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82. Molecular Modeling Related Sites molecular modeling Related Sites. Advanced Chemistry Development ChemSketch3.5 FREE! molecular modeling Institutes and Other Collections of Links. http://www.phc.vcu.edu/link/molmodsites.html

83. Folding@Home Educational Project molecular modeling. Author Tug Sezen. Reference Andrew R. Leach (1996); MolecularModeling Principles and Applications; Addison Wesley Longman Limited. http://folding.stanford.edu/education/molmodel.html

Home Participate (Download) Help! Education ... Glossary MOLECULAR MODELING In a pool table after a cue exerts a force on a ball many balls begin to move as a result of interaction between the balls. If we know the position of each ball using Newton's laws we can predict the motion of all balls with reasonable accuracy, if we simplify the problem to a certain extent (3 body problems have no solutions otherwise). In order to solve such a problem computationally we have to make many simplifications such as assume elastic collisions, and so on. Many of the problems that we would like to tackle in molecular modeling are unfortunately too large to be considered by quantum mechanical methods even for distributed computing. As protein models consist of hundreds or thousands of atoms the only feasible methods of computing systems of such size are molecular mechanics calculations (kind of like playing pool with atoms.) A force field is assigned to each atom in the protein. This figure is a schematic representation of the four key contributions to a molecular mechanics force field: bond stretching, angle bending, torsional terms and non-bonded interactions.

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oinformatics workspace Molecular modeling and the ability to derive a better understanding of structure-function relationships in proteins is contributing to rapid advances in fields such as drug design This release of BioNavigator provides this functionality by incorporating many programs including WHAT IF and ICM Homology Modeling. These programs are, as with all programs and databases in BioNavigator integrated seamlessly into the easy-to-use interface. Additionally there are 6 molecular modeling protocols included in BioNavigator that provide a step-by-step guide to carrying out common molecular modeling analyses, such as: Contact Analysis Find a Homologous PDB Structure Homology Modeling Protein Engineering Protein Structure Mutation Structure Analysis What is molecular modeling? Molecular modeling, within BioNavigator, is used for the analysis, modification, building and display of protein structures. It has applications in structure analysis such as determining contacts between the protein of interest and e.g. a drug; in protein engineering where residues are mutated to perhaps stabilize the structure;and homology modeling, where a three dimensional (3D) structure of a protein, with unknown structure, is built using a homologous protein as a template. Figure: Structure of Lysozyme (PDB: 1l00) generated using ICM and displaying two active site residues and cysteine-97 complexed with Beta-Mercaptoethanol.

85. Applying Molecular Modeling CoMSEF, http//www.comsef.aiche.org/), including links to ChE faculty with researchon molecular modeling, software sources, online literature, images, etc. http://www.wtec.org/loyola/molmodel/

International Comparative Study on Applying Molecular and Materials Modeling The final report is available in Adobe Acrobat format: mm_final.pdf (~3.5 Mb) Traveling panelists (see additional information Phillip R. Westmoreland , Department of Chemical Engineering, University of Massachusetts Amherst (Panel Chair) Measurement and quantum modeling of elementary-reaction kinetics in flames, PECVD plasmas, polymer decomposition, and homogeneous catalysis; founding chair of AIChE Computational Molecular Science and Engineering Forum ; co-chair of 1998 and 2001 AIChE Topical Conference and FOMMS 2000 Peter A. Kollman , Department of Pharmaceutical Chemistry, University of California San Francisco (Panel Vice-Chair) Computational approaches to understand structure, energies and reactions of organic and biochemical molecules; developer of the AMBER force fields ; member of UCSF Molecular Design Institute Anne M. Chaka , Lubrizol during the study; now Group Leader for Computational Chemistry at NIST Industrial chlorination, catalysis, automotive lubricant additives using computational chemistry; Max-Planck-Society Fellowship, 1999-2000 ( Fritz-Haber-Institut (FHI) with Matthias Scheffler) Peter Cummings , Department of Chemical Engineering, University of Tennessee, and Chemical Technology Division, Oak Ridge National Laboratory Molecular simulations for phase equilibrium and rheological properties; parallel supercomputing; co-chair of 1998

86. SGI - Industries: Sciences: Life And Chemical Sciences: Computational Chemistry 260K). Watch a video molecular modeling Video (416 min) StreamingVideo Icon You need javascript turned on to watch a video. In http://www.sgi.com/industries/sciences/chembio/comp_chem.html

Sciences Life and Chemical Sciences Overview SGI Origin Family Servers for Bioinformatics and Chemistry ... Events Application Areas Bioinformatics Computational Chemistry and Molecular Modeling Industry Segments Medicine and Healthcare Research and Education Science Centers, Planetariums, and Museums Related Sites Servers Storage Reality Center Workstations ... 2002 Computational Chemistry Performance Report (PDF 260K) Watch a video: Molecular Modeling Video (4:16 min) You need javascript turned on to watch a video In the following tables you'll find a listing of chemistry applications supported for SGI systems. They are sorted by software developer and application name as well as platform availability. If you cannot find the application software you are looking for or you are a software developer and your product and solutions are not listed, please contact us at chembio@sgi.com Cheminformatics Area Chemistry/Biology Area Chemistry/Biology/ChemInfo Area ... Data Mining and Visualization Area Cheminformatics Area Developer Application IRIX W/S IRIX Servers LINUX NT Accelrys Accord x x Interprobe Chemical Services AUTOBUILD TM x x MDL Chemical Products Information (CPI) file x x MDL ChemInform RXL x x MDL Chemscape x x DAYLIGHT Chemical Information Systems, Inc.

87. Exorga, Inc. - Consultants In Organic Chemistry And Molecular Modeling Exorga, Inc. Consultants in Organic and Environmental Chemistry, andmolecular modeling. Welcome to Exorga, Incorporated's Web-Site! http://ourworld.compuserve.com/homepages/exorga/

Exorga, Inc. - Consultants in Organic and Environmental Chemistry, and Molecular Modeling Welcome to Exorga, Incorporated 's Web-Site! Consultants in chemistry and chemical engineering actively involved in product development, computational, experimental, and environmental organic chemistry. Exorga, Inc. - We are developers of chemistry software Exorga, Inc. has developed " the next generation " of molecular modelers, based on the new QVBMM molecular mechanics force field STR3DI32.EXE and QVBMM32.EXE (and QVBMM.EXE ) will enable you to tackle theoretical problems in organic chemistry that are outside of the reach of all other molecular mechanics based force fields. You'll also be able to explore some problems that cannot be fully resolved by the currently available molecular orbital based methods. Given the power of the CPUs that are commercially available at a modest price, most modest computer purchases now involve machines with CPUs rated at 1 GHz or better, we have added more power to the structure energy minimizing routine and tightened the code considerably. We now present you with STR3DI32.EXE, the 21st Century, Year 2003 Edition, version 2.003.01.H

88. Molecular Modeling And Visualization molecular modeling and Visualization. molecular modeling at NIH en; MolecularModeling in Organic Chemistry Courses (Alan J. Shusterman) en; http://www.chemie.fu-berlin.de/chemistry/index/molmod/

Molecular Modeling and Visualization Please note: Support for this service has been stopped. Use http://www.chemie.de/ instead. Subdirectories References CORINA 3D Coordinates for Chemical Structures [en] Depict - Interactive depiction of SMILES [en] FlexX - a program for automatic prediction of receptor-ligand interactions [en] GROMOS and BIOMOS [en] ... Chemie.DE Chemistry Internet Information Service (under construction) Searchable Chemistry Index Top Level of Hierarchical Chemistry Index

89. Molecular Modeling next previous Next Introduction Previous No Title. molecular modeling.Jan K. abanowski, Ohio Supercomputer Center. Introduction; http://www.arl.hpc.mil/PET/cta/ccm/training/tech-notes/model/node1.html

Next: Introduction Previous: No Title Molecular Modeling Jan K. abanowski, Ohio Supercomputer Center Introduction Computer representation of chemical bonds Computer representation of geometry Molecular surface and volume ... Molecular Comparisons Computational Chemistry Wed Dec 4 17:47:07 EST 1996

90. ISREC Molecular Modeling Page ISREC molecular modeling activities. Andrey Kajava STEREOCHEMICAL ANALYSISAND molecular modeling OF PROTEINLIPID COMPLEXES. Over the http://www.isrec.isb-sib.ch/modeling/modeling.html

ISREC molecular modeling activities Andrey Kajava send an e-mail: akajava@isrec-sun1.unil.ch My main interest is relationship between amino acid sequences of proteins and their 3D structures. Ab initio prediction of protein structures is the most challenging task of this domain of molecular biology. My experience suggests that STRUCTURAL PREDICTION OF PROTEINS WITH REPETITIVE SEQUENCES yields reliable results. The prediction is facilitated by regular spatial arrangement of the repeats, the possibility of distinguishing between structurally and functionally important residue conservation, knowledge of a molecular shape and by indirect experimental evidences. These proteins are of my particular interest. In my previous work, the 3D structures of the bacterial ice nucleation proteins with 48 residue repeats has been predicted and modeled (ref. 10, 14). The coordinates of the structure as well as that of the protein-ice interface are available in the Protein Data Bank ( PDB code and Another structural prediction concerns the extracellular domain of the thyrotropin receptor - a "typical" leucine-rich repeat (LRR) protein (ref.9). The predicted structure can be used to build models for most of the known LRR proteins. The atomic coordinates are available

91. JosseyBass :: Computational Chemistry & Molecular Modeling JosseyBass Chemistry Computational Chemistry molecular modeling. ComputationalChemistry molecular modeling (49), Listings 125 26-49, http://www.josseybass.com/cda/sec/0,,2914,00.html

By Keyword By Title By Author By ISBN By ISSN Shopping Cart My Account Help Contact Us ... Chemistry Computational Chemistry: A Practical Guide for Applying Techniques to Real World Problems by David Young US $78.95 Add To Cart Related Titles Chemical Engineering Speical Topics in Chemistry General Chemistry Electrochemistry Listings: Sort listing by: A-Z Z-A Publication Date Author Refine listing by: All Formats Books Journals BASIC Programming for Chemists: An Introduction by Peter C. Jurs, Thomas L. Isenhour, Charles L. Wilkins Hardcover, September 1987 US $125.00 Add to Cart Chemical Modeling: From Atoms to Liquids by Alan Hinchliffe Hardcover, October 1999 US $110.00 Add to Cart Chemical Modeling: From Atoms to Liquids by Alan Hinchliffe Paperback, October 1999 US $41.95 Add to Cart Chemically Reacting Flow : Theory and Practice by Robert J. Kee, Michael E. Coltrin, Peter Glarborg Hardcover, February 2003

92. WileyEurope :: Computational Chemistry & Molecular Modeling WileyEurope Chemistry Computational Chemistry molecular modeling. ComputationalChemistry molecular modeling (47), Listings 125 26-47, http://www.wileyeurope.com/cda/sec/0,,2914,00.html

Shopping Cart My Account Help Contact Us By Keyword By Title By Author By ISBN By ISSN WileyEurope Chemistry Essentials of Computational Chemistry: Theories and Models by Christopher J. Cramer Add To Cart Recent Title Relativistic Effects in Heavy-Element Chemistry and Physics by Bernd A. Hess (Editor) Add To Cart Related Titles Chemical Engineering Speical Topics in Chemistry General Chemistry Electrochemistry ... Join a Chemistry Mailing List Listings: Sort listing by: A-Z Z-A Publication Date Author Refine listing by: All Formats Books Journals BASIC Programming for Chemists: An Introduction by Peter C. Jurs, Thomas L. Isenhour, Charles L. Wilkins Hardcover, November 1987 Add to Cart Chemical Modeling: From Atoms to Liquids by Alan Hinchliffe Hardcover, August 1999 Add to Cart Chemical Modeling: From Atoms to Liquids by Alan Hinchliffe Paperback, August 1999 Add to Cart Chemically Reacting Flow : Theory and Practice by Robert J. Kee, Michael E. Coltrin, Peter Glarborg

93. Molecular Modeling Page molecular modeling Home Page. molecular modeling as a branch of appliedcomputer science has been developing rapidly over past years http://www.ucsf.edu/shokat/mm/

Molecular Modeling Home Page Molecular modeling as a branch of applied computer science has been developing rapidly over past years gaining its share of success in various fields of scientific research. These impressive advances have been made possible by increasing availability of powerful computational resources and development of new efficient algorithms. We have attempted to use these opportunities to enhance our research possibilities in search for new biologically important compounds as well as potentially useful techniques.

94. Molecular Modeling At UMDNJ molecular modeling at UMDNJ. ACS supports a suite of molecular modelingproducts at UMDNJ including the following. SYBYL. A comprehensive http://www.umdnj.edu/istweb/prodserv/acs_m04.htm

Research Scientific Software Overview Molecular Modeling UNIX Sequence Analysis ... Site Licenses Molecular Modeling at UMDNJ ACS supports a suite of molecular modeling products at UMDNJ including the following SYBYL A comprehensive molecular modeling package Insight II A complementary modeling package. DelPhi . An electrostatic potential/solvation energy tool. Discover A molecular geometry optimization/dynamics tool. Look A suite of homology modeling and sequence alignment tools with compatibility to electronic communication. UMDweb Home ISTweb Home Top

95. CERMM - Centre For Research In Molecular Modeling Announcements. 3rd Annual CERMM Symposium. Photos are now available!!If you have any photos you would like posted on the site, please http://artsci-ccwin.concordia.ca/chem/CERMM/

Announcements 3rd Annual CERMM Symposium Photos are now available!! If you have any photos you would like posted on the site, please e-mail symposium@cermm.concordia.ca Go to: Concordia Home Page Department of Chemistry and Biochemistry Last update: January 2003 Contact us: admin@CERMM.concordia.ca Webmaster: web-CERMM@CERMM.concordia.ca

96. Emerging Technologies--molecular Modeling Internet2 Logo. Macromolecular Crystallography and NMR, molecular modelingand ComputerAided Drug Discovery. Project Director, Glenn Kellog, Ph.D. http://www.at.vcu.edu/etech/i2projects/molec_model.html

Emerging Technologies Day Program Call for Papers Projects/Papers Internet2@VCU MITAC MATR Molecular Modeling Distance Education ... Grant Macromolecular Crystallography and NMR, Molecular Modeling and Computer-Aided Drug Discovery Project Director, Glenn Kellog, Ph.D Another aspect of our project is the storage, manipulation and display of very large crystallographic data sets of biomacromolecular structure between and among I2 institutions Virginia Commonwealth University Academic Technology Last Modified December 3, 2002 Contact AT Webmaster for comments concerning this page.

97. Molecular Modeling Facility At UC Irvine molecular modeling Facility. http://www.chem.uci.edu/facilities/molecular_modeling/

Chem Home facilities Molecular Modeling Facility director info info for new users courses 517 Rowland Hall model@uci.edu Facility Hours: 24 hours Director: HiYoung Yoo , Ph.D. 519 Rowland Hall yooh@uci.edu Work Hours: M-F 9-6 PM The Molecular Modeling Facility maintains Silicon Graphical workstations and various modeling software for visualization, molecular modeling and the calculation of properties of complex molecules. Various research groups subscribe to our facility for their research needs and training software is offered to use proper software for their research projects. Synthetic and biological chemists find computational modeling an important research tool for understanding experimental results and predicting organic reactivity and selectivity.

98. Actelion - Molecular Modeling Structural information on target proteins is used in molecular modelingto guide chemists and biologists in their daily work. For http://www.actelion.com/Apps/WebObjects/Actelion.woa/wa/dp?name=molecular_modeli

99. Molecular Modeling At Middlebury A Chime tutorial on normal modes of Methylene Dichloride molecular modeling StudentProjects Functional Protein Cavities Molecular Dynamics of Carbon Monoxide http://alta1.middlebury.edu/chemistry/molecular/molmod.html

View various molecules using RasMol View CHIME animations Stewart's Organic Chemistry Primer A Chime tutorial on normal modes of Methylene Dichloride Molecular Modeling Student Projects Functional Protein Cavities Molecular Dynamics of Carbon Monoxide Within Myoglobin Heme Dynamics within myoglobin Molecular Dynamics of Heme Within Myoglobin Comments or Suggestions to: Steve Sontum at sontum@panther.middlbury.edu

100. IconBAZAAR - Molecules - WWW Resources On Molecular Modeling Click here to visit our sponsor Selected WWW Resources on molecular modelingChemicals with Pharmaceutical Activity A 3D Structural Database http://www.iconbazaar.com/molecules/resources.html

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