Geometry.Net - Chemistry: Molecular Modeling

Norgwyn Montgomery 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

Extractions: P ractical, affordable software Greetings. Our goal is to provide our customers with quality chemistry software at the most reasonable prices in the business. Norgwyn Montgomery has been selling Chemical Software to Industry and Academia since 1994. We are combing the world for new software to offer in these areas: chemical drawing, molecular modeling, chemical database packages, analytical chemistry aids and education. Our newest program is Molecular Designer, an enterprise-wide client- server Chemical Database and Analysis program. Our current line-up includes the premier physical property calculation program, Molecular Modeling Pro , which calculates over 100 properties from structure and creates databases from them in many formats. It includes a database editor. This program also contains most of the standard 3-D modeling tools such as the MM2 minimizer and a free public domain version of MOPAC 6. Add Molecular Analysis Pro for $200 more and you have a complete chemical structure-property analysis system, good for driving synthesis strategies or designing the next formulation. We throw in a free industrial database of over 800 compounds and 100 associated properties. The complete cost for both programs? $499 ($249 academic). The molecule at the top of the page was drawn with MMP (it created a jpeg file). In 2002
Molecular ART Gallery
molecular modeling Gallery. Polymers and Polymer Simulations. Dendrimers. MolecularRheology Modeling flow and transport properties. Nanotechnology.
http://www.wag.caltech.edu/gallery/art_gallery.html

Extractions: Polymers and Polymer Simulations Dendrimers Proteins and Protein Simulations Molecular Rheology: Modeling flow and transport properties Nanotechnology Ceramics, Semiconductors, Alloys Quantum Chemistry and Electronic Structure Problems with this server should be reported to webmaster@www.wag.caltech.edu
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/

Extractions: 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.
Gallery Of Dendrimers
molecular modeling of Dendrimers. Materials and Process Simulation Center (MSC) hasbeen in the forefront of molecular modeling, characterization of dendrimers.
http://www.wag.caltech.edu/gallery/gallery_dendrimer.html

Extractions: Materials and Process Simulation Center (MSC) has been in the forefront of molecular modeling, characterization of dendrimers. In the course of this work several dendrimers were and are being studied using molecular builders, visualisation and analysis tools along with the Molecular Mechanics and Molecular Dynamics simulations. Below, you'll find pictures and movies of the dendrimers studied at the MSC. The contibutors to the project (past and current) are W. A. Goddard , D. Tomalia, Adel Naylor, Tahir Cagin , Derek Bins and Paul Miklis. Simulation of Dendrimer Box Images and Movies of Dendritic Molecules Collaborations Links to Dendrimer Research Reseources Recently, the encapsulation of bengal rose molecules in the Meijer Dendrimer Box (DBox) has been studied [P. Miklis, T. Cagin and W.A. Goddard, JACS, 1997, 119, pp7458-7462]. Molecular dynamics simulations were performed for the Dendrimer Box and the fifth generation poly(propyleneimine) dendrimer (PPI-5) with both four and six bengal rose molecules. Following links represents the time evolution of the center of mass of six bengal rose molecules in dendrimer box and PPI-5.
Accelrys -- Software For Pharmaceutical, Chemical, And Materials Research
Producer of various molecular modeling and simulation software for both life and materials science research, like cerius, catalyst, insightII, quanta.
http://www.accelrys.com/

Extractions: Stuttgart, Germany More events... E-flash Sign up for a monthly update from Accelrys Smallpox Volunteer your PC to help the fight against smallpox Accelrys provides software solutions for pharmaceutical and chemical research. Through computation, simulation, and the management and mining of scientific data, we accelerate product design, discovery, and development. Our platform technology and consulting services enable enterprise-wide solutions. The result is great science, faster. Our solutions More... Our science More... Our approach More... First AccelrysWorld conference in San Diego IBM, United Devices and Accelrys aid search for smallpox cure Accelrys appoints Chief Science Officer Cerius ... Search
TMMeC - The Molecular Modeling Electronic Conference - TMMeC
Available Issues VOLUME 1, 1997 Issue 1, Apr.Jun. Issue 2, Jul.-Sep. Issue3, Oct.-Dec. VOLUME 2, 1998 Issue 1, Jan.-Feb. Issue 2, Mar.-Apr.
http://fcindy5.ncifcrf.gov/tmmec/
Geometry In Action: Molecular Modeling
molecular modeling. Connections have been growing recently betweenthe molecular modeling community and the computational geometry.
http://www.ics.uci.edu/~eppstein/gina/molmod.html

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

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

Extractions: 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 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.
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

Extractions: 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.
Molecular Modeling Glossary
Search Informatics In silico molecular modeling In Silico molecular modelingglossary Evolving terminology for emerging technologies Suggestions?
http://www.genomicglossaries.com/content/molecular_modeling_gloss.asp

Extractions: Last revised March 06, 2003 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: Fax: document.FrontPage_Form1.interest.value = 'ISB'; http://www.ks.uiuc.edu/Publications/Reports/teraflop/node4.html Related glossaries include Biology Pharmaceutical biology Protein Structure 3D protein structure prediction: See protein structure prediction 3D-QSAR Three-Dimensional Quantitative Structure-Activity Relationships: Involves the analysis of the quantitative relationship between the biological activity of a set of compounds and their three- dimensional properties using statistical correlation methods. [IUPAC Computational] Broader terms: QSAR SAR Structure Activity Relationship Narrower terms: Algorithms CoMFA Comparative Molecular Field Analysis Related term drug design ab initio: From the Latin: from the beginning. In modeling refers to models devised without experimental data?
Linux4Chemistry
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
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/

Extractions: While the CCL is located at the Ohio Supercomputer Center (OSC) , it now runs from a separate domain and enjoys new status as a separate program within the OSC parent organization. If you have problems sending mail to the list, please contact the list administrator directly at jkl@osc.edu and send a copy of your message. It will be eventually resent. Since we are getting a lot of spam mail, we had to blacklist many addresses which originate spam. You can check blacklisted subnets at http://www.ccl.net/spammers.txt . We do admit (and apologize) that most of these addresses are the victims of crackers who used machines in the ajacent subnet to send spam. Even if your address is on the list, you are probably a victim as we all are. The list is ordered by IP address. Please tell us if your address is there, and we will promptly remove it. Note, if you are using some popular mail service, which was compromized by the bad guys at some point, it may be blacklisted, and your messages to CCL may be rejected. Let us know about it (at jkl@osc.edu
Glactone Molecular Modeling
Glactone's molecular modeling Exercises. We are pleased to offer two sets ofmolecular modeling exercises. A short introduction to molecular modeling.
http://chemistry.gsu.edu/glactone/modeling/modeling.html

Extractions: 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 Back to Glactone
Simion Main Page, With Links To Other Pages
SIMION ion optics software and more than 200 scientific software products in mass spectrometry, chromatography, quality control, chemical inventory, MSDS, molecular modeling, database, and plotting. Online ordering.
http://www.sisweb.com/simion.htm

Extractions: Scientific Instrument Services, Inc. Supplies and Services for Mass Spectrometers, Gas Chromatographs and Liquid Chromatographs General What's New Products References ... Request Info SIMION Search: Last Update: unknown The Industry Standard for Ion Optics Simulations SIMION 3D 7.0 Ion and Electron Optics Program - New Windows Version Click here to download latest SIMION 7.0 Demo. (1.1 MB self-extracting file) The software is widely used by manufacturers and designers of mass spectrometers, electron microscopes, electron multipliers and other scientific instruments. Using this software, instrument designs have been perfected and the sensitivities of the instruments have been maximized. Here at Scientific Instrument Services we have been using this software to study mass spectrometer sources and filaments. Using this system we have been able to study the filament shape, the effect of filament shields and the effect of the filament magnet. This information is being used to design new filaments and other mass spec accessories which will be added to our product lines in the future. The original version of SIMION was an electrostatic lens analysis and design program developed by D. C. McGilvery at Latrobe University Bundoora Victoria, Australia, 1977. SIMION for the PC was developed at the Idaho National Engineering Laboratory. SIMION 7.0 is a completely new version which contains major improvements over the previous six versions. User programs have been greatly expanded and are more powerful. A new geometry file option supports highly complex array geometry. Extensive algorithm modifications have greatly improved the computational speed and accuracy. This C based program can model complex problems using an ion optics workbench that can hold up to 200 2-D and/or 3-D electrostatic or magnetic field arrays. These arrays can have up to 50,000,000 points which can be visualized as 3D objects that the user can cut away to inspect ion trajectories and potential energy surfaces.
Molecular Modeling Laboratory-Home Page
Includes information on the software used, one course that uses the laboratory, and links to the personal pages of lab personnel.
http://cesario.rutgers.edu

Extractions: at of Located in: Home of the The molecular modeling laboratory provides students, staff, and faculty the ability to build and graphically manipulate 3-D images of complex molecules such as proteins and nucleic acids using Insight II software developed by Molecular Simulations (now Accelrys ). The premium modules perform complex molecular and quantum mechanical calculation and protein structure homology analysis. Files in standard formats such as that of the Protein Data Bank can be imported. Staffed Hours: M-F 9am-5pm
Molecular Modeling
Click here for books on Molecular Structures. Cool molecular modelingSites, Chemical Computing Group Inc. is a leading worldwide
http://www.ahpcc.unm.edu/~aroberts/main/molmod.htm

Extractions: 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).
Molecular Modeling
Acknowledgements I would like to give special thanks to Denys Bashtovyy for directingme to some interesting websites in molecular modeling and providing some
http://www.ahpcc.unm.edu/~aroberts/myweb2/newpage3.htm

Extractions: = Searchable Site = New Link Index Online Protein Viewers Software Used in Molecular Modeling and Molecular Dynamics Cool Molecular Modeling Sites Acknowledgements: I would like to give special thanks to Denys Bashtovyy for directing me to some interesting websites in molecular modeling and providing some useful comments of this website. Online Protein Viewers Protein Viewer by A.R. Crofts server down 5/22/99 Software Used in Molecular Modeling and Molecular Dynamics AMBER UNIX; proprietary ) at Peter A. Kollman's research group at the University of California San Francisco (Updated 5/22/99). Description: AMBER refers to two things: a molecular mechanical force field for the simulation of biomolecules (which is in general use in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos.(Updated 5/22/99). AMMP Unix, Linux, and PC; Free Downloadable Software ) is a modern full-featured molecular mechanics, dynamics and modeling program. It can manipulate both small molecules and macromolecules including proteins, nucleic acids and other polymers. This software is found at Structural Biology at Jefferson and the Kimmel Cancer Center (Updated 5/22/99).
Molecular Modeling Links
C4, Free molecular modeling Software. RasMol Chime is based on amolecular modeling program called RasMol written by Roger Sayle.
http://c4.cabrillo.cc.ca.us/links.html

Extractions: 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 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 Chime Resources by Eric Martz

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