101. Sdvlapp1 Software: Category: Molecular Modeling Categories molecular modeling, Xray Crystallography. Cerius2. Cerius2 provides an easy-to-use molecular modeling and simulation environment, http://www.msi.umn.edu/user_support/software/MolecularModeling.html

QUESTIONS FEEDBACK HOME Employment Events Links People Publications Welcome Category: Molecular Modeling Programs for the creation, manipulation and viewing of molecular models. Amber Description AMBER: Assisted Model Building with Energy Refinement 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. Home Page http://amber.scripps.edu Tutorial Amber Tutorials Documentation Remote online documentation can be found on the Amber 7 Manuals and Amber 8 Manuals Setting Up Your Environment There are several versions of Amber: serial version, shared-memory parallel (multiprocessor) version (MP) and parallel version that uses MPI message-passing library. The MP version is only available on multi-processor SGI computers. The MPI version is available on SGI Origin computers. Note: Although serial and parallel versions share most of the code base, there are significant differences. In some cases, parallel version may not produce the same results as the serial version. The results for any new problem obtained with a parallel version should be carefully checked against the serial version. The two parallel verions, MP and MPI, are also significantly different from each other. The MP versions supports a richer set of features, but MPI version may provide better performance in certain cases. The MP version is generally more reliable. You must initialize your environment including default paths and environmental variables which the package uses to access the programs and associated files. To do this, enter the following commands:

102. American Chemical Society Publications: Journal Of Chemical Information And Mode Covers topics such as database search systems, use of graph theory in chemical problems, substructure search systems, pattern recognition and clustering, analysis of chemical and physical data, molecular modeling, graphics and natural language interfaces, bibliometric and citation analysis, and synthesis design and reaction databases. http://pubs.acs.org/journals/jcisd8/

Cover Details DELIVERY SUSPENDED The American Chemical Society has suspended delivery of its journals and to areas affected by Hurricane Katrina at the request of the U.S. Postal Service. Full online access to all publications continues. Information on future deliveries will be available at a later date. Read press coverage in regarding a recent publication in JCIM "ZINC - A Free Database of Commercially Available Compounds for Virtual Screening" Review the program and register for ACS ProSpectives' conference on Advances in Structure-Based Drug Discovery , October 17-19, 2005, in Philadelphia. Journal of Chemical Information and Computer Sciences changed its name to Journal of Chemical Information and Modeling in January 2005, to more accurately reflect the journal's content. Journal of Chemical Information and Computer Sciences (now JCIM ) is #2 in total citations among the 78 journals in the Computer Science, Information Systems category (4,885). More citation data... Journal of Chemical Information and Modeling Volume 45 Issue 4 (July 25, 2005)

103. SpringerLink - Publication Publishes articles on the theory and the application of computerbased methods in the analysis and design of molecules. This includes theoretical chemistry, computational chemistry, computer and molecular graphics, molecular modeling, protein engineering, drug design, expert systems, general structure-property relationships, molecular dynamics, and chemical database development and usage. http://www.kluweronline.com/issn/0920-654X

Articles Publications Publishers Home Publication Journal of Computer-Aided Molecular Design Publisher: Springer Science+Business Media B.V., Formerly Kluwer Academic Publishers B.V. ISSN: 0920-654X (Paper) 1573-4951 (Online) Subject: Biomedical and Life Sciences Issues in bold contain content you are entitled to view. Volume 19 Number 4 / 2005 / April 2005 Number 3 / March 2005 Number 2 / February 2005 Number 1 / January 2005 ... Request a sample Volume 18 Number 12 / December 2004 Number 11 / November 2004 Number 10 / October 2004 Numbers 7-9 / July 2004 ... Number 1 / January 2004 Volume 17 Number 12 / December 2003 Number 11 / November 2003 Number 10 / October 2003 Number 9 / September 2003 ... Number 1 / January 2003 Volume 16 Number 12 / December 2002 Number 11 / November 2002 Number 10 / October 2002 Numbers 8-9 / August 2002 ... Number 1 / January 2002 Volume 15 Number 12 / December 2001 Number 11 / November 2001 Number 10 / October 2001 Number 9 / September 2001 ... Number 1 / January 2001 Volume 14 Number 8 / November 2000 Number 7 / October 2000 Number 6 / August 2000 Number 5 / July 2000 ... Number 1 / January 2000 Volume 13 Number 6 / November 1999 Number 5 / September 1999 Number 4 / July 1999 Number 3 / May 1999 ... Number 1 / January 1999 Volume 12 Number 6 / November 1998 Number 5 / September 1998 Number 4 / July 1998 Number 3 / May 1998 ... Number 1 / January 1998 Volume 11 Number 6 / November 1997 Number 5 / September 1997 Number 4 / July 1997 Number 3 / May 1997 ... Number 1 / January 1997 First page

104. Foundations Of Molecular Modeling And Simulation 2006 molecular modeling and Simulation Tools for Innovation FOMMS 2006 is a scientific modeling meeting balanced between molecular simulation and http://www.fomms.org/

Overview Call for Abstracts Important Deadlines Registration Venue Information ... Contact Us Molecular Modeling and Simulation: Tools for Innovation Topics of special interest include the following: Biological Applications Reaction Engineering Educational Methods Polymeric Materials Future Vision FOMMS 2006 is a scientific modeling meeting balanced between molecular simulation and computational chemistry. The format will follow the highly successful FOMMS conferences held in 2000 and 2003. All talks will be invited and will represent state-of-the-art reviews in the particular special topic areas. Two poster sessions will provide opportunities for all attendees to present their work. One afternoon will be devoted to a software/hardware demonstration session for providers to showcase their products and services. In addition, the schedule provides large blocks of time for informal discussions, relaxation, or leisure as well as several receptions to facilitate interaction between conference participants. Each presentation will be rigorously reviewed and edited.

105. Applying Molecular Modeling International Comparative Study on Applying Molecular and Materials Modeling Molecular simulations including hybrid QM/MD methods, modeling of materials 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

106. Molecular Mechanics A tutorial published by the Center for molecular modeling of the U.S. National Institutes of Health. http://cmm.info.nih.gov/modeling/guide_documents/molecular_mechanics_document.ht

Molecular Mechanics Background The "mechanical" molecular model was developed out of a need to describe molecular structures and properties in as practical a manner as possible. The range of applicability of molecular mechanics includes: Molecules containing thousands of atoms. Organics, oligonucleotides, peptides, and saccharides (metallo-organics and inorganics in some cases). Vacuum, implicit, or explicit solvent environments. Ground state only. Thermodynamic and kinetic (via molecular dynamics ) properties. The great computational speed of molecular mechanics allows for its use in procedures such as molecular dynamics, conformational energy searching, and docking, that require large numbers of energy evaluations. Molecular mechanics methods are based on the following principles: Nuclei and electrons are lumped into atom-like particles. Atom-like particles are spherical (radii obtained from measurements or theory) and have a net charge (obtained from theory). Interactions are based on springs and classical potentials. Interactions must be preassigned to specific sets of atoms.

107. Molecular Dynamics A tutorial published by the Center for molecular modeling of the U.S. National Institutes of Health. http://cmm.info.nih.gov/modeling/guide_documents/molecular_dynamics_document.htm

Molecular Dynamics In the broadest sense, molecular dynamics is concerned with molecular motion. Motion is inherent to all chemical processes. Simple vibrations, like bond stretching and angle bending, give rise to IR spectra. Chemical reactions, hormone-receptor binding, and other complex processes are associated with many kinds of intra- and intermolecular motions. The driving force for chemical processes is described by thermodynamics . The mechanism by which chemical processes occur is described by kinetics . Thermodynamics dictates the energetic relationships between different chemical states, whereas the sequence or rate of events that occur as molecules transform between their various possible states is described by kinetics: Conformational transitions and local vibrations are the usual subjects of molecular dynamics studies. Molecular dynamics alters the intramolecular degrees of freedom in a step-wise fashion, analogous to energy minimization. The individual steps in energy minimization are merely directed at establishing a down-hill direction to a minimum. The steps in molecular dynamics, on the other hand, meaningfully represent the changes in atomic position, r i , over time (i.e. velocity).

108. Case Scientific - Industrial Surfactant And Polymer Science, Computational Chemi molecular modeling of surfactants and polymers with an industrial focus. http://www.casescientific.com

Welcome to Case Scientific 125 Main Street Essex Junction VT 05452, USA Consultancy Scientific Journalism Publications Fiona News and Events Nanotech2006: Soft Nanotechnology, Nanostructured Fluids and Self Assembly Symposium Sign up NSTI Workshop on Nanotechnology in Soft Materials Mesoscale Phenomena in Fluid Systems Join the Industrial Fluid Properties Simulation Challenge Questions about this web site should be sent to webmaster@casescientific.com Industrial Surfactant and Polymer Science, Molecular Modeling, Scientific Journalism, Personal Care Produ

109. IconBAZAAR - Molecules - WWW Resources On Molecular Modeling A large collection of 3D molecular models for smelly compounds. The compounds are listed in alphabetical order. Structure Data Base http://www.iconbazaar.com/molecules/resources.html

110. Science Electronic Marketplace: Benchtop: Molecular Modeling Software, Sep. 96 molecular modeling software focuses on programs that enable researchers to visualize Today, with the assistance of sophisticated molecular modeling and http://www.sciencemag.org/feature/e-market/benchtop/bt-molmod.shl

'); document.write(' '); document.write(' ');document.write(' '); document.write(' Molecular Modeling Software: Tools for 3-D Visualization by David Bornstein Advertisers in this Supplement: Apple Informax Molecular Applications Group Tripos M olecular Modeling software focuses on programs that enable researchers to visualize and analyze the structures and interactions of molecules. Computer programs such as these have become important research tools in the fields of combinatorial chemistry and drug design. Researchers can take existing structures or protein-homology-built structures, dock libraries of known molecules (or specifically-designed molecules) one at a time into the receptor sites as they are revealed in the crystal structure, and compute approximate energies of interaction. "We can take large databases and order the molecules and say these are the most likely to give you activity,"explains Cory. "And once we get a lead on a new protein, we can then take those docked molecules, get crystal structures of the molecules bound to the receptor, and use them to develop new product molecules." Perhaps the most notable development in this field today are HIV protease inhibitors, believed by many to be the most promising approach to the treatment of HIV infection and AIDS. "These drugs were developed with extensive use of computer-assisted drug design,"says Cory.

111. Wiley::Molecular Modeling On The PC Computational Chemistry molecular modeling. molecular modeling on the PC Matthew F. Schlecht ISBN 0471-18567-1 Hardcover 763 pages April 1998 http://www.wiley.com/WileyCDA/WileyTitle/productCd-0471185671.html

Location: United States change location Shopping Cart My Account Help ... Contact Us By Keyword By Title By Author By ISBN By ISSN Wiley Chemistry Molecular Modeling on the PC Related Subjects Electrochemistry General Chemistry Special Topics in Chemistry Biochemistry Join a Chemistry Mailing List Related Titles Reviews in Computational Chemistry, Volume 6 (Hardcover) by Kenny B. Lipkowitz (Editor), Donald B. Boyd (Editor) Reviews in Computational Chemistry, Volume 7 (Hardcover) by Kenny B. Lipkowitz (Editor), Donald B. Boyd (Editor) Reviews in Computational Chemistry, Volume 8 (Hardcover) by Kenny B. Lipkowitz (Editor), Donald B. Boyd (Editor) Reviews in Computational Chemistry, Volume 9 (Hardcover) by Kenny B. Lipkowitz (Editor), Donald B. Boyd (Editor) Reviews in Computational Chemistry, Volume 10 (Hardcover) by Kenny B. Lipkowitz (Editor), Donald B. Boyd (Editor) Reviews in Computational Chemistry, Volume 1 (Hardcover) by Kenny B. Lipkowitz (Editor), Donald B. Boyd (Editor) Reviews in Computational Chemistry, Volume 2 (Hardcover) by Kenny B. Lipkowitz (Editor), Donald B. Boyd (Editor) Molecular Modeling on the PC Matthew F. Schlecht

112. Wiley::Molecular Modeling Of Inorganic Compounds, 2nd, Completely Revised And En In many branches of chemistry, molecular modeling is a wellestablished and In the third part, the reader learns how to apply molecular modeling to a http://www.wiley.com/WileyCDA/WileyTitle/productCd-3527299157.html

Location: United States change location Shopping Cart My Account Help ... Contact Us By Keyword By Title By Author By ISBN By ISSN Wiley Chemistry Inorganic Chemistry General Inorganic Chemistry Molecular Modeling of Inorganic Compounds, 2nd, Completely Revised and Enlarged Edition Related Subjects Geology Electronic Materials, Metals and Alloys Bioinorganic Chemistry Join a Chemistry Mailing List Related Titles General Inorganic Chemistry Handbook of Porous Solids (Hardcover) by Ferdi Schuth (Editor), Kenneth S. W. Sing (Editor), Jens Weitkamp (Editor) Inorganic Chemistry Highlights (Hardcover) by Gerd Meyer (Editor), Dieter Naumann (Editor), Lars Wesemann (Editor) Inorganic Experiments, 2nd, Completely Revised and Enlarged Edition (Hardcover) by J. Derek Woollins (Editor) Silicon Chemistry: From the Atom to Extended Systems (Hardcover) by Peter Jutzi (Editor), Ulrich Schubert (Editor) Molecular Clusters of the Main Group Elements (Hardcover) by Matthias Driess (Editor), Heinrich Nöth (Editor) Organosilicon Chemistry V: From Molecules to Materials (Hardcover) by Norbert Auner (Editor), Johann Weis (Editor) The Chemistry of Nanomaterials: Synthesis, Properties and Applications, 2 Volumes (Hardcover)

113. Free Molecular Modeling Software java applets, free software, science projects, interactive chemistry software, molecular modeling. http://www.edinformatics.com/mathmol/mm_software.htm

Today is WHAT IS MOLECULAR MODELING? WHY IS MOLECULAR MOLECULAR MODELING IMPORTANT? VIEW MOLECULES IN 3-D... BIOTECHNOLOGY COMPANIES AND BIOTECHNOLOGY ENCYCLOPEDIA Student and Teacher Travel Student / Teacher Travel Study Abroad Student Travel Spring Break ... Travel Guides Free Molecular Modeling Software Although designed for University level research, the following software packages are ideal to supplement high school and advanced middle school chemistry lessons. The software can also be used as a tool for student science projects. These are all 'free software programs', although many require registration. CHIME RasMol RasMol is a molecular graphics program developed at the University of Edinburgh. The software is intended for the visualization of proteins, nucleic acids and small molecules. The program has the ability to read in PDB as well as several other formats. For more information on RasMol visit the RasMol Home Page SwissPDB Viewer Swiss-PdbViewer is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface. ArgusLab ArgusLab contains: An interactive 3D molecule builder that allows the user to build and manipulate complex structures; and, a rich suite of computational methods, both quantum mechanical and molecular mechanical, for calculating ground and excited states properties. The program is free for academic use

114. NAMD - Scalable Molecular Dynamics NAMD is a parallel molecular dynamics code for large biomolecular systems. Our tutorials show you how to use NAMD for biomolecular modeling. http://www.ks.uiuc.edu/Research/namd/

Overview Research Development Dissemination ... NIH Resource for Macromolecular Modeling and Bioinformatics NAMD, recipient of a 2002 Gordon Bell Award , is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects , NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using gigabit ethernet. NAMD is file-compatible with AMBER, CHARMM, and X-PLOR and is distributed free of charge with source code. You can build NAMD yourself or download binaries for a wide variety of platforms. Our tutorials show you how to use NAMD for biomolecular modeling. NAMD 2.6b1 was released July 30. See what's new and try it today! Spotlight: NAMD in Scienomics Software (Apr 2005) The Materials and Processes Simulations (MAPS) platform from Scienomics Other Spotlights Overview Why NAMD? (in pictures) Steered Molecular Dynamics Interactive Molecular Dynamics Features and Capabilities Performance Benchmarks ... Credits Availability Read the License Download Binaries Build from Source Code Run at NCSA SDSC or PSC NAMD in Scienomics Software Training Charm++ Workshop (Oct 17-19, 2005)

115. Laboratory For Molecular Modeling The Laboratory For Molecular The Laboratory for molecular modeling is a 1500 sq. foot facility. The Laboratory currently acts as a UNC Core molecular modeling facility. http://www.ibiblio.org/pharmacy/mml.html

Laboratory for Molecular Modeling The Laboratory for Molecular Modeling was established in December 1987, by Dean Tom S. Miya of the School of Pharmacy and Dr. J. Phillip Bowen, Assistant Professor of Medicinal Chemistry and the first Director of the Laboratory. The present Director, Dr. Alexander Tropsha , joined the School of Pharmacy in July, 1991. Since its establishment, the Laboratory has gained national and international recognition for its basic and applied research efforts. The Laboratory has also served as a support facility for the first formal graduate course and the first American Chemical Society short course in Molecular Modeling. Beginning in 1993, the Laboratory supports two graduate courses a year - Introduction to Molecular Modeling and Drug Design (Fall Semester) and Macromolecular Modeling (Spring Semester). The graduate program of the Laboratory is of an interdisciplinary nature involving faculties from various departments on the UNC and other campuses as well as guest participants from several industrial organizations. It is a long-term goal and tradition of the Laboratory to assist any ongoing or planned research projects with a molecular modeling component. The Laboratory for Molecular Modeling is a 1500 sq. foot facility. The Laboratory specialized equipment includes: six high-speed

116. The Scientist :: Molecular Modeling - Seeing The Whole Picture With Modeling Sof molecular modeling Seeing the Whole Picture with Modeling Software Packages. By Christopher Smith return to webpage. Want to read more? http://www.the-scientist.com/yr1998/august/profile2_980831.html

Please login or register DAILY E-MAIL RSS HANDHELD CURRENT ISSUE DAILY NEWS UPFRONT FEATURE ... return to webpage Molecular Modeling - Seeing the Whole Picture with Modeling Software Packages By Christopher Smith return to webpage Want to read more? This article is in our premium content section. Gain access to our rich archive containing 17+ years of The Scientist exclusive online-only content, and detailed survey results. Back to top The Scientist support@the-scientist.com

117. Advances Of Molecular Modeling - Perspectives For Soil Research, Vienna, Austria Impact of Genetically Modified Organisms on Soil Microbiology and Nutrient Dynamics, DATE 4 6 November 2002 VENUE Vienna, University of Natural http://www.boku.ac.at/boden/ammsr/ammsr.html

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118. ISREC Molecular Modeling Page STEREOCHEMICAL ANALYSIS AND molecular modeling OF PROTEINLIPID COMPLEXES. AVKajava - molecular modeling of the Three-dimensional Structure of Ice 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

119. FSU - Institute Of Molecular Biophysics Contains information on the Structural Biology Research Emphasis, Center of Excellence, Biomolecular Computer modeling, and Ph.D. Program at Florida State University. http://www.sb.fsu.edu

Institute of Molecular Biophysics - Florida State University Tallahassee, Fl. 32306 Mail code 4380

120. Computational Biology Software Range of biological software for DNA sequencing, molecule modeling, polymerase chain reaction, and taxonomy. http://www.yk.rim.or.jp/~aisoai/soft.html

Molecular Biology Software What's New Home Research Tool LINKS ... Japanese Macintosh Software for the Molecular Biologists GeneSystems www - Creator of Plasmid Artist: Macintosh software for generating publication quality plasmid map diagrams. Genetics Computer Group www - Developers of the Wisconsin Sequence Analysis Package, software aiding researchers in DNA and protein analysis. MolBio Macintosh Site ftp - Server with huge amounts of molbio software at Indiana University (USA) Textco, Inc www - Molecular biology software for the Macintosh. EnzymeX - A program for molecular biologists. For Mac OS X. What's New Home Research Tool LINKS ... General DNA Sequence Analysis Software The BioCatalog: Rel 5.8 www - The BioCatalog is a software directory of general interest in molecular biology and genetics - European Bioinformatics Institute DELILA ftp - Sequence analysis system: Files in this archive are compressed by the Unix compress routine - NCI (USA) Double Digester ftp - Yale University (USA) Gene Construction Kit and Gene Inspector - provided by Textco, Inc

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