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         Molecular Modeling:     more books (100)
  1. Molecular Modeling Basics by Jan H. Jensen, 2010-04-26
  2. Molecular Modeling and Simulation: An Interdisciplinary Guide (Interdisciplinary Applied Mathematics) by Tamar Schlick, 2010-08-25
  3. Molecular Modeling: Basic Principles and Applications by Hans-Dieter Höltje, Wolfgang Sippl, et all 2008-03-18
  4. Molecular Modeling of Proteins (Methods in Molecular Biology)
  5. Molecular Modeling and Simulation by Tamar Schlick, 2002-08-19
  6. Molecular Visions Organic Model Kit with Molecular Modeling Handbook by T. W. Graham Solomons, 1999-08-06
  7. Modeling Dynamic Phenomena in Molecular and Cellular Biology by Lee A. Segel, 1984-03-30
  8. Molecular Modeling in Heavy Hydrocarbon Conversions (Chemical Industries) by Michael T. Klein, Gang Hou, et all 2005-09-28
  9. Introduction to Theoretical Organic Chemistry and Molecular Modeling by William B. Smith, 1996-03
  10. Molecular Gas Dynamics: Theory, Techniques, and Applications (Modeling and Simulation in Science, Engineering and Technology) by Yoshio Sone, 2006-12-12
  11. QSAR and Molecular Modeling Studies in Heterocyclic Drugs II (Topics in Heterocyclic Chemistry) (v. 2)
  12. Computational Chemistry and Molecular Modeling: Principles and Applications by K. I. Ramachandran, Gopakumar Deepa, et all 2010-11-30
  13. Molecular Visions Organic Modeling Kit
  14. Molecular Modeling and Theory in Chemical Engineering, Volume 28 (Advances in Chemical Engineering) (Vol 28) by James Wei, Morton M. Denn, et all 2001-12-24

1. Center For Molecular Modeling
Center for molecular modeling Several tutorials related to molecular modeling, directory of software Category Science Chemistry Computational......

2. Accelrys - Formerly MSI
Develops modeling and visualization software for researchers in materials science and the life sciences. Download trial versions. the combination of a number of leading names in the molecular modeling industry to be the leading company in the area.
@import url(/styles/about2002.css); /*IE and NN6x styles*/ CORPORATE OVERVIEW


About Accelrys
Corporate overview

News room


... About Accelrys
Molecular Simulations Inc. is now Accelrys
Molecular Simulations Inc. (MSI) was renamed Accelrys Inc. on June 1, 2001. Accelrys, the leader in simulation and informatics software for the pharmaceutical and chemicals process industries, was created from the combination of MSI, Oxford Molecular GCG , and Synopsys MSI was the leading provider of simulation and modeling tools for drug discovery and chemical development. For full details of our simulation and modeling products see:
Molecular Simulations History
Founded in 1984, MSI grew through the combination of a number of leading names in the molecular modeling industry to be the leading company in the area. MSI incorporated companies including BioDesign, Biosym, Polygen, Cambridge Molecular Design, and BioCAD. Many of these companies emerged from, or developed close links with, leading Universities Harvard, Cambridge, York and the California Institute of Technology are examples. The company's product-line included the best-known names in modeling for drug discovery: Insight, QUANTA/CHARMm, and Cerius2 as well as the unique tools for materials science modeling in the Cerius2 software environment, now available within Materials Studio.

3. MathMol
Instructional materials related to the use of molecular modeling in the undergraduate chemistry curriculum molecular modeling was introduced at Lebanon Valley College through support by the College and a $49 188 grant titled
MathMol (Mathematics and Molecules) is designed to serve as an introductory starting point for those interested in the field of molecular modeling.
Quick Tour
What is molecular modeling? Why is molecular modeling important? Why the math in MathMol? This link contains numerous images and MPEG files.
More about MathMol
Where is MathMol being developed? What are the objectives of MathMol? Why is this site so important to education?
Public Domain Software
What is the latest public domain software available for PC's, Mac's and Unix workstations? Where can this software be obtained? (Software found here can be used to read all the files in the the MathMol Library.)
Library of 3-D Molecular Structures
The MathMol Library of Molecular Structures contains GIF, PDB and 3-D (VRML) files of molecules that are found in most introductory biology and chemistry textbooks (e.g., water and ice, carbon, hydrocarbons, amino acids, nucleotides, lipids, sugars, photosynthetic pigments and drugs).
Water Module
This site contains background information on water and ice, MPEG files of computer simulations of water molecules in motion, and water and ice databases.

4. Journal Of Molecular Modeling
German journal presents papers on computeraided modeling, using color, and 3D images. View the table of contents and abstracts. Journal of molecular modeling. Probably the most successful electronic journal in chemistry
Journal of Molecular Modeling
Probably the most successful electronic journal in chemistry
You are looking for a good scientific journal on the molecular modeling field?
You want brand new information about todays current topics?
You expect an electronic journal to be a serious publication?
You think that color graphics and 3D-data files should be part of an innovative publication?
But you also like classical printed journals?
Then give the Journal of Molecular Modeling a try.
Don't miss to have a look at our list of abstracts of published papers and feel free to get your personal copy of selected papers. The Journal of Molecular Modeling is the first journal in chemistry to offer network, print based and CD-ROM editions. The Journal is fully citeable with CAS-abstract, ISI-entry and ISSN (0948-5023). Dont't hesitate:
here is your opportunity to compare three different presentation technologies and to get insight into the impact the WWW is going to have upon your daily scientific work. If you want to keep pace with leading edge research in the field of molecular modeling and experience the rapid development of scientific publishing the Journal of Molecular Modeling is a must for you.

5. Molecular Modeling Home Page
Links to information on chemical structures, graphics, slide shows, and modeling experiments.
You should go to a

6. NCBI Structure Group
MMDB, the molecular modeling Database, contains experimentally determined biopolymer structures obtained from the
PubMed BLAST OMIM Taxonomy ... Entrez Structure Search Entrez PubMed Protein Nucleotide Structure Conserved Domains 3D-Domains Genome PopSet Taxonomy OMIM for
What's New?
MMDB NCBI's structure database 3D-structure viewer CDD Conserved Domain Database VAST Structure comparisons VAST Search Submit structure database searches PDBeast Taxonomy in MMDB Research Research topics and staff
The NCBI Structure Group .. maintains MMDB, a database of macromolecular 3D structures, as well as tools for their visualization and comparative analysis. MMDB, the Molecular Modeling Database, contains experimentally determined biopolymer structures obtained from the Protein Data Bank ( PDB Structure highlights Semi-automated annotation of taxonomic sources in MMDB has resulted in taxonomy links for about 38.000 molecules with 3D structure information. This allows for organism-based queries in Entrez's structure division. More..
Text searches in MMDB (use the search toolbar at the top of this page) will yield Structure Query pages, providing access to entries which matched the keywords.

7. Springer LINK: Journal Of Molecular Modeling - Contents
Molecular, protein, peptide and drug design, computational modeling, molecular mechanics/dynamics Category Science Biology Publications Journals Fulltext J......Springer LINK, Forum Springer Journal of molecular modeling. ForumWhat's New Search Orders Helpdesk Up. Online First 2003 9/1, 2002
TM Example of a published paper in HTML and PDF format Example of a protein structure available in the journal
Last update: 14 March 2003
LINK Helpdesk

8. Representation Models In Molecular Graphics
Concepts in Science through molecular modeling Activities for Students and Teachers Concepts in Mathematics through molecular modeling
The Representation of Molecular Models
Rendering Techniques
Part I
The Representation of Molecular Models
Part II
Rendering Techniques.
This page has been accessed times since the 1rst January 1995 (after six months accessibilty) thank you very much for your interest.
Part I
1. Structural models.
1.1 The wire-frame model.
1.3 The space-filling model.
1.4 The stick model. ...
7. Future.
Part II
1. Shading techniques.
1.1 Classical illumination model of a polygon mesh
1.2 Shading :
1.2.1 Constant shading. ...
Chemistry on the Internet: The best of the Web 1995!
Other local servers
Same document in French
Have a look at the public defense of my Ph. D
Crystal in Europe
University of Geneva
FTP access to the SGI file format images of the current document
New All the gif images used in theses documents!
Table 1
Table 2
Servers list dealing with chemistry ... Bridge BCC Group of Professor J. Weber, Department of Physical Chemistry, University of Geneva 30, quai Ernest Ansermet CH-1211 Geneva 4 tél.: +4122 702 65 32

9. 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.
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
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)

10. Welcome To Hypercube, Inc.
Producer of HyperChem, a molecular modeling package for windows and HyperNMR, a program for prediction of onedimensional NMR spectra.
What's New? Hardware Lock Licensing for Release 7 P urchase a Product Online! Products, Free Software and Demos Novell Server? Please Read This Page First Product Updates ... And the Winner of the Third Annual Hypercube Classic Golf Tournament is.... The tournament was held at the Sanibel Symposium, Wednesday, February 26, 2003 Special Upgrade Pricing for Release 5 and Lower! Special Pricing Extended Until March 31, 2003!! Upgrade from Release 5, 4, 4.5, 3, 2 or 1 for only $495.00 academic, $860.00 commercial! Contact or one of our Authorized Dealers today! Visit Our Scripts Page Did you know that HyperChem is scriptable? We are soliciting script contributions to post on our new Scripts Page! HyperChem Now Networks With Pocket HyperChem Pocket HyperChem Release 1.1 and HyperChem Release 7.01 communicate! Update to Release 7.01

11. Form For PDB Query
Search engine for visualizing 3D biomolecular models.
Welcome to the NIH Molecules R US Utililty . This facility combines a full text search of the PDB database with a FORM interface to customize the format ( TEXT, IMAGE, INTERACTIVE ) of the selected structure. Please read the instructions! Initiate a PDB query. What's NEW

12. Introduction To Molecular Modeling
Read an indepth introduction to molecular modelling with diagrams, equations, and notes. What is molecular modeling? molecular modeling, also known as molecular mechanics, is a method to calculate the
What is Molecular Modeling?
In a very crude sense molecular modeling treats a molecule as a collection of wieghts connected with springs, where the weights represent the nuclei and the springs represent the bonds.
A force field is used to calculate the energy and geometry of a molecule. It is a collection of atom types (to define the atoms in a molecule), parameters (for bond lengths, bond angles, etc.) and equations (to calculate the energy of a molecule). In a force field a given element may have several atom types. For example, ethylbenzene contains both sp -hybridized carbons and aromatic carbons. sp -Hybridized carbons have a tetrahedral bonding geomtery, while aromatic carbons have a trigonal bonding geometry. The C-C bond in the ethyl group differs from a C-C bond in the phenyl ring, and the C-C bond between the phenyl ring and the ethyl group differs from all other C-C bonds in ethylbenzene. The force field contains parameters for these different types of bonds. Some of these parameters are given below. The total energy of a molecule is divided into several parts called force potentials, or potential energy equations. Force potentials are calculated independently, and summed to give the total energy of the molecule. Examples of force potentials are the equations for the energies associated with bond stretching, bond bending, torsional strain and van der Waals interactions. These equations define the potential energy surface of a molecule.

13. CAChe Group/Fujitsu | Chemistry Products
Experimental chemists use CAChe to view and predict 3D molecular structure, to predict properties and to analyze the relationship between structure and properties or structure and reactivity. CAChe is a tool for medicinal, polymer, process and synthetic chemists.
CAChe Group is a leading provider of computer-aided chemistry software and services for predicting molecular structure, properties, spectra, reactions, thermodynamics, and kinetics.
What's new

14. TINKER Molecular Modeling Package
A free molecular modeling package for molecular mechanics and dynamics, with some special features Category Science Chemistry Software Biomolecular...... The TINKER molecular modeling software is a complete and general package for molecularmechanics and dynamics, with some special features for biopolymers.
TINKER Home Page
TINKER - Software Tools for Molecular Design
Current Major Version: TINKER 3.9 Major Release Date: June 2001 Last Minor Revision: December 20, 2001
    The TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. TINKER has the ability to use any of several common parameter sets, such as AMBER ff94 and ff96, CHARMM 19 and 27, MM2(1991), MM3(2000), OPLS-UA and OPLS-AA. Parameter sets for other standard force fields such as UFF, ENCAD and MM4 are under consideration. In addition, we are actively developing our own AMOEBA force field based upon polarizable atomic multipole electrostatics.
Current Release
    The curent release, version 3.9 contains the following new features and updates from version 3.8: (1) improved nucleic acid building from sequence and automated conversion of nucleic acid PDB files to and from the TINKER format, (2) a new rigid body dynamics facility, (3) ability to handle infinite polymer lattices such as diamond and graphite, (4) treatment of intramolecular polarization via the Thole method, (5) a new utility program to compute molecular polarization, (6) an improved RasMol-based viewer that accepts TINKER coordinate files, allows atom selection, etc., (6) an optional Andersen stochastic collision thermostat for MD, (7) where appropriate TINKER programs such as ANALYZE, SUPERPOSE and SPACEFILL accept multiple coordinate set "archive" files as input, (8) updated parameter sets for various of the supported force fields.

15. Center For Molecular Modeling

16. Molecular Modelling
Summary of lecture course which aims to introduce the hierarchy of computational modeling methods used in Organic Chemistry. Links to background and supplemental information.
c) Henry Rzepa. 1995-2003.

17. Springer LINK: Journal Of Molecular Modeling
The Journal of molecular modeling is the perfect medium for publishing of researchresults produced by frequent and sophisticated use of computational methods
Editor-in-Chief: Tim Clark Would you like to automatically receive every new table of contents of Journal of Molecular Modeling ? Then register with our free-of-charge mail service LINK Alert by checking the appropriate box(es) and enter your email address here: Online First Articles only
Printed issues only You will receive confirmation via email.
ISSN: 0948-5023

18. B Home Page
B (formerly known as Biomer) is a Javabased molecular modeling program for small organic molecules and biopolymers. Supports nucleic acids (DNA/RNA), polypeptides, polysaccharides, the AMBER force field, geometry optimization, simulated annealing. Exports jpeg, gif, and ppm images.

19. Molecular Modeling Heidelberg
Category Science Chemistry Computational
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20. 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.
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 To influence and advise government departments and agencies
Forthcoming Events Click here to search the chemsoc Conferences and Events database for meetings organised by the Molecular Modelling Group Submit details of a Group meeting to the chemsoc Conferences and Events database Annual Events

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