41. Norgwyn Montgomery Software Inc. Molecular Modeling Software NGMSI sells software for 3D molecular modeling, chemical database creation and manipulation, 2-D publication quality drawing, calculation of over 100 physical properties from structure, automatic chemical internet database generation, and QSAR and QSPR analysis as well as chemical databases. http://www.norgwyn.com

NGMSI Norgwyn Montgomery Software Inc. Practical, affordable software for working chemists What's New NGMSI creates and markets molecular modeling and chemical database software. Our programs were developed and tested by industrial research chemists. This software is primarily used in the design of new compounds, and in formulation optimization. Founded in 1995, NGMSI sells a full line of molecular modeling, chemical database, chemical drawing and traditional QSAR tools. We have formed an alliance with Pyramid Learning, the makers of ChemSite, to further our goal of creating a complete line of chemical software that can supply all the basic needs of the research chemist. We are dedicated to bringing to our customers, quality programs at a reasonable cost. NGMSI will provide training in the field of molecular design. We can bring experienced industrial researchers to your site for seminars or complete courses in molecular design which includes (but is not limited to) use of our software. We do contract programming in the areas of our expertise.

42. Molecular Modeling Links C4, Free molecular modeling Software. RasMol Chime is based on a molecular modeling program called RasMol written by Roger Sayle. http://c4.cabrillo.cc.ca.us/links.html

Free Molecular Modeling Software RasMol Chime is based on a molecular modeling program called RasMol written by Roger Sayle. Rasmol is driven by a relatively simple but powerful scripting and command language. Chime has inherited many features from its parent program. Chime has many new features that Rasmol lacks, but Rasmol is available for more platforms - Unix and Linux in addition to Windows and MacOS. Like Chime, it is free. Download Marco Molinari of UC Berkeley has developed UCB-Rasmol which adds a graphical interface for model manipulation tools. UCB-Rasmol can also load up to five molecules at a time and move them independently. However, it does not work well with stereo or with most Rasmol scripts. Download ChemOffice This commercial molecular modeling package is available from CambridgeSoft Corporation. The free version is called CS ChemOffice Net . Although limited in functionality, this package includes viewers that can be used to view both 2D and 3D molecular structures. Download How to Find Sites Using Chime Chime Resources by Eric Martz This is the premier site for anyone wanting to learn how to use Chime. In addition to maintaining this site and the

43. Home 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/

molecular modeling, and pharmaceutical industries. See our poster on ArgusDock, Planaria's new drug docking program, at the American Chemical Society meeting in Philadelphia, August 22-26. We also distribute the popular ArgusLab molecular modeling program, used by thousands in industry and education around the world. ArgusLab is free for qualified academic students, and faculty. Contact Information Planaria PO Box 55207 Seattle, WA 98155 FAX: 206-440-3305 General Information: info@planaria-software.com Sales: sales@planaria-software.com

44. C4: Computers In Chemistry At Cabrillo College compatible browser. molecular modeling Links Recommended internet resources for molecular modeling information and models. Molecular http://c4.cabrillo.cc.ca.us/

WebMO Demonstration: Access and Instructions Instructions and guest access to the C4 Consortium installation of WebMO Pro. Molecular Library 2.0 A set of over 400 molecular models, plus three Java-enhanced viewers: the MonoViewer, DuoViewer, and MacroViewer. The old version is still available as well. A Chime Tutorial Includes problem set. Chime Student Exercises Sets of chemistry problems incorporating Chime models. Assigned as student homework in 5 different undergraduate courses. Insulin: Structure of a Protein Hormone A Chime-based tutorial examining the structure of the protein insulin. Chime Toolbox A package of Java applets for educational developers to use in making their own Chime web pages. Includes online documentation and examples! Download C4 Software You can download our completed tutorials or other projects here, for use offline. About the C4 Project We are developing visualization and instructional software for chemistry instructors and students. Chime Help Center How to get set up with Chime and a compatible browser.

45. SpringerLink - Publication Molecular, protein, peptide and drug design, computational modeling, molecular mechanics/dynamics in the fields of Life Sciences and Chemistry. http://link.springer.de/link/service/journals/00894/tocs.htm

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...

46. Molecular Modeling Click here for books on Molecular Structures. Cool molecular modeling Sites. Chemical Computing Group Inc. is a leading worldwide http://www.ahpcc.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).

47. CACHE Molecular Modeling CACHE. molecular modeling Task Force. The courses; Conference Foundations of molecular modeling and Simulation FOMMS 2000, FOMMS 2003; http://zeolites.cqe.nwu.edu/Cache/

CACHE Molecular Modeling Task Force The CACHE Molecular Modeling Task Force (MMTF) was formed to promote the use and distribution of molecular modeling tools in the chemical engineering curriculum. Current Activities Web-based textbook on molecular modeling and simulation Web-based modules to introduce molecular modeling concepts into existing undergraduate chemical engineering courses Conference: Foundations of Molecular Modeling and Simulation: FOMMS 2000 FOMMS 2003 PowerPoint presentation of Task Force activities. Presented by Dave Kofke at the 2000 ASEE Meeting in St. Louis. Task Force Members Arup Chakraborty , University of California, Berkeley Ariel A. Chialvo , University of Tennessee/Oak Ridge National Laboratory Henry D. Cochran, Jr. , Oak Ridge National Laboratory Peter T. Cummings , Vanderbilt University/Oak Ridge National Laboratory Juan J. DePablo , University of Wisconsin, Madison James Ely , Colorado School of Mines Kristen Fichthorn , Pennsylvania State University David Ford David A. Kofke

48. Molecular Modeling Reference Quick Reference Guide to Computational Chemistry Acronyms, Methods, Parameters, Accuracy, and Software. Compliments of CHAMOT LABS, INC. http://www.chamotlabs.com/Freebies/ModelRef.html

Quick Reference Guide to Computational Chemistry Acronyms, Methods, Parameters, Accuracy, and Software Compliments of: CHAMOT LABS, INC. Chemical Research and Consulting METHODS: Geometry OPTIMIZATION TERMS: SOFTWARE: PARAMETERIZATIONS: by Element (Grain of Salt) The information above has been collected from various published results, documentation, and personal experience. (Accuracies are averages of typical literature comparisons.) This list is updated as information comes to my attention and as time allows, but as rapidly as methods evolve (and companies merge), some info is no doubt out of date and/or incomplete. Consequently, these compilations are meant more as an aid to jog one's memory on keywords and capabilities, rather than as a complete and authoritative reference. Return Link to Chamot Labs Home Page 3/13/03 Ernie Chamot / Chamot Labs /

49. Geometry In Action: Molecular Modeling molecular modeling. Connections have been growing recently between the molecular modeling community and the computational geometry. http://www.ics.uci.edu/~eppstein/gina/molmod.html

Molecular Modeling Connections have been growing recently between the molecular modeling community and the computational geometry. Many questions in molecular modeling can be understood geometrically in terms of arrangements of spheres in three dimensions. Problems include computing properties of such arrangements such as their volume and topology, testing intersections and collisions between molecules, finding offset surfaces (related to questions of accessability of molecule subregions to solvents such as water), data structures for computing interatomic forces and performing molecular dynamics simulations, and computer graphics algorithms for rendering molecular models accurately and efficiently (taking advantage of their special geometric structure). Classical molecular modeling has dealt with biological molecules which generally have a tree-like structure, but applications to nanotechnology require dealing with more complicated diamond-like structures; it is unclear to what extent this affects the relevant algorithms. Algorithms for finding the axis of a helix , J. Christopher, R. Swanson, and T. Baldwin. The authors use this problem to detect structural patterns in protein molecules.

50. Glactone Molecular Modeling Glactone s molecular modeling Exercises. We are pleased to offer two sets of molecular modeling exercises. A short introduction to molecular modeling. http://chemistry.gsu.edu/glactone/modeling/modeling.html

Glactone's Molecular Modeling Exercises We are pleased to offer two sets of molecular modeling exercises. One set is designed for undergraduate general and organic chemistry students, and the other set is designed for advanced undergradate to graduate level organic and physical organic students. While the modeling exercises in these pages are intended to be used with any molecular modeling package, they have been tested with only PCMODEL. Consequently, hints and instructions on how to actually draw the structures and perform the caculations are specific to PCMODEL. PCMODEL is a product of Serena Software E TOTAL = E STRETCH + E BEND + E S-B + E TORSION + E vdW Undergraduate Molecular Modeling Exercises Graduate Molecular Modeling Exercises A short introduction to molecular modeling Back to Glactone

51. Introduction To Molecular Modeling What is molecular modeling? Molecular out. Problems, suggestions, comments? webmaster@wolf.gsu.edu. Back to Glactone molecular modeling. http://chemistry.gsu.edu/glactone/modeling/MMintro.html

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. E TOTAL = E STRETCH + E BEND + E S-B + E

52. Biosiris - Votre Partenaire En Modélisation Moléculaire Bioinformatics company specialising in molecular modeling. http://www.biosiris.com/en/index.html

change the language : Fr En search go Home Company profile presentation ... Contact us Your partner in molecular modeling Biosiris is active in the molecular modeling field. It aims to collaborate with pharmaceutical, cosmetic, biotechnological and food companies in developing research activities. Its specificity is the study of structure-activity relationships of proteins and drugs in membranes and water. Biosiris’ skill is based on scientific expertise and an in-house technology platform.

53. COSMOS Home Page Der Hersteller von Software f¼r molecular modeling, NMRSpektroskopie und Kristallographie informiert ¼ber die Produkte und bietet Demos und Molek¼l-Viewer zum Download an. http://www.cosmos-software.de/

Wir über uns Produkte Forschung Galerie ... Email Your browser don´t support frames! Please install a new version. You can work without frames. Please select : About us Products Science Galery ... Email

54. Molecular Modeling Pro Interactive molecular modeling and drawing software to build, study, and present molecules, including crystallography. molecular modeling Pro TM http://www.chemsw.com/13052.htm

Molecular Modeling Pro TM This advanced molecular modeling program is the result of over 20 years of development at a major chemical company. Developed first for main-frame computers, it now is available for Windows. Molecular Modeling Pro has most of the advanced features available in expensive PC-based molecular modeling programs and more! It probably has the most physical property calculations from structure of any program sold for the PC. Molecules are easily constructed with your mouse and pull-down menus. The program can display molecules as wire frame, ball and stick, spheres and dot surface models. Up to 5000 atoms and 40 molecules can be displayed on the screen at a time and minimized using the MOLY minimizer. In addition, for those with WIN 95/98 or WIN NT an MM2 minimizer and minimization with MOPAC 6.0 is also included. The AMBER minimizer in ChemSite Pro is also accessible from within MMP (requires ChemSite Pro ). Routines for conformational analysis are also included.

55. PPL Contents And Abstracts Publishes on all aspects of protein and peptide research, including structural studies, recombinant expression, function, synthesis, enzymology, immunology, molecular modeling, and drug design. http://www.bentham.org/ppl/pplconts.html

[Back to Home Page] [Instructions for Authors] Contents and Abstracts Follow the links to view the contents and abstracts of the listed issues. Protein and Peptide Letters, Volume 11, 2004 [Volume 11, Number 2] [Volume 11, Number 1] Protein and Peptide Letters, Volume 10, 2003 [Volume 10, Number 6] [Volume 10, Number 5] [Volume 10, Number 4] [Volume 10, Number 3] ... [Volume 10, Number 1] Protein and Peptide Letters, Volume 9, 2002 [Volume 9, Number 6] [Volume 9, Number 5] [Volume 9, Number 4] [Volume 9, Number 3] ... [Volume 9, Number 1] Protein and Peptide Letters, Volume 8, 2001 [Volume 8, Number 6] [Volume 8, Number 5] [Volume 8, Number 4] [Volume 8, Number 3] ... [Volume 8, Number 1] Protein and Peptide Letters, Volume 7, 2000 [Volume 7, Number 6] [Volume 7, Number 5] [Volume 7, Number 4] [Volume 7, Number 3] ... [Volume 7, Number 1] Protein and Peptide Letters, Volume 6, 1999 [Volume 6, Number 6] [Volume 6, Number 5] [Volume 6, Number 4] [Volume 6, Number 3] ... [Volume 6, Number 1] Protein and Peptide Letters, Volume 5, 1998 [Volume 5, Number 6]

56. Chapter 5. Quantum Chemistry In Molecular Modeling Chapter 5. Quantum chemistry in molecular modeling. 5.1 Why use Quantum Chemical methods ? Quantumchemical methods are more general http://www.caos.kun.nl/~borkent/compcourse/fred/ch5.html

Chapter 5. Quantum chemistry in Molecular Modeling 5.1 Why use Quantum Chemical methods ? Quantum-chemical methods are more general than empirical methods The recipe for the calculation of the electronic wavefunction 5.3 Hartree-Fock SCF theory Part a: The independent particle approximation Part b :Molecular Orbitals, basis sets 5.4 Limitations of the HF method; Electron correlation CI, MP2 and MCSCF 5.5 Energy calculations Conversion of absolute energies to heats of formation Isodesmic reactions 5.6 Quality of ab initio results Performance of low-level methods for organic molecules 5.7 Semi-empirical quantum chemistry Further approximations and introduction of empirical parameters 5.8 Quality of semi-empirical results Low-level ab initio methods are usually better, but much more time-consuming 5.9 Solvation The medium can be represented as a dielectric continuum 5.10 Atomic charges Not a physical concept ! Several methods exist for attributing charge to individual atoms 5.1 Why use Quantum Chemical methods ? Many aspects of molecular structure and dynamics can be modeled using classical methods in the form of molecular mechanics and dynamics. The classical force field is based on empirical results, averaged over a large number of molecules. Because of this extensive averaging, the results can be good for standard systems, but there are many important questions in chemistry that can not at all be addressed by means of this empirical approach. If one wants to know more than just structure or other properties that are derived only from the potential energy surface, in particular properties that depend directly on the electron density distribution, one has to resort to a more fundamental and general approach : quantum chemistry. The same holds for all non-standard cases for which molecular mechanics is simply not applicable.

57. Molmodl.html molecular modeling, Viewing and Drawing. Intoduction to molecular modeling (A thorough mathematical and conceptual treatment from Georgia State University). http://ep.llnl.gov/msds/orgchem/molmodl.html

Molecular Modeling, Viewing and Drawing Useful Resources General Background Lists/Pointers Programs/Applications Most Useful Resources: RasMol FREE , easy to use desktop Molecular Viewer , widely adopted, many sites and structures; Shallow learning curve, Instructions, Complete documentation, Downloadable: Windows, Mac and UNIX , ver. 2.5 and 2.6 Beta) SEE: Graphics and Animations Data Bases for examples. RasMol Homepage University of Massachusettes RasMol Home page , downloading site, extensive information and examples. Also, information on Chemscape, a Chime plug-in for On-Line viewing. RasMol applied to VSEPR UC Berkeley examples using RasMol to examine VSEPR models. RasMol used in illustrating Amino Acids Structures of the common twenty amino acids for viewing. RasMol Introductory Chemistry Assignment Molecular Visualizations and the Chemistry of Smell UC Berkeley Tutorial: Using RasMol Scripts with Chime How to use Chime and RasMol in a document. MDL Chemscape Chime FREE Plug-in Viewer: Windows and Mac. SEE Topics: Graphics and Animations Data Bases for additional examples.)

58. Interprobe Chemical Services - Molecular Modelling Offers a variety chemical software focusing on molecular modeling, visualization and analysis of proteins/peptides. Free for academic use. http://interchem.chem.strath.ac.uk/inter/interprobe.html

INTERPROBE CHEMICAL SERVICES INTERPROBE CHEMICAL SERVICES provides quality computer software for the handling of chemical structure information. It had a forerunner in INTERPROBE CHEMICAL SERVICES Ltd; a Limited Liability Company set up by the University of Strathclyde in 1985 to market the original version of INTERCHEM. There were two directors of this company; - Dr. Robin Breckenridge and Dr. Peter Bladon. Both were employed by the University at the time . Subsequently Robin left the University to go and work first for CNRS at Gif-sur-Yvette in France, and later at Sandoz Pharma in Basel Switzerland. The limted company INTERPROBE was wound up in 1990. In 1991 Peter Bladon retired from the University although he still retains an honorary appointment. Collaboration continued between the two directors of the former company , and the result was the new version of INTERCHEM, a version entirely rewritten specifically for Silicon Graphics Inc. workstations. When it came to distributing this program the name INTERPROBE CHEMICAL SERVICES was retained for the "sole trader" organisation . Operating in this way means that overhead expenses are kept to a minimum and so the price of the software can be kept low. More background information on INTERPROBE Several programs are available at present: INTERCHEM This is a general-purpose molecular modelling program which uses the graphics facilities of Silicon Graphics workstations for display of structures, and for molecular-mechanics and quantum-chemistry calculations. It is suited to calculations on both low- and high-molecular weight systems, and has many features incorporated for treating protein and enzyme structures. It is the cornerstone software to which many of the other programs are linked.

59. MoluCAD MoluCAD a molecular modeling and visualization tool. MoluCAD Educational software for chemistry students.MoluCAD is a fullfeatured http://www.kinematics.com/molucad/

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, "

60. Ilya Balabin Works on largescale computational biochemistry and biophysics, bioinformatics, molecular modeling and design, and molecular machines at UIUC. http://www.ks.uiuc.edu/~ilya/

Overview Research Development Dissemination ... Theoretical and Computational Biophysics Group Ilya Balabin NIH Resource for Macromolecular Modeling and Bioinformatics Research Interests Current Research Representative Publications ... Contact Information Research Interests Molecular modeling and design, molecular motors Biomolecular electronics and engineering Nanoscale materials, structures, and devices Development of methods and software Current Research Energy Conversion in F-ATPases Biopolymer Imaging Representative Publications A. Aksimentiev, I. A. Balabin , R. H. Fillingame, and K. Schulten. Insights into the Molecular Mechanisms of F o ATP Synthase.To appear in Biophys. J. M. L. Tan, I. A. Balabin , and J. N. Onuchic. Dynamics of Electron Transfer Pathways in Cytochrome c Oxidase. To appear in Biophys. J. I. A. Balabin and J. N. Onuchic. Dynamically Controlled Protein Tunneling Paths in Photosynthetic Reaction Centers. Science PDF I. A. Balabin and J. N. Onuchic. New Framework for Electron Transfer Calculations - Beyond the Pathways-like Models. J. Phys. Chem.

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