121. 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. 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

122. The Molecular Sciences Institute Independent nonprofit research laboratory combining genomic experimentation and computer modeling, Berkeley, California, USA. http://www.molsci.org/

MSI and Amnis Announce Collaboration The Alpha Project Announces the Third Annual Research Symposium: June 16-17, 2005 MSI Releases "Moleculizer" - a new approach to simulation of intracellular biochemical networks More News... MSI and Amnis Announce Collaboration The Alpha Project Announces the Third Annual Research Symposium: June 16-17, 2005 MSI Releases "Moleculizer" - a new approach to simulation of intracellular biochemical networks More News...

123. Molecular ART Gallery molecular Rheology modeling flow and transport properties Nanotechnology Ceramics, Semiconductors, Alloys Quantum Chemistry and Electronic Structure http://www.wag.caltech.edu/gallery/art_gallery.html

Molecular Modeling Gallery Polymers and Polymer Simulations Dendrimers Proteins and Protein Simulations Molecular Rheology: Modeling flow and transport properties Nanotechnology Ceramics, Semiconductors, Alloys Quantum Chemistry and Electronic Structure Problems with this server should be reported to webmaster@www.wag.caltech.edu

124. 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

125. 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 recent 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. I have a number of original paintings for sale. For more information, please see my personal site at http://homepage.mac.com/dgoodsell. 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?

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

127. 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 homepage Login My account ... Browse by subject Search This journal All of nature.com 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 September 2005 - Vol 8 No 9 Risk-sensitive neurons in cingulate Wnts repel spinal axons via Ryk receptors Disrupting repetition priming with TMS Current issue table of contents ... Advance online publication CURRENT ISSUE CURRENT ISSUE Thalamic multimodal integration Article by Komura and colleagues Combining sensory cues across modalities can enhance the quality and accuracy of our percepts. In rat auditory thalamus, visual cues as well as reward size influence neural responses to auditory stimuli, showing that these effects are present early in this sensory pathway. Attention boosts size, not speed Article by McDonald and colleagues We perceive attended objects more quickly than unattended ones, even when they appear at the same time, but does attention actually speed up sensory processes? A study in humans now finds an increase in the magnitude of neural responses to cued objects but no change in their timing. CURRENT ISSUE ADVANCE ONLINE PUBLICATION Modulating neuroendocrine secretion Article by Chen and colleagues Reduced suppression with age Brief Communication by Gazzaley and colleagues A new fMRI study finds that older and younger adults show enhanced activation when asked to memorize scenes, but the older adults have reduced activation suppression when asked to ignore scenes. Age-related memory deficits are therefore due to inadequate suppression of irrelevant information, not due to inadequate enhancement of relevant information.

128. 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 GTK2), 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 are provided by the package (Public Domain). 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**. Ghemical also uses the OpenBabel package for importing and exporting many different file formats (as well as for other tasks).

129. 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.ru.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 5.2 is available WHAT IF license holders can now get WHAT IF 5.2. 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 5.2 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

130. ZMM Software Inc. modeling tool for theoretical studies, employing molecular mechanics approach in combination with Monte Carlo energy minimization algorithm. Downloads on secure server, and contacts in Flamborough, Ontario. http://www.zmmsoft.com/

MOLECULAR MODELING PROGRAM ZMM Home About ZMM Downloads Register ... Contact Template © by H Home Profile People Research ... Contact WELCOME ZMM is a molecular modeling program for theoretical studies of systems of any complexity: small molecules, peptides, proteins, nucleic acids, and ligand-receptor complexes. ZMM searches optimal structures in the space of generalized coordinates: torsion angles, bond angles, bond lengths, positions free molecules and ions, and orientation of free molecules. Any generalized coordinate may be kept fixed. Molecules and fragments that are not expected to undergo significant conformational changes may be treated as rigid bodies. Popular molecular modeling programs usually work in the space of Cartesian coordinates of atoms. During energy minimization of a big system, many Cartesian coordinates-variables move collectively. For example, rotation of a benzene ring around the C-Ph bond in the Cartesian-coordinates space involves collective motion of 33 variables. In the generalized-coordinates space, this rotation involves variation of just one torsion angle. In ZMM, any fragment of a molecular system may be treated as either rigid or flexible. The generalized-coordinates method saves large computational resources if only a small part of a system is considered flexible. Examples are ligand-protein and protein-protein interactions. The savings occur because the sampling space is reduced and because molecular interactions within rigid fragments are not computed.

131. Accelrys: History - Oxford Molecular molecular Biologists • Polymer Scientists • Protein Modelers • R D Executives Data Pipelining • Life Sci modeling • Materials modeling. Reference http://www.accelrys.com/about/oxmol.html

Search Accelrys for... About Accelrys Overview Careers Investors Locations News Room Our Network Contact Legal Info 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 ... History Oxford Molecular The software businesses of the Oxford Molecular Group were incorporated into Accelrys Inc. on June 1, 2001. Oxford Molecular was a leading provider of cheminformatics tools. Founded in 1989, Oxford Molecular was listed on the London Stock Exchange in 1994. The Oxford Molecular Group grew aggressively through internal growth and the acquisition of software and experimentation-based companies. Acquired companies included Chemical Design Limited, MLR Automation, and the Genetics Computer Group Oxford Molecular's primary expertise was in the area of cheminformatics, and in the consulting services associated with building enterprise informatics systems. The foundation of this offering was the RS3 discovery information management system, now integrated into the Accord family.

132. StatMechMolSim Groups Web Page Biophysics multiscale computer simulation group, active in method development and applications from detailed firstprinciples simulations, to mesoscopic and coarse-grained modeling (Stockholm, Sweden). http://www.fos.su.se/physical/aatto/smms/

WELCOME TO THE S TATISTICAL M ECHANICAL M OLECULAR S IMULATION GROUPs WEB PAGE STOCKHOLM UNIVERSITY ARRHENIUS LABORATORY Physical Chemistry Division

133. 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 Post-Doc Opening Graduate Student Opening Bioinformatics Seminar Series Journal Club

134. 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

135. ScienceDirect - Computational Biology And Chemistry - List Of Issues Publishes original papers and reviews in all areas of computational life sciences, such as nucleic acid and protein sequence research, molecular evolution, molecular genetics (functional genomics and proteomics), theory and practice of either biologyspecific or chemical-biology-specific modeling, and structural biology of nucleic acids and proteins. http://www.sciencedirect.com/science/journal/14769271

Register or Login: Password: Athens/Institution Login Quick Search: within This Journal All Journals All Full-text Sources Computational Biology and Chemistry Bookmark this page as: http://www.sciencedirect.com/science/journal/14769271 Formerly known as Volume 29 Volume 29, Issue 4 , Pages 259-308 (August 2005) Volume 29, Issue 3 , Pages 183-258 (June 2005) Volume 29, Issue 2 , Pages 83-181 (April 2005) Volume 29, Issue 1 , Pages 1-82 (February 2005) Volume 28 Volume 27 Alert me when new Journal Issues are available Add this journal to My Favorite Journals Sample Issue Online More Publication Info Information for Authors Contact Us ... Elsevier B.V.

136. Molecular Library Library of 3D molecular Structures World of Molecules contains text information along with images. Chemistry at Okanagan University College Simple, http://www.nyu.edu/pages/mathmol/library/

Welcome To the MathMol Library Water and Ice Carbon Hydrocarbons Amino Acids ... Textbook These pages are being designed at the New York University Scientific Visualization Center We welcome feedback and comments at mr23@nyu.edu Library of 3-D Molecular Structures If you are using CosmoPlayer click on the above image of a water dimer About the Database To enter the library, click on the appropiate buttons below. Links to Other Molecular Databases Java Applets of Molecules this database contains links to Java Applets for a large number of molecules. No plug-in or software is needed if your computer is java enabled. World of Molecules contains text information along with images. Chemistry at Okanagan University College Simple, Common, and Interesting Molecules from Indiana University Molecular Structure Center (includes VRML and Java images) Molecular database without transition elements These files were made with the atom's coordinates to respect the experimental values. So, these files permit the illustration of classical geometries learnt in the VSEPR method. The 3-D Structure of Minerals IMB Jena Image Library of Biological Molecules -Includes VRML images Amino Acids Monosaccharide Browser NIH (NCI) Drug Information System 3D Database Has over 400,000 structures

137. Representation Models In Molecular Graphics Rendering Techniques with many examples of inorganic compounds. 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

138. Molecular Modelling (c) Henry Rzepa. 19952003. http://www.ch.ic.ac.uk/local/organic/mod/

c) Henry Rzepa. 1995-2003.

139. Antas.agraria.uniss.it/ molecular Modelling Toolkit (MMTK)Home page for MMTK, the molecular Modelling Toolkit, a free library for molecular simulations. http://antas.agraria.uniss.it/

140. Welcome To The Biocomputing Pages Of The Center For Computing Services The European molecular Biology Open Software Suite. Databases. Get information on the different local databases. Accelrys Pages http://www-bio.unizh.ch/

Biocomputing SW Databases Documentation Visualization ... ZI Home Last modified: Sep 09 2005 17:56 / go Welcome to the Biocomputing pages of the IT Services Attention! We will change from GCG to EMBOSS Biocomputing Biocomputing Software starting point: Start wEMBOSS 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. Accelrys Pages You can find documentation on how to install Accelrys 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

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