81. ISREC Molecular Modeling Page ISREC molecular modeling activities. Andrey Kajava STEREOCHEMICAL ANALYSIS AND 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

82. 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).

83. Molecules From Chemistry At Okanagan University College Search Results in the Bio Netbook molecular modelling classification molecular modelling, cristallography http//bsmcha1.biochem.ucl.ac.uk80/~martin/ ANTAS ANTAS molecular modeling research group at Disaaba. http://www.ouc.bc.ca/chem/molecule/molecule.html

Index to the Models I. Recent Additions II. Functional Group: Alcohols Aldehydes Alkanes Alkenes ... Phenols III. Molecular Type or Origin: Inorganic Acids (Organic) Chiral Molecules Cyclic Molecules (Non-Aromatic) ... Molecular Fragments (short topics) IV. Indexes: Formula Index (large file). JavaScript search engine Alphabetical Indexes: A B C D ... T to Z For help with General/Organic Chemistry, go to Main Index Page. The Molecular Model files in .pdb, .mol or .xyz format are 1995-2003 by Dave Woodcock. Notes The models are intended for use where exact interatomic distances and conformations (as might be determined by X-ray analysis for example) are not required. I am using them with beginning students in organic chemistry as educational aids and in tutorials on this site. I use a commercial programme to obtain x,y,z coordinates and convert these into the pbd format by first using the format interconversion programme, Babel, then using a Perl script followed by hand editing to produce the final pdb file. pdb files may be viewed using the ChemScape Chime plug-in or by using the stand-alone programme Rasmol (This site also has lots of information on RasMol, Chime and Protein Explorer.)

84. Molecular Modeling And Bioinformatics http//www.h6.dion.ne.jp/~ksugino/ http://www.biwa.ne.jp/~k-sugino/

http://www.h6.dion.ne.jp/~k-sugino/ http://www.h6.dion.ne.jp/~k-sugino/

85. Table Of Contents For Molecular Modeling And Simulation Applications Table of Contents for molecular modeling and Simulation Applications. CNS Dynamics Simulation (Local Only) DOCK Most Favorable http://www.csb.yale.edu/model_toc.html

CSB Home Search Table of Contents General Information Table of Contents for Molecular Modeling and Simulation Applications CNS : Dynamics Simulation (Local Only) DOCK : Most Favorable Ligand/Receptor Binding GROMACS : Dynamics for Molecular Modeling ISIS/DRAW : Chemical Structure Drawing package MAIN : Model Building and Refinement NAMD : Dynamics for Molecular Modeling NAMOT : Nucleic Acid Modeling Tool O : Model Building and Refinement REDUCE : Build Hydrogens on your Model RNAView : Quickly generate display of RNA/DNA secondary structures with tertiary interactions TINKER : Molecular Modeling, Dynamics and Analysis TurboFrodo : Model Building and Refinement : Model Building and Refinement Xplor : Dynamics Simulation Xtalview : Model Building and Refinement CSB Home Search Table of Contents General Information Center for Structural Biology ( www.csb.yale.edu ), Yale University ( www.yale.edu Contact: webadmin(at)mail^csb^yale^edu Last Modified: Monday, 24-May-2004 09:37:17 EDT by P. Fleming

86. School Of Medicine: Research: Core Facilities: BIMCORE: Molecular Modeling Softw molecular modeling Software at BimCore. Icon Key. Homepage, Download, Kinemage. PostScript, Reference/ Manual, Graphics, Tutorial. http://www.bimcore.emory.edu/home/SoftwareMM.html

Emory University: School of Medicine: Research: Core Laboratories ... Links Molecular Modeling Software at BimCore Icon Key : Homepage : Download : Kinemage : PostScript : Reference/ Manual : Graphics : Tutorial UNIX denotes that a local login to BimCore's Unix workstations is required. Molecular Visualization Name Description Download Reference/ Manuals Tutorials/ Examples Grasp surface representations UNIX N/A N/A Midas Plus interactive graphics display for macromolecules UNIX N/A N/A Mage display and viewing of kinetic images of molecules Molscript ref Web Interface UNIX Web Rasmol manual 3D molecular graphics viewer ( ref Ribbons converts molecular coordinates into black and white postscript ( ref UNIX Sybyl biomolecular visualization, manipulation, building, design, and analysis ( ref contact Tripos UNIX N/A View visualization and calculation program UNIX N/A N/A Homology Modelling Name Description Download Reference/ Manuals Tutorials/ Examples Composer, Sybyl comparative structural modelling, T. Blundell contact Tripos UNIX N/A Matchmaker, Sybyl inverse folding, tertiary structure prediction, J. Skolnick

87. Modeling Molecules, Particles & Plantary Systems With VRML & Java3d Particles and Planetary Systems Animated with VRML,Java3d and VRML Loaders for Java3d. molecular modeling with Java3d VRML on Linux. http://www.frontiernet.net/~imaging/molecular_modeling.html

The "Java Molecular Viewer" (JMV) is a molecule viewer program written in Java and Java3D developed by the NIH ( the US National Institute Of Health ). It is designed to be an easy-to-use, platform neutral molecular visualization tool which can be used standalone or integrated into a larger program. It provides several molecular representations, multiple coloring styles, lighting controls, and stereoscopic rendering capabilities. It loads VRML and PDB files over the web, from the RCSB protein databank, from BioCoRE filesystems, and from local filesystems. http://freshmeat.net/projects/jmv/ Run the Demo Java3d required Java Source Code is available: Download here For additional information see the JMV page at the Theoretical and Computational Biophysics Group Virtual Chemistry Lab implemented with VRML, Java3d, XML, with the Sun VRML Loaders 3d VRML Modeling with Animation on Linux ( Red Hat 7.2 ): 7 instances of my Java3d VRML Viewer program Your browser is not configured to run Java ! Gallium Arsenide Crystal ( Java enabled browser required ) Gallium Arsenide Crystal VRML Model : molecule_GaAs.wrl

88. Orville.ucsc.edu/cgi-bin/ferinczbin/convert Center for Biomolecular modelingThe MSOE Center for Biomolecular modeling (along with 3D Molecular Designs) creates handheld molecular models in a variety of types and formats to assist in http://orville.ucsc.edu/cgi-bin/ferinczbin/convert

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

Today is Read About WHAT IS MOLECULAR MODELING? WHY IS MOLECULAR MODELING IMPORTANT? VIEW AND READ ABOUT SOME COMMON MOLECULES: DNA, ASPIRIN, CAFFEINE... Our Sponsors: TheFreeDictionary.com FreeEncyclopedia TheFreeLibrary.com Our Sponsors: TheFreeDictionary.com FreeEncyclopedia TheFreeLibrary.com Webster Dictionary 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.

90. Academic Sites (145) and molecular dynamics calculations. A molecular modeling program running in Windows 95 and NT, has backends to run in UNIX boxes. http://www.chemoinformatics.com/free/molmod-sites.html

This is our own collection of Web sites related to Theoretical and Computational Chemistry. Please e-mail to the WebMaster any changes or additions to the list (you can verify the status of your favorite country in the text file country_list.txt ). Notice that there is a collection of Universities around the World at the Braintrack University Index where you can eventually find more information. Academic Sites (145) Argentine Australia Austria Belgium ... Venezuela Selected Computational Chemistry Software Integrated Packages Hyperchem Hyperchem Release 5 provides 3-D visualization and animation, quantum chemical (semiempirical, ab initio), molecular mechanics and molecular dynamics calculations. A molecular modeling program running in Windows 95 and NT, has backends to run in UNIX boxes. Spartan Spartan 5.0 (for UNIX machines) provides molecular mechanics, ab initio and density functional calculations, conformational searches, graphical interface, etc. Macintosh and PC versions are al;so available. Databases TAPP TAPP is a database of thermochemical and physical properties of pure chemical compounds. TAPP contains properties for over 11,000 solid compounds and over 6,000 fluids and includes data for both organic and inorganic compounds. The database also contains more than 1,500 binary and ternary phase diagrams. TAPP runs under MacOS or Windows.

91. Applying Molecular Modeling CoMSEF, http//www.comsef.aiche.org/), including links to ChE faculty with research on molecular modeling, software sources, online literature, images, etc. http://itri.loyola.edu/molmodel/welcome.htm

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

92. Cssj.chem.sci.hiroshima-u.ac.jp/molda/molda.htm The molecular modeling Toolkit Conference The molecular modeling Toolkit a case study of a large scientific application in Python. Konrad molecular modeling. The term http://cssj.chem.sci.hiroshima-u.ac.jp/molda/molda.htm

93. Molecular Modeling Core Guide A Users Guide for the molecular modeling Core Facility. 5.3.6. Molden DOCU. 5.4 molecular modeling 5.4.1. Full graphics programs 5.4.1.1. http://inka.mssm.edu/endo/guide.html

94. Molecular Modeling Core Facilities The major objective of the molecular modeling Laboratory is to provide a basis for integrating computational and experimental methodologies, allowing faculty http://bims.unmc.edu/MMC/fac_mmc.html

95. Springer-Verlag - Chemistry Journal of molecular modeling Computational Chemistry Life Sciences - Advanced Materials - New Methods Editor-in-Chief T. Clark ISSN 1610-2940 (print http://www.springeronline.com/sgw/cda/frontpage/0,10735,4-135-70-1116860-0,00.ht

Please enable Javascript in your browser to browse this website. Select your subdiscipline Analytical Chemistry Biochemistry Biotechnology Inorganic Chemistry Organic Chemistry Polymer Science Home Chemistry Select a discipline Biomedical Sciences Chemistry Computer Science Engineering Environmental Sciences Geosciences Law Life Sciences Materials Mathematics Medicine Statistics preloadImage('/sgw/cda/pageitems/designobject/cda_displaydesignobject/0,10885,4-0-17-900120-0,00.gif'); preloadImage('/sgw/cda/pageitems/designobject/cda_displaydesignobject/0,10885,4-0-17-900180-0,00.gif'); preloadImage('/sgw/cda/pageitems/designobject/cda_displaydesignobject/0,10885,4-0-17-900170-0,00.gif'); preloadImage('/sgw/cda/pageitems/designobject/cda_displaydesignobject/0,10885,4-0-17-900190-0,00.gif'); preloadImage('/sgw/cda/pageitems/designobject/cda_displaydesignobject/0,10885,4-0-17-900200-0,00.gif'); All Author/Editor Title ISBN/ISSN Series preloadImage('/sgw/cda/pageitems/designobject/cda_displaydesignobject/0,10885,4-0-17-900050-0,00.gif'); preloadImage('/sgw/cda/pageitems/designobject/cda_displaydesignobject/0,10885,4-0-17-900070-0,00.gif');

96. Www.chem.vt.edu/YIP/Mmodel.html molecularmodeling software, data, conferences, jobs, quantum chemistry, molecular mechanics, molecular dynamics, QSAR, molecular graphics, molecular modeling, and associated http://www.chem.vt.edu/YIP/Mmodel.html

97. Molecular Modeling Secton Home Page The molecular modeling Section Home Page. Design and development of molecular graphics and other software tools for molecular modeling. http://www3.cancer.gov/intra/lmb/mms.htm

The Molecular Modeling Section Home Page Figure: Designed disulfide bond (yellow) between the heavy and light chains of mouse monoclonal antibody B3. Affiliation: Molecualr Modeling Section Laboratory of Molecular Biology National Cancer Institute National Institutes of Health Research: Origin and magnitude of the hydrophobic effect. Design and development of molecular graphics and other software tools for molecular modeling. Design of mutations on a class of immunotoxins that will improve their property and biological activity. Protein structure prediction and comparison. About our group: Who we are and how to reach us Selected Publications Resources: Software Available for Downloading Fun molecule pictures NIH home page

98. CERMM - Centre For Research In Molecular Modeling Announcements. Please note that this site has moved to cermms.concordia.ca. Go to Concordia Home Page; Department of Chemistry and Biochemistry. http://artsandscience.concordia.ca/chem/CERMM/

Announcements Please note that this site has moved to: cermm-s.concordia.ca Go to: Concordia Home Page Department of Chemistry and Biochemistry Last update: January 2004 Contact us: admin@CERMM.concordia.ca Webmaster: web-CERMM@CERMM.concordia.ca

99. The Scientist - Molecular Modeling In The Genomics Era ); //. PROFILE. molecular modeling in the Genomics Era. For more information on molecular modeling, CASP, and prediction methods, see references 1014. S. http://www.the-scientist.com/yr2001/mar/profile_010305.html

The Scientist 15[5]:24, Mar. 5, 2001 PROFILE Molecular Modeling in the Genomics Era New tools open windows into protein structure and function By Christopher M. Smith Molecular Modeling, Visualization, and Structure Prediction Software (Additional material not included in the print edition) Courtesy of Theoretical Biophysics Group Beckman Institute University of Illinois at Urbana-Champaign The photosynthetic reaction center of the purple bacterium, Rhodopseudomonas viridis (rendered using VMD) The aim of some life science researchers is to understand human physiology and the various diseases and mutations that can cause the body to go haywire. Accomplishing this goal requires a thorough understanding of the workhorse of all biological systems, the protein. Currently, a tremendous amount of effort is spent on proteomics research as scientists map protein-protein interactions (proteomics tools and technologies will be profiled in LabConsumer on April 2, 2001). Yet there is also a push to map the structural features of proteins, and the structural basis of protein-protein, protein-ligand, and protein-drug interactions. This effort requires the development and enhancement of software capable of carrying out molecular modeling, structure visualization, structure prediction, and protein folding and energetics calculations. Research

100. Chemistry-software.com: Specializing In Organic Chemistry Software, Mass Spectro Open GL graphics for stunning visuals! HyperChem is a sophisticated molecular modeling environment that is known for its quality, flexibility, and ease of use. http://www.chemistry-software.com/

Software for chemistry, biochemistry and laboratory management Home demo download buy contact us ... price list Software categories Chemical Inventory MSDS Management Molecular modelling / drawing Chemical databases ... How to order (866) 571-1976 (USA, toll free) 01737 822144 (UK) Worldwide software sales and support Top Products Molsearch Pro Easy to use chemical database system. Fast and easy creation of databases with up to 10,000,000 records. Search databases by (sub)structure and any other field. Structure editor built in, no need for other software. Over 165 pre-drawn structure template or, create your own. Model Chemlab A complete laboratory simulation. Its a great alternative to dangerous, expensive or environmentally hazardous labs. Model ChemLab is a unique product incorporating both an interactive simulation and a lab notebook workspace with separate areas for theory, procedures and student observations. Commonly used lab equipment and procedures are used to simulate the steps involved in performing an experiment. Users step-through the actual lab procedure while interacting with animated equipment in a way that is similar to the real lab experience. Cyber ed Courses for introductory and advanced Chemistry instruction This impressive series of engaging chemistry programs will help your students quickly learn complex chemistry concepts using the power of 3D animations and audio-narration.

Page 5     81-100 of 134    Back | 1  | 2  | 3  | 4  | 5  | 6  | 7  | Next 20