61. MDL Information Systems - Scientific Software And Databases For The Life Science Databases, molecular modeling, and structureactivity relationship software for Windows. Covers glasses, polymers, proteins, toxicology, and oncology. http://www.scivision.com

We're redesigning the MDL Web site to make it easier to use. Read about the new Web site and the latest discovery informatics solutions from MDL in the 25th Anniversary Edition of Molecular Connection Product Finder: Select a product or database AutoNom AIDS Database ChemInform Reaction Library CrossFire Beilstein CrossFire Gmelin Current Synthetic Methodology Derwent Journal of Synthetic Methods (formerly RX-JSM) DiscoveryGate Environmental, Health, and Safety Hazard Communication Integrated Major Reference Works Material Safety Data Sheets MSDS Authoring and Delivery National Cancer Institute Databases OHS Safety Series ORGSYN Database Download No-fee Software! American Chemical Society Meeting March 24-26 Drug Discovery Technology March 31-April 3 MDL US User Conference 2003 May 4-8 White Paper on MDL's Enhanced Stereochemical Representation MDL assembles Scientific Advisory Board MDL and SciTegic form strategic alliance MDL delivers custom chemical registration system for Aventis Special offer for academic institutions in North America. About MDL Support Newsmagazine Products ... Jobs Other sites in the Elsevier Science family: MDL GmbH Elsevier Science ScienceDirect ChemWeb.com

62. Chapter 5. Quantum Chemistry In Molecular Modeling Chapter 5. Quantum chemistry in molecular modeling. 5.1 Why use QuantumChemical methods ? Quantumchemical methods are more general http://www.caos.kun.nl/~borkent/compcourse/fred/ch5.html

Chapter 5. Quantum chemistry in Molecular Modeling 5.1 Why use Quantum Chemical methods ? Quantum-chemical methods are more general than empirical methods The recipe for the calculation of the electronic wavefunction 5.3 Hartree-Fock SCF theory Part a: The independent particle approximation Part b :Molecular Orbitals, basis sets 5.4 Limitations of the HF method; Electron correlation CI, MP2 and MCSCF 5.5 Energy calculations Conversion of absolute energies to heats of formation Isodesmic reactions 5.6 Quality of ab initio results Performance of low-level methods for organic molecules 5.7 Semi-empirical quantum chemistry Further approximations and introduction of empirical parameters 5.8 Quality of semi-empirical results Low-level ab initio methods are usually better, but much more time-consuming 5.9 Solvation The medium can be represented as a dielectric continuum 5.10 Atomic charges Not a physical concept ! Several methods exist for attributing charge to individual atoms 5.1 Why use Quantum Chemical methods ? Many aspects of molecular structure and dynamics can be modeled using classical methods in the form of molecular mechanics and dynamics. The classical force field is based on empirical results, averaged over a large number of molecules. Because of this extensive averaging, the results can be good for standard systems, but there are many important questions in chemistry that can not at all be addressed by means of this empirical approach. If one wants to know more than just structure or other properties that are derived only from the potential energy surface, in particular properties that depend directly on the electron density distribution, one has to resort to a more fundamental and general approach : quantum chemistry. The same holds for all non-standard cases for which molecular mechanics is simply not applicable.

63. PPL Contents And Abstracts Publishes on all aspects of protein and peptide research, including structural studies, recombinant expression, function, synthesis, enzymology, immunology, molecular modeling, and drug design. http://www.bentham.org/ppl/pplconts.html

[Back to Home Page] [Instructions for Authors] Contents and Abstracts Follow the links to view the contents and abstracts of the listed issues. Protein and Peptide Letters, Volume 10, 2003 [Volume 10, Number 1] Protein and Peptide Letters, Volume 9, 2002 [Volume 9, Number 6] [Volume 9, Number 5] [Volume 9, Number 4] [Volume 9, Number 3] ... [Volume 9, Number 1] Protein and Peptide Letters, Volume 8, 2001 [Volume 8, Number 6] [Volume 8, Number 5] [Volume 8, Number 4] [Volume 8, Number 3] ... [Volume 8, Number 1] Protein and Peptide Letters, Volume 7, 2000 [Volume 7, Number 6] [Volume 7, Number 5] [Volume 7, Number 4] [Volume 7, Number 3] ... [Volume 7, Number 1] Protein and Peptide Letters, Volume 6, 1999 [Volume 6, Number 6] [Volume 6, Number 5] [Volume 6, Number 4] [Volume 6, Number 3] ... [Volume 6, Number 1] Protein and Peptide Letters, Volume 5, 1998 [Volume 5, Number 6] [Volume 5, Number 5] [Volume 5, Number 4] [Volume 5, Number 3] ... [Volume 5, Number 1] Protein and Peptide Letters, Volume 4, 1997 [Volume 4, Number 6] [Volume 4, Number 5] [Volume 4, Number 4] [Volume 4, Number 3] ... [Volume 4, Number 1] Protein and Peptide Letters, Volume 3, 1996 [Volume 3, Number 6]

64. 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

65. Molecular Modeling molecular modeling. Some of the pages in the Molecular Nanotechnology section also deal with molecular modeling. NanoCAD, A Freeware http://www.lucifer.com/~sean/n-mm.html

Molecular Modeling Some of the pages in the " Molecular Nanotechnology " section also deal with molecular modeling. NanoCAD , A Freeware CAD System for Nanotechnology: this is an exciting project to develop a computer program to simulate the behavior of atoms and molecules engaging in chemical reactions, particularly the controlled reactions discussed in the nanotech literature. The user would be able to build hypothetical molecules and watch how they interact with other molecules. [who knows, this might evolve into the nanotech design tool someday Sean] Viseur is a program that can help G-Protein Coupled Receptor modelling. The 3D molecular view can be written as an OpenInventor file and translated (ivToVRML tool) to VRML with hyperlinked amino-acids. David Eppstein's (ICS, UC Irvine) molecular modeling page, " Geometry in Action Mailing lists and electronic journals/magazines Journal of Computer-Aided Molecular Design Journal of Molecular Modeling Molecular Structure Laboratory , Department of Chemistry at the University at Stony Brook (NY): samples of molecular graphics produced using CHEM-RAY and related programs developed at the laboratory. molecular modeling oriented information resource at the National Institutes of Health (NIH) Molecules R US - an interactive interface to facilitate access (browsing, searching and viewing) of the molecular structure data contained within the Brookhaven Protein Data Bank (PDB).

66. 3D Genoscience - Drug Discovery And Development Of Molecules To Fight HIV And He Genmol is a 3D molecular modeling software for measuring resistance/affinity between a ligand and a target, used for Disease Management, Drug Discovery and Development of molecules. http://www.3dgenoscience.com/index.php

Genoscience 23 rue de Friedland 13 006 Marseille France Tel : +33.4.91.29.95.14 Fax : 33.4.91.79.20.44 Genmol 3D molecular modeling software , as the standard tool for measuring resistance/affinity between a ligand and a target, with significant implications in Disease Management, Drug Discovery and Development. Introduction of our technologies by Dr Mark Wainberg : "Solutions for Disease Management and Development of Drugs to Fight Viruses" in the section " our technologies HIV Protease Inhibitor : video simulation Docking in the active site I Welcome I I Meet the company I I Our Technologies I I Our Products I I Investors Information I I In the News I I Join Our Team I I Contact us I Terms of Service Designed and Produced by E-MedHosting.com Inc.

67. DDL Main Page molecular modeling resources, software and projects. Home of the programs Vega and BioDock. http://users.unimi.it/~ddl/

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68. Molecular Modeling At Virginia Tech General References for molecular modeling. Listed below are some generalreferences that pertain to molecular modeling. References http://www.biochem.vt.edu/courses/modeling/

Home Page Topics Evaluation Assignments ... News Home Page General Information These Web pages are designed primarily for a course entitled "Molecular Modeling of Proteins and Nucleic Acids" taught in the Department of Biochemistry at Virginia Tech by Dr. David R. Bevan. The purpose of the course is to prepare students to read and interpret the molecular modeling literature and to apply molecular modeling in their research. The Web pages serve as a guide to students in the course, though they also may be of interest to other molecular modelers. For several of the topics, on-line references are already available and can be accessed from links that are provided. Most notably, the excellent on-line resource developed at the NIH is referenced several times. For some topics, on-line material is not available or is unsuitable for this course. In these cases, a more comprehensive review has been prepared. Topics UNIX Protein Structure and Proteomics Nucleic Acids Visualization ... Docking Student Presentations General References for Molecular Modeling Listed below are some general references that pertain to molecular modeling. References to on-line and printed resources that pertain to the specific topics are given with the topics.

69. ChemSW Chemistry Software For Windows Offers commercial chemistry software for inventory management, chromatography, mass spectrometry, molecular modeling, physical properties, reaction kinetics, and radioactive decay. http://www.chemsw.com/

The leading provider of chemical inventory management systems, MSDS systems and chemistry laboratory software. Products New Support Order ... Quality Control ChemSW is the leader in asset management software for laboratories worldwide, providing inventory and laboratory solutions since 1991. Our software is installed in thousands of laboratories including the smallest of chemical stockrooms and the largest enterprise environments. We pride ourselves in the best customer service and support available and our knowledgeable staff will be glad to assist you in solving any of your laboratory needs. Products in the news New module for CISPro Chemical Inventory System produces accurate, formatted HMIS reports. ( read more New drug discovery software tool for the life science research community is now available - Visual Cloning (read more) Portable Inventory Manager Controls Security and Movement of Stock Room Chemicals (read more) New Version of Chemical Inventory System Integrates with SQL Server* (read more) Configurable Signature Event for Chemical Inventory System Further Enhances 21 CFR Part 11 Compliance (read more) New NIST/EPA/NIH 2002 database is now available! The first upgrade in 4 years: an increase by 46,078 spectra!

70. CACHE Molecular Modeling CACHE. molecular modeling Task Force. The courses; Conference Foundationsof molecular modeling and Simulation FOMMS 2000, FOMMS 2003; http://zeolites.cqe.nwu.edu/Cache/

CACHE Molecular Modeling Task Force The CACHE Molecular Modeling Task Force (MMTF) was formed to promote the use and distribution of molecular modeling tools in the chemical engineering curriculum. Current Activities Web-based textbook on molecular modeling and simulation Web-based modules to introduce molecular modeling concepts into existing undergraduate chemical engineering courses Conference: Foundations of Molecular Modeling and Simulation: FOMMS 2000 FOMMS 2003 PowerPoint presentation of Task Force activities. Presented by Dave Kofke at the 2000 ASEE Meeting in St. Louis. Task Force Members Arup Chakraborty , University of California, Berkeley, arup@templeton.cchem.berkeley.edu Ariel A. Chialvo , University of Tennessee/Oak Ridge National Laboratory, achialvo@utk.edu Henry D. Cochran, Jr. , Oak Ridge National Laboratory, hdc@ornl.gov Peter T. Cummings , University of Tennessee/Oak Ridge National Laboratory, ptc@utk.edu

71. Sdvl Software: Category: Molecular Modeling . Babel is a program designed tointerconvert a number of file formats currently used in molecular modeling....... Category molecular modeling. BABEL. http://www.msi.umn.edu/user_support/software/MolecularModeling.html

QUESTIONS FEEDBACK HOME Employment Events Links People Programs Publications Support 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://www.amber.ucsf.edu/amber/ Tutorial Amber Tutorials Documentation Remote online documentation can be found on the Amber 6 Manuals and Amber 7 Manuals Local documentation in PDF and HTML format can be found in /usr/local/amber/amber6-serial/doc/ 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 Origin computer. 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:

72. Mathub Features current and background information about molecular modeling and informatics for chemistry and materials science. http://www.mathub.com/

ABOUT MATHUB REGISTER SITE MAP CONTACT US About Mathub Mathub is the focal point for computational materials science on the web, providing a gateway to scientific information about modeling and informatics. If you're interested in in silico materials science this site is just what you've been looking for. Register Free registration is required to access the Mathub site. Register now Features Modeling at Continental Tire - an Interview Computational Chemistry in the Fine Chemicals Industry Theoretical and Computational Chemistry at University College London Nanoscale Modeling. More Features... WebWatch WebWatch reviews the best of the web for computational materials science. Current Mathub WebWatch is MatWeb Computational Materials Science News Carbon Nanotube Conductance Study wins NASA Award Computational and Experimental Search for Polymorphs of Parabanic Acid Matinformatics Tools on the PC Materials Studio 2.2 Released

73. Molecular Modeling Pro molecular modeling Pro TM. This advanced molecular modeling program is theresult of over 20 years of development at a major chemical company. http://www.chemsw.com/13052.htm

The leading provider of chemical inventory management systems, MSDS systems and chemistry laboratory software. Home Products New Support ... Search 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 is also accessible from within MMP (requires CHEMSITE). Routines for conformational analysis are also included. (Requires Windows 3.1 , 95, 98, 2000 or NT). The Molecular Modeling Pro program is: a physical property estimation program a 3-D chemical structure drawing program a chemical data base creation program (used with the companion Molecular Analysis Pro program)

74. 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).

75. Molecular Drawing And Modeling Software Material Science. Molecular Drawing Modeling. Quality Control. Molecular Drawing Modeling Section. molecular modeling Pro. Molecular Analysis Pro. MolSuite. http://www.chemsw.com/molecmod.htm

The leading provider of chemical inventory management systems, MSDS systems and chemistry laboratory software. Home Products New Support ... ChemSite 3D Molecular Visualization Software ChemSite Pro CS ChemOffice Ultra CS ChemOffice Pro CS ChemDraw ... About ChemSW, Inc. 420 F Executive Ct N Fairfield, CA 94585-4019 Tel: 707-864-0845 Fax: 707-864-2815 Email: info@chemsw.com ©1991-2002 ChemSW, Inc. All rights reserved

76. 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.

77. CAChe Molecular Modeling Tutorial http://www.chem.ox.ac.uk/course/cache/default.html

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78. Molecular Modeling Reference Quick Reference Guide to Computational Chemistry Acronyms, Methods, Parameters,Accuracy, and Software. Compliments of CHAMOT LABS, INC. http://www.chamotlabs.com/Freebies/ModelRef.html

Quick Reference Guide to Computational Chemistry Acronyms, Methods, Parameters, Accuracy, and Software Compliments of: CHAMOT LABS, INC. Chemical Research and Consulting METHODS: Geometry OPTIMIZATION TERMS: SOFTWARE: PARAMETERIZATIONS: by Element (Grain of Salt) The information above has been collected from various published results, documentation, and personal experience. (Accuracies are averages of typical literature comparisons.) This list is updated as information comes to my attention and as time allows, but as rapidly as methods evolve (and companies merge), some info is no doubt out of date and/or incomplete. Consequently, these compilations are meant more as an aid to jog one's memory on keywords and capabilities, rather than as a complete and authoritative reference. Return Link to Chamot Labs Home Page 3/13/03 Ernie Chamot / Chamot Labs / (630) 637-1559 /

79. Center For Molecular Modeling CMM Home Research People Publications Links Resources Contact the CMM. http://www.cmm.upenn.edu/

CMM Home Research People Publications CMM Home Research People Publications ... Contact the CMM

80. Molecular Modeling Section Research Origin and magnitude of the hydrophobic effect. Design and developmentof molecular graphics and other software tools for molecular modeling. http://rex.nci.nih.gov/RESEARCH/basic/lmb/mms.htm

Related information: B.K. Lee, Chief, MMS MMS Contact Information MMS Publications and Supplements MMS Gallery ... Laboratory of Molecular Biology Research: Origin and magnitude of the hydrophobic effect. Design and development of molecular graphics and other software tools for molecular modeling. Design of mutations to improve the property and biological activity of protein molecules. Protein structure prediction and comparison. Gene discovery by EST analysis Go to: Laboratory of Molecular Biology National Cancer Institute National Institutes of Health

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