41. Biosiris - Your Partner In Molecular Modeling 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.

42. 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.

43. 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

44. Molecular Modeling Glossary The Resource brings the most advanced molecular modeling, bioinformatics, and computational molecular modeling, molecular modelling A technique for the http://www.genomicglossaries.com/content/molecular_modeling_gloss.asp

You are here Biopharmaceutical Glossary homepage/Search In silico In Silico Evolving terminology for emerging technologies Suggestions? Comments? Questions? mchitty@healthtech.com Last revised June 29, 2005 View a Printer-Friendly Version of this Web Page! Registration policy has details Mr. Ms. Mrs. Dr. Prof. First: Last: Title: Dept.: Company: Address: City: State: Zip: Country: Email: Opt-out of Email YES NO Telephone: Would you like to receive CHI event updates via fax? Yes No Fax: document.FrontPage_Form1.interest.value = 'ISB'; An understanding of the behavior of biological systems at each level of their organization can only be achieved by careful study of the complex dynamical interactions between the components of these systems. For this understanding to be quantitative it is necessary to develop structurally, biochemically and biophysically detailed mathematical models. Once developed, these models can be simulated, analyzed, and visualized through application of modern engineering and computational approaches. IBM, Functional Genomics and Systems Biology Overview http://www.research.ibm.com/FunGen/index.html

45. Molecular Modeling Software - NGMSI NorGwyn Montgomery Software Inc 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

What's New? Products Molecular Modeling Pro Molecular Modeling Pro Plus ... Contact Us 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. Our specialties are molecular drawing, physical property calculations from structure, substructure searching and chemical database creation. Feel free to contact us if you have further questions.

46. Molecular Chemistry Models - Darling Models Molecular models are as vital a tool for the study of chemistry as calculators We would encourage you to download a copy of our molecular modeling Guide http://www.darlingmodels.com/

47. MMTK Home Page Free library for molecular modeling applications. Written in Python, with a few portions in C. Downloads, examples, documentation, and wiki. http://starship.python.net/crew/hinsen/MMTK/

Sections Documentation Examples Download Useful links See also MMTK Wiki Python ScientificPython DomainFinder Contact hinsen@llb.saclay.cea.fr The Molecular Modelling Toolkit The Molecular Modelling Toolkit (MMTK) is an Open Source program library for molecular simulation applications. In addition to providing ready-to-use implementations of standard algorithms, MMTK serves as a code basis that can be easily extended and modified to deal with standard and non-standard problems in molecular simulations. The three most common usage patterns of MMTK are Writing Python scripts that make use of MMTK functions for standard simulation and modelling applications. This is similar to using other simulation packages with a scripting language (i.e. CHARMM or Gromos), but with the added advantage of having access to lots of useful Python modules from elsewhere. The example section shows what such scripts look like. Writing modules that interact closely with MMTK (and perhaps other packages) to solve problems for which no standard solution exists. For example, adding a particular force field term or a particular simulation or analysis algorithm. There is not much competition for MMTK in that domain. Writing application programs in Python that use MMTK internally, for users that do not need to know anything about such internals. Those programs can provide easy-to-use graphical interfaces (see e.g.

48. Altoris - Innovation In Drug Discovery, Research And Development Consultants in chemoinformatics for computer aided drug design. Areas of expertise include design of chemical libraries for high throughput screening, structure guided drug design, molecular modeling, virtual screening, predictive toxicology, and software development. http://www.altoris.com/

Home About Us Professional Services Employment We are a progressive, young company fostering new concepts in Life Sciences research. We have active programs in-house to discover pharmacological agents in therapeutic areas as diverse as oncology, metabolic disorders, cognitive impairment, and infectious diseases. All of this by targeting a single protein class: oxidoreductases. At the same time, we make available to others some of the technologies we have found useful in our research. We comercialize tools for research informatics and offer professional services in drug discovery. Our professional services help new companies, in areas as diverse as Screening, Design of Chemical Libraries or Information Management among others. Our technical expertise, and years of work in the biotechnology and pharmaceutical industries provides you with practical, inexpensive solutions. Our Chemical Information Software is down to earth. The tools we are developing deal with simple daily problems, initially for medicinal and computational chemists and screeners. Our years of experience in the frontlines of drug discovery have allowed us to identify areas where simple and sensible solutions could greatly improve efficiency. Behind a simple friendly user interface, we provide sophisticated state of the art solutions to aid in drug discovery Site by Interking Media LLC

49. Molecular Modeling bullet, Software Used in molecular modeling and Molecular Dynamics bullet, molecular modeling for Beginners Tutorial new.GIF (3043 bytes) provides an 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).

50. 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 GmbH ISSN: 1610-2940 (Paper) 0948-5023 (Online) Subject: Biomedical and Life Sciences Chemistry and Materials Science Issues in bold contain content you are entitled to view. OnlineFirst Volume 11 Number 3 / June 2005 Number 2 / March 2005 Number 1 / February 2005 Request a sample Volume 10 Numbers 5-6 / December 2004 Number 4 / August 2004 Number 3 / June 2004 Number 2 / April 2004 ... Number 1 / February 2004 Volume 9 Number 6 / December 2003 Number 5 / October 2003 Number 4 / August 2003 Number 3 / June 2003 ... Number 1 / February 2003 Volume 8 Number 12 / December 2002 Number 11 / November 2002 Number 10 / October 2002 Number 9 / September 2002 ... Number 1 / January 2002 Jump to volumes: Most Recent 7 to 4 3 to 1 First page Previous page Next page Last page Jump to Volumes Most Recent 7 to 4 3 to 1 Linking Options About This Journal Editorial Board Manuscript Submission Quick Search Search within this publication...

51. CCL Home A resource for computational chemists. Discussions on chemistry software, data, conferences, jobs, quantum chemistry, molecular mechanics, molecular dynamics, QSAR, molecular graphics, molecular modeling, and associated archives http://www.ccl.net/chemistry/

Page supported by: http://www.ccl.net/chemistry/index.shtml CCL Home About CCL Rules Instructions Contributing Material ... Send E-mail to CCL Administrators Welcome to the CCL Website! If you have problems sending mail to the list of subscribers or to CCL administrators, please use the CCL MAIL WEB FORM . It skips the agressive spam filters. Please suggest improvements, report deficiences, bad links, etc. We also do not mind receiving praise when deserved CHECK IT OUT!!! Greylisting to fight spam http://www.ccl.net/cca/software/UNIX/greylisting/README.shtml Updating RedHat Linux without pain with yum http://www.ccl.net/cca/software/UNIX/updating-redhat-with-yum/index.shtml How to back-up your data on the DVD-R, DVD+R, and DVD+RW with the Sony DRU-510A http://www.ccl.net:/cca/software/ UNIX/Sony_DRU-510A_DVD+RW_burner/README-DRU-510A.shtml Installing webmail (squirrelmail) on RedHat Linux 9 to access your e-mail via browser http://www.ccl.net/cca/software/UNIX/webmail-on-redhat/README.shtml Updating RedHat Linux without pain with apt http://www.ccl.net/cca/software/UNIX/updating-redhat/index.shtml

52. Molecular Modeling Reference Quick Reference Guide to Computational Chemistry Acronyms, Methods, Parameters, Accuracy, and Software. 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 /

53. MoluCAD MoluCAD is a fullfeatured molecular modeling and visualization tool designed for Windows. Originally conceived as an aid for students of organic chemistry, 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, "

54. Molecular Conceptor A multimedia course for Windows that teaches drug design and molecular modeling. http://www.molecular-conceptor.com/

55. CAChe Molecular Modeling Tutorial http://www.chem.ox.ac.uk/course/cache/default.html

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56. Dynamol Program for molecular modeling with the Amber force field, minimization, conformational search, and visualization. http://www.dynamol.com/

Dynamol Inc. Home About Us Contact Us Main Menu Features Screen Shots About Us Contact Us Forums BUGS Suggestions Science Dynamol Beta 3 Download Dynamol Beta 3 Linux Version Windows Version What is Dynamol? Dynamol is my attempt to create a computational drug discovery platform which encompasses public domain algorithms that I feel are important for my day to day drug discovery research. On one hand I started Dynamol to gain a deeper understanding of computational chemistry methods. One the other hand I simply enjoy building and designing large projects. I have been programming since I was about 12 years old when my parents gave me my first computer. A Commodore 64! Dynamol will always remain free for academic use. Some of the features such as network database searches will ultimately have to generate income or the servers will get turned off. Thus I will have to charge a fee for these features (yes even academics). If and when I believe dynamol is ready for commercial usage I will allow people from industry to purchase a license if there is interest. At this point Dynamol is really more of a hobby for me. Will it ever become a viable company? Who knows, but I am certain to learn a lot and have fun during the process. While I enjoy the process of software development it is the application of the software to discover new drugs that I am most concerned with.

57. CAChe Molecular Modeling Tutorial http://www.chem.ox.ac.uk/courses/dp/

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58. 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/

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59. Glactone Molecular Modeling We are pleased to offer two sets of molecular modeling exercises. One set is designed for undergraduate general and organic chemistry students, 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

60. Introduction To Molecular Modeling molecular modeling, also known as molecular mechanics, is a method to calculate the In a very crude sense molecular modeling treats a molecule as a 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

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