21. ArgusLab Molecular Modeling And Drug Docking Software A free molecular modeling program for Windows9x operating systems with 3Dbuilder, various ab initio calculation modules and simple molecular mechanics. http://www.planaria-software.com/

ArgusLab Computational Chemistry Software A molecular modeling, graphics, and drug design program ArgusLab is freely licensed Please use this citation for ArgusLab in your publications: ArgusLab 4.0.1 Mark A. Thompson mark@arguslab.com Planaria Software LLC, Seattle, WA http://www.arguslab.com [ Home ] Mark Thompson ArgusLab 4.0 Screen Shots Tutorials ... Company Email

22. Eximias Pharmaceutical Corporation Announces Results Of Phase III the firstmolecularly targeted products, using a highresolution crystal structure ofthe TS target and molecular modeling techniques to design http://tmsyn.wc.ask.com/r?t=an&s=hb&uid=24312681243126812&sid=343126

23. Rasmol In Neuem Gewand Der Bericht beschreibt, welche neuen Funktionen in Rasmol 2.6AB implementiert wurden und beleuchtet ein wenig die Bedeutung und Entstehung des Programms. Beispielgrafiken deuten die F¤higkeiten des Programmes an und eine Linkliste weist den Weg zu weiteren RasMolSites. http://www.dkfz-heidelberg.de/spec/linux/rasmol/

Molecular Modeling mit RasMol von Andreas Bohne und Henryette Roth Der Bericht beschreibt, welche neuen Funktionen in Rasmol 2.6AB implementiert wurden und beleuchtet ein wenig die Bedeutung und Entstehung des Programms. Wie alles begann Wie es weitergeht Beliebt, weil benutzbar xmkmf make setzt das Programm dann zusammen. Neben ein paar #ifdefs im Code resultierte diese Manko durch die Vordefinition der Farbtiefe mittels eines typedefs . Da Rasmol in Bezug auf die Abarbeitungsgeschwindigkeit optimal programmiert wurde, bedeutet dies im Klartext, dass Pointer verwendet werden, und je nach typedef Rasmol und die Browser macro1.scr Andere Ansichten Autoren myemail("a.bohne") chemical/x-ras Rasmol (PDB/Expasy) chemical/x-pdb Eine PDB-Datei application/x-rasmol Rasmol (PDB German Mirror) application/x-spt Rasmol-Script chemical/x-gaussian-cube Gaussian Cube chemical/x-gaussian-input Gaussian Input chemical/x-mdl-tgf MDL Scretch chemical/x-mdl-rxnfile MDL RXN chemical/x-mdl-molfile MDL MOL chemical/x-jcamp-dx JCAMP-DX chemical/x-mopac-input MOPAC-Input chemical/x-xyz XMOL xyz-file Links 1) Rasmol 2.6AB (nur Unix)

24. Tripos Online Producer of sybyl, a computational tool kit for molecular design and analysis. http://tmsyn.wc.ask.com/r?t=an&s=hb&uid=24312681243126812&sid=343126

25. TINKER Molecular Modeling Package A free molecular modeling package for molecular mechanics and dynamics, with some special features for biopolymers. Distributed as source code and as http://tmsyn.wc.ask.com/r?t=an&s=hb&uid=24312681243126812&sid=343126

26. Molecular Modeling molecular modeling. *molecular modeling. Protein Modeling PDB The Protein Data Bank, is hosted by the Research Collaboratory for Structural Bionformatics http://amanda.uams.edu/mm.html

Molecular Modeling Protein Modeling PDB The Protein Data Bank, is hosted by the Research Collaboratory for Structural Bionformatics use this resource for the latest crystal structures of proteins, nucleic acids and carbohydrates. QSAR Quantum Mechanics Example Molecules Links to related topics Send the BVC your Questions/Comments Underlined Topics are HotLinks Note: More to come.

27. 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 ... CTBP

28. 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 . If you have problems with Chime, the link below (World Index of Molecular Visualization Resources) should be helpful. Check the requirements link on the Chemscape Chime download page to determine which browsers are compatible with the latest version of 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 ... World Index of Molecular Visualization Resources Directions for Manipulating the Display Click on the name of the molecule to see the Chemscape Chime model of that molecule.

29. Periodic Table Of Computational Chemistry Basic This table lists and describes some well documented and validated parameter sets available for modeling each element by Molecular Mechanics and Quantum Mechanics molecular modeling methods. http://www.chamotlabs.com/Freebies/Table/parameters-table.html

Periodic Table of Parameters This Periodic Table of the Elements serves as a guide to summarize which Force Fields ( FF ), Semiempirical Parameterizations ( Semi ), and ab initio Basis Sets ( Basis ) have been developed and are documented and available for modeling each element. Group 8 Alkali Metals Noble Gases H FF Semi Basis Alkaline Earth Metals Main Group He FF Basis Li FF Semi Basis Be FF Semi Basis B FF Semi Basis C FF Semi Basis N FF Semi Basis O FF Semi Basis F FF Semi Basis Ne FF Basis Na FF Semi Basis Mg FF Semi Basis Early Transition Metals Late Transition Elements Al FF Semi Basis Si FF Semi Basis P FF Semi Basis S FF Semi Basis Cl FF Semi Basis Ar FF Basis K FF Semi Basis Ca FF Semi Basis Sc FF Semi Basis Ti FF Semi Basis V FF Semi Basis Cr FF Semi Basis Mn FF Semi Basis Fe FF Semi Basis Co FF Semi Basis Ni FF Semi Basis Cu FF Semi Basis Zn FF Semi Basis Ga FF Semi Basis Ge FF Semi Basis As FF Semi Basis Se FF Semi Basis Br FF Semi Basis Kr FF Basis Rb FF Basis Sr FF Basis Y FF Semi Basis Zr FF Semi Basis Nb FF Semi Basis Mo FF Semi Basis Tc FF Semi Basis Ru FF Semi Basis Rh FF Semi Basis Pd FF Semi Basis Ag FF Semi Basis Cd FF Semi Basis In FF Semi Basis Sn FF Semi Basis Sb FF Semi Basis Te FF Semi Basis I FF Semi Basis Xe FF Basis Cs FF Basis Ba FF Basis Hf FF Semi Basis Ta FF Semi Basis W FF Semi Basis Re FF Basis Os FF Basis Ir FF Basis Pt FF Basis Au FF Basis Hg FF Semi Basis Tl FF Semi Basis Pb FF Semi Basis Bi FF Semi Basis Po FF Basis At FF Basis Rn Basis Fr Basis Ra Basis Rf Ha Sg Ns Hs Mt Noble Metals Lanthanide Series La FF Basis Ce Basis Pr Basis Nd FF Basis Pm Basis Sm Basis Eu FF Basis Gd FF Semi Basis Tb FF Basis Dy Basis Ho FF Basis Er Basis Tm Basis Yb FF Basis Lu FF Basis Actinide Series Ac Basis Th Basis Pa Basis U Basis Np Basis Pu FF Basis Am Cm Bk Cf Es Fm Md No Lr Return Backup level to Modeling Reference Page Link to

30. 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 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.

31. Molecular Modeling Lernsystem molecular modeling der Arbeitsgruppe von Prof. Dr. Rainer Herges am Institut f¼r Organische Chemie der Universit¤t Kiel. http://scholle.oc.uni-kiel.de/herges/modeling/gliederung.html

Lernsystem Molecular Modeling START Autoren: Lehrveranstaltung: Vorlesung Molecular Modeling Erstelldatum: seit Oktober 1998 Erstellt im Rahmen des BMBF-Leitprojekts "Vernetztes Studium - Chemie" sponsored by

32. Laboratory For Computational And Applied Chemistry Molecular and engineering catalysis. molecular modeling and drug design. http://lcac.ku.ac.th/

33. Molecular Modelling Toolkit The Molecular Modelling Toolkit (MMTK) is a program library for molecular It emphasizes Python programming aspects rather than molecular modeling. http://starship.python.net/crew/hinsen/mmtk.html

The Molecular Modelling Toolkit European mirror This page describes an older version of MMTK which is still available for compatibility reasons. See the new MMTK home page for the current version. 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 program in a PTUI window using VMD for visualization This software is MMTK is developed in and around Python , a high-level object-oriented general-purpose programming language. In fact, MMTK consists of nothing more than a collection of Python modules, most of which written in Python itself, with only a small time-critical part (e.g. energy evaluation) written in C. MMTK applications are Python programs that make use of these modules. Python was chosen because it allows rapid code development and testing, while providing a very convenient C interface for dealing with time-critical calculations. MMTK is based on an object-oriented model of molecular systems. A system is made up of molecules, complexes, and atoms, all of which are defined in a central database of definition files, which themselves are (very simple) Python programs. A molecule, for example, is defined in terms of atoms, functional groups, bonds, force field parameters etc. It is possible to introduce specialized versions of these objects; for example, MMTK has special support for proteins, which are basically chemical complexes, but can be handled in terms of peptide chains, residues, sidechains etc.

34. 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!

35. Uwmml.pharmacy.wisc.edu/ link.springerny.com/link/service/journals/00894/ molecular modeling of Proteinsmolecular modeling of proteins and mathematical prediction of protein structure Mathematics and Molecules (movies and images on molecular modeling) http://uwmml.pharmacy.wisc.edu/

36. Center For Molecular Modeling Supplier of molecular modeling resources and expertise to the NIH research community. Development and application of theoretical and computational http://cmm.cit.nih.gov/modeling/

37. Computational Chemistry And Molecular Modeling Service f¼r die Berechnung von Molek¼lstrukturen und Molek¼leigenschaften sowie Erstellung von Molek¼lbildern. Es werden Beispiele gezeigt und die F¤higkeiten der verwendeten Programme erl¤utert. http://www.comchem.de/

Home deutsch english deutsch ... 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

38. An Introduction To Molecular Modeling This article introduces the concepts of molecular modeling and contains references Computational chemistry/molecular modeling is the science (or art) of 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.

39. NetSci: Chemistry Display Software NetSci Software Listing for Display of Data From molecular modeling and Computer Assisted Drug Design. http://www.netsci.org/Resources/Software/Modeling/Viewers/

Welcome to NetSci's List of Molecular Display and Visualization Software Notice: The Software Section of NetSci is accessed by hundreds of scientists every week. Our goal is to make this resource as comprehensive as possible. If your software program is not included, please send e-mail with a brief description, the categories under which your program should appear, the platforms supported, and contact information. For programs currently listed in NetSci , please check the table and description and notify us of any changes or additions. - A, B, C - CACTUS: a universal, networked visual chemistry data manager for computation, analysis and visualization of arbitrary chemical information. ChemCraft is graphics software for the visualization of molecular structures, vibrational modes, molecular orbitals and other properties from log files produced by GAMESS, Gaussian ab initio packages. chemVISION : Reads in 3D molecular structure files in many formats, renders them in a variety of styles, and manipulates them in full 3D space. You can also query the structure interactively to identify chemical, geometric, and file content information, displaying the results with color-coded labels. Use the ZOOMING magnifying glass to highlight and enlarge portions of complex structures. Transfer 3D graphics into virtually all graphics-capable Windows and DOS programs. Available from Molecular Arts Corporation Hanover Corporate Centre 1532 East Katella Avenue, Suite 1000

40. 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

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