101. Molecules And Molecular Modeling Organic Structures and molecular modeling. Programs for Viewing Molecular Structure Files. Viewing 3D views of molecular structures http://www.chem.tamu.edu/organic/six.html

Organic Structures and Molecular Modeling Programs for Viewing Molecular Structure Files Viewing 3-D views of molecular structures require addition of appropriate 'helper applications' or 'plug-ins' to a standard Web Browser. Free-ware or shareware versions of appropriate programs are available. For viewing molecular structure, either the plug-in Chemscape Chime or the helper application Rasmol may be used. Chemscape Chime shows the structures directly in the Browser page if the source page is set up for Chime. Rasmol can be used as a stand-alone application to view structure files downloaded from any of a variety of sources (see below). Chemscape Chime From MDL Information Systems Ltd. (Free for All Users) Chemscape Chime . Chime supports most of the popular structure display formats that scientists use including MDL Information Systems, Inc. Molfile and many of the popular 3D display formats such as the Brookhaven Protein Databank (pdb) format. Rasmol and RasMac Enhanced by the MultiCHEM Facility, UC Berkeley RasMol is an excellent and free pdb viewer available for Windows, Macintosh and UNIX platforms. This site includes links to Quick Help and Basic Instructions for Rasmol as well as links to download original version of Rasmol..

102. Using Fuzzy Logic For Molecular Modeling Modeling and Simulation, Part I Overview Using Fuzzy Logic for molecular modeling. David A. Ress FUZZY molecular modeling. Figure 3. http://www.tms.org/pubs/journals/JOM/9908/Ress/Ress-9908.html

This article is one of four papers on modeling and simulation (part one) to be presented exclusively on the web as part of the August 1999 JOM-e JOM The second part of this topic supplements the September issue. The coverage was developed by Steven LeClair of the Materials Directorate Air Force Research Laboratory Wright-Patterson Air Force Base The following article appears as part of JOM-e http://www.tms.org/pubs/journals/JOM/9908/Ress/Ress-9908.html JOM is a publication of Modeling and Simulation, Part I: Overview Using Fuzzy Logic for Molecular Modeling David A. Ress TABLE OF CONTENTS INTRODUCTION FUZZY SET THEORY FUZZY MOLECULAR MODELING Fuzzy Lines ... References Since fuzzy logic is, by definition, imprecise, it is a natural means of representing the imprecision of lattice parameters and bond angles. Fuzzy lattice parameters are created by collecting parameter values from the literature. From the minimum, maximum, and average of these parameter values, a fuzzy number is created that represents the imprecision in that parameter. Then, through the use of fuzzy arithmetic operators and recently developed fuzzy trigonometric functions, fuzzy atom locations within the unit cell and bond angles can be calculated. The benefit of using fuzzy logic in this manner is that it directly enables representation and calculation with the imprecision found in chemical compounds, which arises from measurement variability due to measurement error, structural defects, and thermal and vibrational characteristics. INTRODUCTION

103. Folding@Home Educational Project molecular modeling. Author Tug Sezen. Reference Andrew R. Leach (1996); molecular modeling Principles and Applications; Addison Wesley Longman Limited. http://www.stanford.edu/group/pandegroup/folding/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.

104. Molecular Modeling Of Polymer Membranes molecular modeling of Polymer Membranes. Ridgway HF and KI Ishida. 1996. molecular modeling of Organics Adsorption to Polymer Separation Membranes. Proc. http://www.micromemanalytical.com/MolMod/MolecMod.htm

Molecular Modeling of Polymer Membranes Brief Description of Technique Basic Information Provided Key Measurements Examples of Results ... Some Interesting Molecular Modeling Web Sites to Visit Brief Description of the Technique Molecular modeling provides visually rich information concerning the theoretical structure, energetics, and dynamics of your commercial or experimental membrane systems at the atomistic scale. Membrane molecular models can be used to predict the most important theoretical structural attributes of new polymer membrane materials (e.g., density, surface energy, etc.) and to forecast key membrane performance properties such as water flux and solute rejection. Molecular modeling of membranes is performed using modern molecular mechanics and semi-empirical force fields that are parameterized optimally for your system. Custom software is then created to automatically build and optimize your membrane system. Molecular dynamics is subsequently employed to simulate water and solute diffusion within the membrane matrix or to model the energetics and kinetics of the adsorption of organic species to the membrane surface to quantitatively predict basic surface fouling properties.

105. 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

106. Group Theory and methods of computational modeling, alphabetical software and database directory. Krak³w, Poland. http://www.mol.uj.edu.pl/modmol/

Molecular Modelling Group Group research curses publications events ... contact The Group The main aim of our research is to elucidate the basic mechanisms of the biophysical aspects of the cell membrane functioning. The tool we use is molecular modelling at the atomic level. Our particular interests are: the organisation of the membrane/water interface and hydrocarbon chain region in membranes built of phospholipids with saturated and mono-unsaturated chains the influence of selected sterols, terpenoids and local anaestethics on the interface and the non-polarcore of the membrane antibacterial activity and selectivity of magainin-2 peptide signal transduction of vasopressin V2 receptor in the membrane lipid - peptide, lipid - protein interactions In addition to membranes studies, we also apply molecular modelling to the study of dimerisation and polymerisation of alpha1-antitrypsin, a serum protein. August 2003

107. T-10 At LANL The Theoretical Biology and Biophysics Group (T10) at Los Alamos National Laboratory focuses on the modeling of biological systems and the analysis and informatics of molecular and cellular biological data. http://www.t10.lanl.gov/

T-10 Theoretical Division Los Alamos National Laboratory Contact Site Map ... Jobs Research Highlights The Influenza Sequence Database is a curated database of nucleotide and amino acid sequences. It is intended to provide the research community with easy sequence deposit and retrieval capabilities, together with tools tailored, in particular, to the analysis of hemagglutinin and neuraminidase sequences. , the new group leader of T-10, and colleagues have developed an off-lattice minimalist model to describe the effects of pressure on the folding kinetics of proteins ( PNAS ). The model captures the combined effects of the folding transition state and chain configurational diffusion on activation volume changes in pressure-induced protein folding and unfolding. Notable News and Announcements Four of the ten most cited LANL publications between 1995-1999 , including the most cited article, were contributed by T-10. George Bell , former group leader of T-10 and director of T Division, died May 28, 2000. Bell, a Laboratory Senior Fellow, came to Los Alamos in 1951, joining T Division's effort to design and develop the world's first thermonuclear weapons. Bell later co-founded T-10 and was at the forefront of the human genome project. He is also remembered as a world-class mountaineer. Life in Northern New Mexico Balloon Fiesta Bandelier National Monument Santa Fe Tent Rocks

108. AMMP Home Page AMMP is a modern fullfeatured molecular mechanics, dynamics and modeling program http://www.cs.gsu.edu/~cscrwh/ammp/ammp.html

AMMP Home Page Welcome to AMMP AMMP is a modern full-featured molecular mechanics, dynamics and modeling program. It can manipulate both small molecules and macromolecules including proteins, nucleic acids and other polymers. In addition to standard features, like numerically stable molecular dynamics, fast multipole method for including all atoms in the calculation of long range potentials and robust structural optimizers, it has a flexible choice of potentials and a simple yet powerful ability to manipulate molecules and analyze individual energy terms. One major advantage over many other programs is that it is easy to introduce non-standard polymer linkages, unusual ligands or non-standard residues. Adding missing hydrogen atoms and completing partial structures, which are difficult for many programs, are straightforward in AMMP. It is written in C and has been ported to many different computers. The source code is available under the GNU "copyleft" so that it is easy to follow exactly what the program is doing. Another major advantage over commercial software is that AMMP can be easily included in another program to supply molecular mechanics function. The program and modeling methods are under active development. User feedback is appreciated and incorporated in the program. A graphical interface is available for Linux and Unix with the openGL graphics language and for windows 95/98/NT

109. Home Of David S. Goodsell Attempt to add esthetic appeal to molecular graphics and modeling research by author of Lexitropsin; DNA informationreading molecules, at Scripps Institute, La Jolla, California. http://www.scripps.edu/pub/goodsell/

Home of David S. Goodsell "Nature" is what we see - The Hill - the Afternoon - Squirrel - Eclipse - the Bumble bee - Nay - Nature is Heaven - Nature is what we hear - The Bobolink - the Sea - Thunder - the Cricket - Nay - Nature is Harmony - Nature is what we know - Yet have no art to say - So impotent Our Wisdom is To her Simplicity. Emily Dickinson I have recently completed a large commission for the new Center for Integrative Molecular Biosciences. To take a look, click here. My new book on BioNanoTechnology is now available. For ordering information, click on the picture above. "Molecular Machinery: A Tour of the Protein Data Bank," a poster showing a selection of molecules, is now available online. Research Illustration and Education "The Molecular Perspective" "Molecule of the Month" at the Protein Data Bank 1994 and 1998 Molecular Graphics Art Shows Book Extracts What's New at my Home Page? I invite comments and welcome correspondence with scientists and artists interested in molecular subjects. I may be reached at goodsell@scripps.edu

110. Journal Home - Nature Neuroscience Nature Neuroscience welcomes contributions in molecular, cellular, systems and cognitive neuroscience, as well as psychophysics, computational modeling and diseases of the nervous system. http://www.nature.com/neuro

@import "/neuro/style.css"; NATURE.COM NATUREJOBS NATUREEVENTS Help USERNAME: PASSWORD: Save password Forgotten password? SEARCH JOURNAL Advanced search Journal home Advance online publication Current issue ... For librarians NPG Resources Nature Nature Reviews Neuroscience Nature Cell Biology Nature Medicine ... Browse all publications June 2004 - Vol 7 No 6 Motion-sensitive microcircuitry Prostaglandins and development of sexual behavior Navigational landmarks in the parahippocampal gyrus Current issue table of contents ... Advance online publication CURRENT ISSUE CURRENT ISSUE A navigational neuron Article by Haag and Borst Neurons in the fly head ganglion aid its flight control. Haag and Borst unravel the microcircuitry of motion-analyzing cells, suggesting a mechanism for their receptive field tuning. See also: News and Views by Zeck and Masland Landmarks in navigation Article by Janzen and van Turennout As subjects navigate virtually through a computer-generated space strewn with objects, BOLD activity in the parahippocampal gyrus reflects the relevance of those objects as navigational landmarks. See also: News and Views by Spiers and Maguire CURRENT ISSUE CURRENT ISSUE Placebo affects Parkinson's neurons Brief Communication by Benedetti and colleagues Single-cell recordings in Parkinson's patients show that placebo injections not only alleviate clinical symptoms, they also reduce hyperactivity in the subthalamic nucleus.

111. GRAMM (Global Range Molecular Matching) A program for modeling protein docking. http://reco3.musc.edu/gramm/

112. WHAT IF Protein structure analysis software for Linux, SGI/IRIX, Windows NT. Performs mutant prediction, structure verification, homology modeling and molecular visualization. Links to the documentation in HTML. Commercial software. http://www.cmbi.kun.nl/whatif/

WHAT IF Introduction WHAT IF is a versatile protein structure analysis program that can be used for mutant prediction, structure verification, molecular graphics, etc. We distribute 4-6 times per year. Delivery times will therefore range from 2-12 weeks. Emails requesting speedy delivery, confirmation of arrival of the order form, demo versions, etc., will not even be answered. As we say in The Netherlands: "Geduld is ene schone zaak...". WHAT IF 5.0 is available WHAT IF license holders can now get WHAT IF 5.0. If you are a valid WHAT IF license holder, and you have a valid WHAT IF user-number (which is printed on the bill you received with the WHAT IF distribution), you can proceed and request the WHAT IF 5.0 update. Yes I am a WHAT IF license holder and I have a valid user-number No I am not yet a WHAT IF license holder, but I want to buy WHAT IF The WHAT IF course For more information on the WHAT IF course click here References If you use WHAT IF, please refer to: WHAT IF: A molecular modeling and drug design program. G.Vriend

113. Ghemical Homepage An easyto-use molecular editor and modeling package with all-atoms molecular mechanics, reduced protein models and links to many common chemistry programs. Ghemical is released under the GNU GPL and includes source code. http://www.uku.fi/~thassine/ghemical/

This page is mirrored at: www.bioinformatics.org www.uku.fi A molecular modelling package released under the GNU GPL. Authors thassine@messi.uku.fi Introduction Ghemical is a computational chemistry software package released under the GNU GPL . It means that full source code of the package is available, and users are free to study and modify the package. Ghemical is written in C++. It has a graphical user interface (which is based on GNOME), and it supports both quantum-mechanics (semi-empirical and ab initio) models and molecular mechanics models (there is an experimental Tripos 5.2-like force field for organic molecules). Also a tool for reduced protein models is included. Geometry optimization, molecular dynamics and a large set of visualization tools are currently available. Ghemical relies on external code to provide the quantum-mechanical calculations. Semi-empirical methods MNDO, MINDO/3, AM1 and PM3 come from the package (Public Domain), and are included in the source distribution. The MPQC package (GNU GPL) is used to provide ab initio methods: the methods based on Hartree-Fock theory are currently supported with basis sets ranging from STO-3G to 6-31G**. The MPQC code is not included in the source distribution. In order to use the MPQC-based ab initio methods in Ghemical, you must first compile and install the MPQC program for your system, and then compile Ghemical using some specific settings that link the programs together; see the INSTALL file for more information. Ghemical also contains the

114. Lab Of Hui Lu: Computational Proteomics - The lab involves all current aspects of research into protein structure and function including molecular dynamics, ab initio folding, machinelearning based fold recognition, protein-protein interaction, and theoretical modeling of protein mechanics. http://proteomics.bioengr.uic.edu

Research Areas Biomolecular Mechanics Protein Structure Prediction Protein-Protein Interactions Computational proteomics is the genome-scale modeling of protein structure, dynamic s, and function. While experimental methods are still the best way to determine a protein's structure and function, the time and money spent is substantial enough to encourage computer-based solutions. Indeed, computational proteomics involves all current aspects of research into protein structure and function including: molecular dynamics, ab initio folding, machine-learning based fold recognition, protein-protein interaction, and theoretical modeling of protein mechanics. Currently we are collaborating with Julio M. Fernandez 's group from Columbia Universtiy and Klaus Schulten 's group from UIUC on force-induced protein reconfiguration. Other collaborations are with Mike Johnson on Drug design and with Yang Dai on kernal-based protein structure prediction. Announcements Journal Club Structure modeling of SANT domains

115. BUMC: Division Of Graduate Medical Sciences Research in molecular biology, clinical trials, computer modeling, pharmaceutical products at the School of Medicine, Division of Graduate Medical Sciences, the School of Public Health, and the Goldman School of Graduate Dentistry. http://www.bumc.bu.edu/Departments/HomeMain.asp?DepartmentID=86

116. Molecular Modelling molecular Modelling. The threedimensional structures of molecules help determine the physical Shell Electron Pair Repulsion Theory. Bond and molecular Polarity. Intermolecular Forces http://www2.gasou.edu/chemdept/general/molecule

117. MathMol Home Page MathMol home page This Internet site is meant to provide grade K to 12 students and teachers (along with researchers and the general public) information about the growing field of molecular http://rdre1.inktomi.com/click?u=http://www.nyu.edu/pages/mathmol/&y=027AB77

118. Representation Models In Molecular Graphics The Representation of molecular Models. Rendering Techniques. Part I. The Representation of molecular Models. Part II. Rendering Techniques. http://scsg9.unige.ch/fln/eng/toc.html

The Representation of Molecular Models Rendering Techniques Part I The Representation of Molecular Models Part II Rendering Techniques. This page has been accessed times since the 1rst January 1995 (after six months accessibilty) thank you very much for your interest. Part I 1. Structural models. 1.1 The wire-frame model. 1.3 The space-filling model. 1.4 The stick model. ... 7. Future. Part II 1. Shading techniques. 1.1 Classical illumination model of a polygon mesh 1.2 Shading : 1.2.1 Constant shading. ... Chemistry on the Internet: The best of the Web 1995! Other local servers Same document in French Have a look at the public defense of my Ph. D Crystal in Europe University of Geneva FTP access to the SGI file format images of the current document New All the gif images used in theses documents! Table 1 Table 2 Servers list dealing with chemistry francois.savary@chiphy.unige.ch ... Bridge BCC Group of Professor J. Weber, Department of Physical Chemistry, University of Geneva 30, quai Ernest Ansermet CH-1211 Geneva 4 tél.: +4122 702 65 32

119. Welcome To The Biocomputing Pages Of The Center For Computing Services SeqWeb, Start SeqWeb (web interface for GCG) from this page. EMBOSS, The European molecular Biology Open Software Suite. Databases, http://www-bio.unizh.ch/

Biocomputing SW Databases Documentation Visualization ... ZI Home Last modified: Sep 24 2003 07:58 / go Welcome to the Biocomputing pages of the IT Services Biocomputing Biocomputing Software starting point: Start www2gcg and SeqWeb from this page. SeqWeb Start SeqWeb (web interface for GCG) from this page. EMBOSS The European Molecular Biology Open Software Suite. Databases Get information on the different local databases. MSI Pages You can find documentation on how to install MSI software and the Token Licenses here Bitplane You can find information on the Bitplane Licenses here Documentation You can find documentation and links to documentation of biocomputing software installed on the zisgi here. Visualization You can find information and links to documentation on installed visualization packages here. Links Linkslist to other biocomputing resources. zisgi.unizh.ch Information on Software (coming soon) and Hardware of the zisgi. Search bio.unizh.ch

120. SpringerLink - Publication www.springerlink.com/link.asp?id=100529 molecular Modelling(c) Henry Rzepa. 19952003. http://www.springerlink.com/openurl.asp?genre=journal&issn=1610-2940

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