61. Accelrys Producer of various molecular modeling and simulation software for both life and materials science research, like cerius, catalyst, insightII, quanta. http://www.accelrys.com/

Search Accelrys for: About Accelrys • Company overview • Careers • Contact Us • Investors ... • Our Network Products • All Products • Accord • Catalyst • Chemical Databases ... • Webstore Services • Overview • Contract Research • Custom Services • Customer Support ... • Training Solutions for... • Analytical Chemists • Bioinformaticians • Chemists/Engineers • Comput'l Chemists ... • Development Technologies • Overview • Bioinformatics • Cheminformatics • Data Pipelining ... • Materials Modeling Reference • Index • Case Studies • Gallery • Glossary ... • White Papers Events • AccelrysWorld • Conferences • Seminars • Training Workshops ... • Webinars Solutions for... Bioinformaticians Molecular Biologists Protein Modelers Structural Biologists ... Webstore Reference Materials Index White Papers Publications Case Studies ... References About Accelrys Overview News Contact Investors ... Contact us

62. 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/

63. Center For BioMolecular Modeling The MSOE Center for Biomolecular modeling (along with 3D Molecular Designs) creates handheld molecular models in a variety of types and formats to assist http://www.rpc.msoe.edu/cbm/

September 17, 2005 Science Education Models Research Models Center for BioMolecular Modeling At the Center for BioMolecular Modeling (CBM), teachers truly do come first. We work closely with talented science educators from across the US to create innovative instructional materials that make the molecular world real for students. Synergy between Physical Models and Computer Visualization Tools We believe that the invisible world of molecules becomes real when students have an opportunity to hold physical models in their hands. This is true for flexible models made from Toobers, or accurate models made by rapid prototyping technologies . In both cases, the physical models function as thinking tools that stimulate questions that are then addressed using computer visualization tools. Keeping Busy Our hard-working staff and students keep busy running: Professional Development Courses for Teachers Special Workshops for School Districts and other groups The SMART Team program for students A Protein Modeling Event for the Science Olympiad Competition Borrow or Buy All models and activities created by CBM are available to borrow from our Model Lending Library , or to purchase from our sister organization, 3D Molecular Designs A Little Help from our Friends Our work is supported by grants from the NIH National Center for Research Resources SEPA program and the NSF CCLI program.

64. BALL - Biochemical Algorithms Library — The BALL Website C++ framework for rapid software prototyping in molecular modeling. http://www.bioinf.uni-sb.de/OK/BALL/

Skip to content Small Text Normal Text Large Text Search The BALL Website BALL Biochemical Algorithms Library Sections News Overview Documentation Support ... Search Personal tools You are not logged in Log in Join You are here: Home Navigation Home Documentation Gallery Members Overview Support Log in Name Password Forgot your password? New user? BALL - Biochemical Algorithms Library Document Actions What is BALL? Rapid Software Prototyping can significantly reduce development times in the field of Computational Molecular Biology and Molecular Modeling. BALL (Biochemical Algorithms Library) is an application framework in C++ that has been specifically designed for this purpose. It provides an extensive set of data structures as well as classes for Molecular Mechanics, advanced solvation methods, comparison and analysis of protein structures, file import/export, and visualization BALL has been carefully designed to be robust, easy to use, and open to extensions. Especially its extensibility which results from an object-oriented and generic programming approach distinguishes it from other software packages. BALL is well suited to serve as a public repository for reliable data structures and algorithms. Based on BALL we have developed a stand-alone tool for molecular visualization

65. Molecular Modeling Links Chime is based on a molecular modeling program called RasMol written by Roger Sayle. This commercial molecular modeling package is available from http://c4.cabrillo.edu/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

66. Computational Chemistry Resources On The WWW Directory of links related to computational chemistry. Offers several tutorials for understanding the basics of molecular structure and molecular modeling techniques. http://www.chem.swin.edu.au/chem_ref.html

WWW Computational Chemistry Resources This list of resources is designed to provide computational chemists, students and other people interested in the CAUT Computational Chemistry project with a list of useful web sites related to computational chemistry and molecular modelling This list is not intended to be a definitive list of chemistry pages on the web, but rather to provide links to some of the more most useful sites on the Web. Please let us know of any changes or suggestions for this list. The resources are divided into: General chemistry Chemistry education Computational chemistry Resources Molecular modelling ... The URL update form Interesting general chemistry resources The Australian Chemistry Network Beilstein Information Systems The Free University, Berlin Chemistry Index (very comprehensive) The Yahoo Chemistry Index Chemistry Databases Links for Chemists; University of Liverpool including World Wide Web Virtual Library: Chemistry The Information Retrieval in Chemistry The SDSU Chemistry Information Reference Silicon Graphics' Chemistry and Biological Sciences resources WebElements - The periodic table via WWW MIME types for Chemistry Network Science - an electronic journal for those in the chemical, pharmaceutical and biotechnology industries

67. C4: Computers In Chemistry At Cabrillo College Recommended internet resources for molecular modeling information and models. A selection of eight different sample molecular models for Chime. http://c4.cabrillo.edu/

C4's Consortium WebMO Pro Implementation Login portal for C4 Consortium Members. 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. Molecular Modeling Links Recommended internet resources for molecular modeling information and models.

68. Interprobe Chemical Services 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

69. Molecular Modeling Pro Interactive molecular modeling and drawing software to build, study, and present molecules, including crystallography. 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.

70. Molecular Modeling And Drawing Software And Databases molecular modeling and drawing software, structural databases, build, study, and present molecules, including crystallography. http://www.chemsw.com/molecularmodeling.htm

Molecular Drawing and Modeling Software Molecular Modeling Pro™ Molecular Modeling Pro™ Plus Molecular Modeling Pro™ Plus - Enterprise Molecular Modeling for Educators ... ChemSite 3D Molecular Visualization Software ChemSite Pro Structural Databases that can be used with the above programs Amphibian Ecotoxicity Database ChemicaElectrica Database Herbal Pharmacological Database Human/Animal Developmental Toxicity Database ... E-Notebook Ultra

71. Jerome Baudry's Page. Molecular Modeling, Drug Design Applications of molecular modeling and computational chemistry to biophysics of large, integrated biosystems. http://www.ks.uiuc.edu/~jerome/

Jerome Baudry Our research IN THE NEWS Present position: Senior Research Scientist School of Chemical Sciences Computer Applications and Network Services Noyes Lab, Room 150 University of Illinois at Urbana-Champaign e-mail : jerome@scs.uiuc.edu See Resume (updated May 2004) E-mail at Beckman: jerome@ks.uiuc.edu Education: December 1997 : Ph.D., Molecular Biophysics (Tres Honorable avec Felicitations du Jury - summa cum laude). Title : Theoretical study of H-bonded systems : from peptide dynamics to the function of Bacteriorhodopsin Paris-6 University, France. Under supervision of Prof. Jeremy C. Smith and Prof. Paul Vigny. Research Interests: Computational Chemistry, Drug Design and Molecular Modeling of Biomolecules. Functional Genomics/Proteomics: from protein sequence to function and structure. Structure and Function of an integral functional biomolecular unit in its natural environemnt. Free Energy Calculations. Computational drug discovery: Combinatorial library design, diversity/similarity characterization, binding site characterization, virtual docking, QSAR and HT-'Binary'-QSAR. Links to public and private biotech sites.

72. Geometry In Action: Molecular Modeling Connections have been growing recently between the molecular modeling community Many questions in molecular modeling can be understood geometrically in 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.

73. Facio The 3D-Molecular Modeling Software 3Dmolecular modeling Software, available at no charge for the Windows platform. Has functions for visualization of biomolecules and results from GAMESS QM calculations, and for aligning and modifying structures. http://www1.bbiq.jp/zzzfelis/Facio.html

Facio 3D-Graphics program for Molecular Modeling and Visualization of Quantum Chemical Calculations Facio is publicly available at no charge, but only for Windows platform Download Current Version : Facio 9.8.3 (released on August 27, 2005) Japanese Page Facio is an OpenGL -based 3D-graphics program for molecular modeling and visualization of quantum chemical calculations ( GAMESS and Gaussian SSH / SFTP client is also implemented. Through SSH / SFTP connection, Gaussian job can be submitted to batch job system on the remote server and calculation results can be retrieved form the server. Supported batch job systems are LoadLeveler and NQS Since Facio internally uses PDB (Protein Data Bank) format, it can also display a 3D-structure of biological macromolecules, such as proteins and nucleic acid with emphasizing their secondary or quaternary structures. Note Facio is tested on Windows 98SE, Me, NT, 2000 and XP. But it is reported that sometimes Facio does not work properly. In that case, follow the instructions below to disable or constrain 3D graphics accleration (2) Double click on the System Icon, in the Control Panel.

74. SIMION 3D 7.0 - The Ion And Electron Optics Simulator 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

Scientific Instrument Services, Inc. Supplies and Services for Mass Spectrometers, Gas Chromatographs and Liquid Chromatographs Search: Home Products Catalog Machining ... Employment SIMION SIMION Overview Brochure (PDF) SL Toolkit (NEW) SIMION.com Ordering SIMION The Industry Standard for Ion Optics Simulations www.SIMION.com We invite you to visit our new www.simion.com web site, which contains many more resources and hosts the SIMION Users Group for discussions between SIMION users. Windows Version Click here to download latest SIMION 7.0 Demo. 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.

75. Biodesigner Molecular Modeling And Visualization Program Biodesigner molecular modeling and Visualization Program. http://www.pirx.com/biodesigner/index.shtml

July, 20th, 2002 After a long break, a new version of Biodesigner (0.70) is available. This release supports CASP5 tertiary structure (TS) format. Several rendering bugs and memory leaks are fixed, as well. Download the new version. May, 5th, 2001 The new Biodesigner website has just started. New version of Biodesigner (0.60) including user's manual is available now !!! Make sure to check the feature tour page and the renewed picture gallery Biodesigner is powered by: visitors since Nov, 13th, 2003 INTRODUCTION OVERVIEW FEATURES TOUR GALLERY ... Piotr Rotkiewicz

76. The Hanessian Group Total synthesis. Medicinal chemistry and drug design. Immunochemistry and drug targeting. Glycosidic linkage in life processes. Computer aided chemistry and molecular modeling. http://osiris.corg.umontreal.ca/index.shtml

Welcome! The Hanessian group presently comprises 1 postdoctoral associates, Ph.D. students, M.Sc. students, 1 computer scientist, 1 LCMS specialist and 2 group technicians for a total of The group occupies the entire ninth floor of the chemistry building and enjoys an "institute-like" atmosphere. A wide-cross section of research interests are pursued in organic, bioorganic and medicinal chemistry. A selection of published work can be found in the accompanying pages. Contact Information Professor Stephen Hanessian Department of Chemistry Université de Montréal C.P. 6128, Succursale Centre-Ville Montréal Québec H3C 3J7, CANADA Phone: (514) 343-6738 F ax email: stephen.hanessian@umontreal.ca URL: http://osiris.corg.umontreal.ca webmaster

77. Collaboratory For Structure-Based Drug Design complex threedimensional molecular models for applications such as drug was constructed based on the MidasPlus molecular modeling system and was http://www.cgl.ucsf.edu/Research/collaboratory/

Overview: The Resource for Biocomputing, Visualization, and Informatics , a NCRR Resource Center, has created a software system to support collaborative studies of molecular structure among scientists at multiple remote locations. This "collaboratory" allows scientists to share and interactively manipulate complex three-dimensional molecular models for applications such as drug design and protein engineering. An early prototype collaboratory with limited functionality was constructed based on the MidasPlus molecular modeling system and was demonstrated at NETAMORPHOSIS in Washington, D.C. on March 11-13, 1998, sponsored by the White House Office of Science and Technology Policy and the National Economic Council. (See this UCSF Daybreak news article for details.) However, our current work is based on Chimera , and it is this version of the software which we are now distributing. Additional Information Available: Project overview (PDF file from 10/27/00 NCRR workshop presentation) Detailed project description User's Guide Documentation Guide to desktop videoconferencing What is structure-based drug design?

78. The Computer-Aided Nanodesign Site - MatHub Features current and background information about molecular modeling and informatics for chemistry and materials science. http://www.mathub.com/

The Computer-Aided Nanodesign Site ComputeNano.com Background Technology Glossary ... Home MatHub is Now Retired After 5 successful years, MatHub has been retired and in its place ComputeNano.com has been launched. To view the majority of the site please register your details (your MatHub log-in details will not work): Contact Us Conditions Glossary

79. QuantumBio Inc -- A Next Generation Of CAMM & CADD Develops solutions for ComputerAssisted molecular modeling and Computer-Assisted Drug Design, with emphasis on semiempirical quantum mechanics and bioinformatics. http://www.quantumbioinc.com/

QuantumBio provides Pharmaceutical and Biotech companies with patent pending fast Quantum Mechanical (QM) solutions for Lead Optimization! QuantumBio offers the following lead optimization capabilities for your drug discovery investment: Use QM based Scoring Function to predict protein-ligand binding affinities on a daily basis. Study protein-ligand complexes containing metals. Predict ligand-induced NMR (Nuclear Magnetic Resonance) Chemical Shift Perturbation on protein. Study large biomolecules of 500 or 15,000 atoms with QM. Understand the Pair-Wise Energy Decomposition of protein-ligand complex interaction. Improve QSAR (Quantitative Structure-Activity Relationships) understanding with Quantum Chemistry Molecular Field Analysis (MFA). August 23, 2004 QuantumBio at Fall 2004 ACS in Philadelphia. July 19, 2004 QuantumBio releases DivCon Discovery Suite 2.1.5. May 31, 2004 BioInform highlights QuantumBio. May 2004 Start-Ups magazine profiles QuantumBio. ... March 2004 QuantumBio featured in the LSGPA Accelerator newsletter.

80. Jay Ponder Lab Home Page Graphical user interface to suites of molecular modeling tools, providing an integrated environment for engineering applications. Contacts for the group at Washington University School of Medicine in Saint Louis, Missouri. http://dasher.wustl.edu/

Jay Ponder Lab Home Welcome to the Home Page for the Jay Ponder Lab in the at the Washington University School of Medicine in Saint Louis, Missouri. We are located in the recently renovated Center for Computational Biology building on the Medical School campus. Our group is primarily interested in computational chemistry, especially the development of new algorithms and their application to problems in structural biology. We develop, maintain and distribute several software packages which are described below. For a more complete description of our work, please see the abstract in the Research Interest Book which is published annually by the . Publications and dissertations from the lab are available from Jay Ponder's Home Page Software Distributed by the Lab TINKER A complete package for molecular mechanics, dynamics and modeling of molecules, especially biomacromolecules. TINKER has the ability to use any of several common parameter sets, such as Amber (ff94, ff96, ff98, ff99), CHARMM (19 and 27), Allinger MM (MM2-1991 and MM3-2000), OPLS (OPLS-UA, OPLS-AA and OPLS-AA/L), as well as our own AMOEBA polarizable atomic multipole force field. TINKER implements a variety of novel algorithms including distance geometry with fast metrization and Gaussian trial distances, Elber's reaction path method, global optimization via our Potential Smoothing and Search algorithms, molecular dynamics with simulated annealing and stochastic dynamics options, particle mesh Ewald summation, Monte Carlo minimization, atomic multipole treatment of electrostatics with explicit dipole polarizability, Eisenberg-McLachlan ASP and GB/SA continuum solvation models, and truncated Newton TNCG local energy minimization.

Page 4     61-80 of 163    Back | 1  | 2  | 3  | 4  | 5  | 6  | 7  | 8  | 9  | Next 20