch english deutsch ... english Email: stefan@comchem.de Links modeling, modelling, computer, computational, chemistry, render, molecule, molecular, pictures, animation, picture, 3D, animations, VRML, pdb, Molekülbilder, Molekuelbilder, Bilder, Modell, Modelle, Molekuelmodelle, Molekülmodelle, Molekülmodell, Molekuelmodell, Molekuel, molekuel, Molekül, molekül, 3 D, räumlich, raeumlich, struktur, structure, Strukturen, Struktur, strukturen, Molekuelstruktur, molekuelstrukturen, Molekülstrukturen, molekülstrukturen, molecular, structures, organisch, organische, Chemie, chemie, chemistry, Chemistry, anorganische, Anorganische, Bio, bio, Computerbilder, Computergrafik, inorganic, organic, semi, empirisch, empirical, DFT, dft, abinitio, ab initio, Kraftfeld, Geometrie, optimierung, optimize, Computergrafik Service fuer Computerchemie - Molekuelbilder und Animationen. - Computational chemistry and molecular modelling service, Molekülbilder, Computergrafik, Art, chemical, molecular modeling, chemische Struktur

29. Molecular Modelling Group One of the Specialist Interest Groups of the Royal Society of Chemistry. Links to research groups, meeting reports, software archives, selected articles. http://www.rsc.org/lap/rsccom/dab/ind006.htm

RSC Members Press Releases Register Jobs ... Public Activities Special Interest Groups Join the Group Contacts Secretary of the Group RSC Staff contact ... Committee Members Annual Report Newsletter Future Group Meetings Future ITF Group Meetings Annual Events ... Submit an Event Awards Research Interests Other activities Software Downloads Useful Links RSC members: register your email address ... Further information Molecular Modelling Group Mission Statement "To stimulate the use and application of molecular modelling and related methods in Industry" Aims To raise awareness of molecular modelling To promote the cost-effectiveness of molecular modelling and related methods in experimental programs of research across all industrial sectors To facilitate the use of molecular modelling and related methods by Small and Medium Enterprises (SMEs) across the UK by arranging seminars and meetings for research managers and technical personnel To identify expertise in problem solving and the provision of appropriate molecular modelling solutions for industrial research applications To inform members of advances in the applications and development of molecular modelling and to update members on the performance of hardware and software To promote the synergistic interaction of this Specialist Interest Group with others, both within the RSC and outside, in industry and academia, in the UK and abroad

30. Molecular Modeling Of Proteins molecular modeling of Proteins. Journal of Molecular Biology. Journal of molecular modeling (the first fully electronic journal in chemistry). Protein Science. http://solon.cma.univie.ac.at/~neum/protein.html

Molecular Modeling of Proteins ``It is God's privilege to conceal things, but the kings' pride is to research them.'' (Proverbs 25:2; ascribed to King Solomon of Israel, ca. 1000 B.C.) The protein folding problem entails the mathematical prediction of (tertiary, 3-dimensional) protein structure given the (primary, linear) structure defined by the sequence of amino acids of the protein. It is one of the most challenging problems in current biochemistry, and is a very rich source of interesting problems in mathematical modeling and numerical analysis, requiring an interplay of techniques in eigenvalue calculations, stiff differential equations, stochastic differential equations, local and global optimization, nonlinear least squares, multidimensional approximation of functions, design of experiment, and statistical classification of data. Even topological concepts like the Morse index and invariants in knot theory (Jones polynomials) have been discussed in this context. An extensive recent report from the U.S. National Research Council

31. MathMol MathMol (Mathematics and Molecules) is designed to serve as an introductory starting point for K12 students and teachers interested in the field of molecular modeling and its application to mathematics. http://www.nyu.edu/pages/mathmol/K_12.html

The K-12 Activity MathMol Page is designed to serve as an introductory starting point K-12 students interested in the field of molecular modeling. If your browser supports JavaScript you will be taken to our new location at http://www.edinformatics.com/mathmol/ in a few seconds. If your browser doesn't support JavaScript, you may click to the above address. Please inform the webmaster of the site that linked you here to update their link. Thanks!

32. Accelrys -- Software For Pharmaceutical, Chemical, And Materials Research Provider of molecular modeling and simulation software and services for both life and materials science research. http://www.accelrys.com/

CORPORATE OVERVIEW NEWSROOM EVENTS EMPLOYMENT ... CONSORTIA MEMBERS Nanotech Guide Accelrys' nanotechnology applications guide Request your free copy E-flash Sign up for a monthly update from Accelrys Product Updates AEI 5.3 new enterprise cheminformatics solution MS Modeling 3.0 materials simulation on the PC Software for pharmaceutical, chemical, and materials research More about Accelrys... Events Molecular Modeling for Generic Drug Product Development Structure Based Design Methodologies Materials science seminars - Materials Innovation On The PC More events Press releases Pharmacopeia changes name to Accelrys and appoints Mark Emkjer new chief executive officer Pharmacopeia and PDD announce March 2004 quarter financial results Pharmacopeia completes spin-off of Pharmacopeia Drug Discovery More news... WebStore Desktop solutions Bioinformatics Cheminformatics Modeling/Simulations Chemical databases Or call toll-free Free Publications Quinoline binding site on malaria pigment crystal: A rational pathway for antimalaria drug design Buller et al.

33. SpringerLink - Publication antas.agraria.uniss.it/ molecular modelingmolecular modeling. Protein Modeling. PDB The Protein Data Bank, is hosted by the Research Collaboratory for Structural Bionformatics http://link.springer-ny.com/link/service/journals/00894/

Articles Publications Publishers Home Publication Journal of Molecular Modeling Publisher: Springer-Verlag Heidelberg ISSN: 1610-2940 (Paper) 0948-5023 (Online) Subject: Chemical Sciences Life Sciences Medicine Physics and Astronomy Issues in bold contain article full text that you are entitled to view. Online First Volume 10 Number 3 Number 2 Number 1 Request a sample Volume 9 Number 6 Number 5 Number 4 Number 3 ... Number 1 Volume 8 Number 12 Number 11 Number 10 Number 9 ... Number 1 Volume 7 Number 12 Number 11 Number 10 Number 9 ... Numbers 1-3 Volume 6 Number 12 Numbers 10-11 Number 9 Numbers 7-8 ... Number 1 Volume 5 Number 12 Number 11 Number 10 Number 9 ... Number 1 Volume 4 Number 12 Number 11 Number 10 Number 9 ... Number 1 Volume 3 Number 12 Number 11 Number 10 Number 9 ... Number 1 Volume 2 Number 12 Number 11 Number 10 Number 9 ... Numbers 1-2 Volume 1 Number 4 Number 3 Number 2 Number 1 Publication 1 of 1 Previous Publication Next Publication Linking Options About This Journal Editorial Board Manuscript Submission Quick Search Search within this publication...

34. Chemistry Molecular Models molecular modeling for Chemical Education Lebanon Valley College; NIH molecular modeling Home Page - Easy Access to Biochemical Structures; http://www.uwsp.edu/chemistry/pdbs/

Chemistry Molecular Models This page is maintained by Dr. Tom Zamis. Please email any comments: This page will link you to an awesome collection of chemical structure files in PDB (Protein Data Bank) format that will be displayed in 3D by a plug-in developed by MDL Information Systems Inc. called Chemscape Chime RasMol Many of the structure files appearing in this collection were obtained from other structures collections. Please visit these sites for additional structures. Molecular Modeling for Chemical Education - Lebanon Valley College NIH Molecular Modeling Home Page - Easy Access to Biochemical Structures Protein Data Bank - Rutgers University Klotho: Biochemical Compounds Declarative Database - Washington University, St. Louis ... The Three-dimensional Drug Structure Databank - NIH Directions for Manipulating the Display Click on the name of the molecule to see the Chemscape Chime model of that molecule. If you are using a Macintosh, put the pointer on the graphic and hold down the mouse button to obtain a menu of options that control the molecule display. If you are using a PC, put the pointer on the graphic and hold down the right mouse button to obtain the menu. You can manually rotate the molecule on its x or y axis by dragging on the graphic.

35. UWMML At Pharmacy Click here Tripos/Sybyl course announcement. Sybyl molecular modeling software is available as a seat on the University of Wisconsin site license. http://uwmml.pharmacy.wisc.edu/

UWMML Web Page University of Wisconsin Molecular Modelling Laboratory, Rm. 7205 School of Pharmacy, 777 Highland Ave., Madison, Wisconsin 53705-2222 Professor Dan Rich dhrich@facstaff.wisc.edu Associate Scientist Ken Satyshur satyshur@wisc.edu 608-262-9403. Or contact me on my cell phone: 608-215-5207, Which also takes e-mail: 6082155207@vtext.com Serving the Pharmacy community since 20/Sep/1994:13:32:29. Last modified Sept. 28,2003 OUR EIGHTH ANNIVERSARY!! This is a composite stereo picture. This is the CORRECT kind of stereo image to publish in a journal. If you see crossed stereo, view the middle and right images. If you see relaxed stereo, view the left and middle images. If you don't know which method you use to see stereo, view the images and note if the phenyl under the yellow dots comes toward you or away from you. Find out the answer by clicking here!! How to See Stereo Modelling Pictures! Sybyl Modeling Web Page Click here: Tripos/Sybyl course announcement. Sybyl molecular modeling software is available as a seat on the University of Wisconsin site license. Sybyl, by Tripos Corp (www.tripos.com), is a full featured modeling package that is used to create, manipulate, and display molecules and polymers. It is especially suited to biological compounds with the "biopolymer" module. Proteins, DNA, and RNA can be displayed andmanipulated in various formats, including sticks, surfaces and ribbons. High quality images can be saved in various formats for publication in print, as html, or for input to powerpoint. There are 14 seats now in use for students and faculty. The site is sponsored by the Chemistry department (prof. Dan Rich) and is served by Melissa Lucero (lucero@chem.wisc.edu) and Ken Satyshur (satyshur@uwmml.pharmacy.wisc.edu). Please contact them if you wish to join the site license.Things to do at this site:

36. Fred K. Friedman, Ph.D. Structure, function, mechanism and regulation of the drug and carcinogen metabolizing cytochrome P450 enzymes are studied by biochemical, biophysical and enzymology approaches, and by molecular modeling. http://rex.nci.nih.gov/RESEARCH/basic/lm/fkf.htm

Center for Cancer Research National Cancer Institute National Institutes of Health The web address for Dr. Fred K. Friedman's home page has changed. Please click here for the new address and update your bookmarks. Last revised on September 18, 2002 by Linda Byrd Return to Laboratory of Metabolism

37. Center For Molecular Modeling http://cmm.cit.nih.gov/modeling/

38. GLMAC Homepage Information about current research in bioremediation, soil contaminant sorption and desorption, molecular modeling techniques, and related fields. Michigan, USA. http://www.engin.umich.edu/dept/cee/research/HSRC/

GREAT LAKES MID-ATLANTIC CENTER FOR HAZARD OUS SUBSTANCE RESEARCH University of Michigan Michigan State University Howard University Mission Statement The mission of the Great Lakes Mid-Atlantic Center for Hazardous Substance Research is to foster and support integrated, interdisciplinary, and collaborative efforts that advance the science and technology of hazardous substance management to benefit human and environmental health and well-being. To this end, the center coordinates the research efforts of a world-class team of investigators from the University of Michigan, Michigan State University, and Howard University. Investigators from the three universities join forces to tackle issues surrounding the development and application of bioremediation technologies for contaminated soils and groundwater. Current research projects include studies of soil contaminant sorption, desorption, and sequestration properties aimed at developing molecular modeling techniques, and the development and field application of surfactant-enhanced remediation and in-situ microbial remediation technologies. Targeted Research Area Collaborations, or TRACs, encourage research groups to share ideas, data, and other resources, thereby increasing productivity and accelerating the transfer of technologies to end-users.

39. An Introduction To Molecular Modeling An Introduction to molecular modeling. Allen B. Richon. This article introduces the concepts of molecular modeling and contains references for further reading. http://www.netsci.org/Science/Compchem/feature01.html

An Introduction to Molecular Modeling Allen B. Richon Molecular Solutions, Inc. 1116 Miller Mountain Road Saluda, NC 28773-8677 E-mail:abrichon@molsol.com This article originally appeared in Mathematech http://www.netsci.org/Science/Compchem/feature01.html Introduction Drug design is an iterative process which begins when a chemist identifies a compound that displays an interesting biological profile and ends when both the activity profile and the chemical synthesis of the new chemical entity are optimized. Traditional approaches to drug discovery rely on a step-wise synthesis and screening program for large numbers of compounds to optimize activity profiles. Over the past ten to twenty years, scientists have used computer models of new chemical entities to help define activity profiles, geometries and reactivities. This article introduces the concepts of molecular modeling and contains references for further reading. Photo 1 Ferrodoxin rendered from a Brookhaven PDB file Iron complexed to sulphur containing residues highlighted Computational chemistry/molecular modeling is the science (or art) of representing molecular structures numerically and simulating their behavior with the equations of quantum and classical physics. Computational chemistry programs allow scientists to generate and present molecular data including geometries (bond lengths, bond angles, torsion angles), energies (heat of formation, activation energy, etc.), electronic properties (moments, charges, ionization potential, electron affinity), spectroscopic properties (vibrational modes, chemical shifts) and bulk properties (volumes, surface areas, diffusion, viscosity, etc.). As with all models however, the chemist's intuition and training is necessary to interpret the results appropriately. Comparison to experimental data, where available, is also important to guide both laboratory and computational work.

40. The Babel Home Page A program designed to interconvert a number of file formats currently used in molecular modeling. http://smog.com/chem/babel/

Babel - A Molecular Structure Information Interchange Hub by Pat Walters and Matt Stahl Research Advisor Prof. Dan Dolata Artificial Intelligence in Chemistry Lab Department of Chemistry University of Arizona Tucson, AZ 85721 babel@mercury.aichem.arizona.edu Babel is a program designed to interconvert a number of file formats currently used in molecular modeling. The program is available for Unix (AIX, Ultrix, Sun-OS, Convex, SGI, Cray, Linux), MS-DOS, and on Macs running at least System 7.0. Babel is capable of assigning hybridization, bond order, and connectivity when these elements are not present in the input file. Supported Input Formats Supported Output Formats View the README file Download A Copy of Babel ... Register your copy of Babel Babel was designed so that new file formats could be easily added by the end user. The addition of a file format to Babel typically consists of merely creating the "reader" and/or "writer" routines and adding a few lines of code to the main program. For those interested in adding new file formats we have produced The Babel Developer's Guide

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