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Molecular Modeling: more books (100)

Molecular Modeling on the PC by Matthew F. Schlecht, 1997-03-15
Saratov Fall Meeting 2001: Laser Physics and Photonics, Spectroscopy, and Molecular Modeling II (Proceedings of Spie) (Vol 4706) by Vladimir L. Derbov, Leonid A. Melnikov, et all 2002-06-03
Molecular Modeling and Theory on Chemical Engineering (Advances in Chemical Engineering) by Arup Chakraborty, 2001-12-27
Molecular Modeling of Inorganic Compounds by Peter Comba, Trevor W. Hambley, et all 2009-10-20
Molecular Modeling of Polymer Structures and Properties by Bruce R. Gelin, 1994-09
Guidebook on Molecular Modeling in Drug Design
Applying Molecular and Materials Modeling
Electron Collisions with Molecules in Gases: Applications to Plasma Diagnostics and Modeling, Volume 44 (Advances in Atomic, Molecular and Optical Physics)
The molecular modeling workbook for organic chemistry by Warren J Hehre, 1998
Theoretical Aspects and Computer Modeling of the Molecular Solid State
Maruzen Molecular Modeling Kit Version 2 by Maruzen International Co., 2002-05
Chemtutor Student Molecular Modeling Kit by Sigma-Aldrich Inc;,
Mathematical modeling of the molecular weight distribution of polypropylene produced in a loop reactor.: An article from: Polymer Engineering and Science by Zheng-Hong Luo, Yi Zheng, et all 2007-10-01
Molecular Modeling for the Design of Novel Performance Chemicals and Materials

lists with details

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/

Extractions: 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...
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/
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/

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

Extractions: Forgot your password? New user? Document Actions 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
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

Extractions: 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 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 Chime Resources by Eric Martz
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

Extractions: 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
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/
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
Molecular Modeling Pro
Interactive molecular modeling and drawing software to build, study, and present molecules, including crystallography.
http://www.chemsw.com/13052.htm

Extractions: 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.
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
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/
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

Extractions: 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.
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
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

Extractions: Scientific Instrument Services, Inc. Supplies and Services for Mass Spectrometers, Gas Chromatographs and Liquid Chromatographs Search: Home Products Catalog Machining ... Employment SIMION 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.
Biodesigner Molecular Modeling And Visualization Program
Biodesigner molecular modeling and Visualization Program.
http://www.pirx.com/biodesigner/index.shtml
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

Extractions: 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
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/

Extractions: 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. 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?
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/

Extractions: The Computer-Aided Nanodesign Site ComputeNano.com Background Technology Glossary ... Home 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
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/

Extractions: 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: 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.
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/

Extractions: 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.

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