81. Linux4Chemistry An up-to-date website with the links to Linux software for chemistry including computational, visualization, graphic, molecular modeling, both free and commercial software useful in different fields of chemistry. http://www.redbrick.dcu.ie/~noel/linux4chemistry/

82. Molecular Modeling | GPU Computing Welcome to the Molecular Modeling community. This community covers the full range of molecular modeling applications on GPUs. I invite group members to post links to recent http://gpucomputing.net/?q=node/67

83. VeraChem LLC Illustrates firm that designs molecular modeling applications utilized by scientists in computational chemistry tasks. http://verachem.com

Vconf Vconf is a powerful and flexible conform- ational search application which processes an SDfile of drug-like compounds with arbitrary initial 2D or 3D conformations. The user may designate atoms to be kept fixed during the search. Vfilter and Vrms Vfilter compares multiple conformations of a molecule and removes repeats, accounting for alternate resonance forms and symmetry. Vrms provides the symmetry-corrected root-mean-square deviation (RMSD) between a series of test conformations of a drug-like m olecule and a reference conformation. Vcharge Vcharge calculates accurate, conformation- independent, "ab initio-like" partial atomic charges for an SDfile of drug-like compounds in ~0.1 second per compound. It is useful for a wide range of modeling and QSAR applications. - All VeraChem software is free for academic and nonprofit use - designed by nextdaysite.com

84. Home - CCR Web - The Center For Computational Research CCR offers courses in high-performance computing and molecular modeling, training and workshops in specific aspects of high-end computing. University at Buffalo, State University of New York . http://www.ccr.buffalo.edu/display/WEB/Home

85. Form For PDB Query Search engine for visualizing 3-D biomolecular models. From the Center for Molecular Modeling, NIH, Maryland. http://molbio.info.nih.gov/cgi-bin/pdb/

Site formerly known as Molecules R Us Welcome to the NIH Molecules To Go Utililty . This facility combines a full text search of the PDB database with a FORM interface to customize the format ( TEXT, IMAGE, INTERACTIVE ) of the selected structure. Please read the instructions! Initiate a PDB query: What's NEW

86. BSP :: Protein & Peptide Letters 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/

87. 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/

Jay Ponder Lab Welcome to the Home Page for the Jay Ponder Lab in the at the Washington University School of Medicine in Saint Louis, Missouri. We are located in the recently renovated Center for Computational Biology building on the Medical School campus. Our group is primarily interested in computational chemistry, especially the development of new algorithms and their application to problems in structural biology. We develop, maintain and distribute several software packages which are described below. A summary of our research work is in the Faculty Research Abstract maintained by the . Publications and dissertations from the lab are available from Jay Ponder's Home Page Software Distributed by the Lab 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.

88. Software For Bio-molecular Modeling Program for bio-molecular modeling, particularly for molecular graphics and dynamics with implicit and explicit water models. http://www.biomolecular-modeling.com/Abalone/

Contacts Purchase License Gallery ... Home Biomolecular simulations with "Abalone" Biomolecular dynamics simulations of proteins, DNA, ligands Molecular graphics Molecular model building Geometry optimization Molecular dynamics simulations Hybrid Monte Carlo Adaptive Temperature Hybrid Monte Carlo Replica exchange Implicit and explicit water models Software for Simulations Molecular Building Tutor Protein folding ... Site map var MerchantID = 'AGILEM'

89. Ascalaph Designer Program for creating molecular models, molecular mechanics simulations and development of the force fields by quantum chemical methods. http://www.biomolecular-modeling.com/Ascalaph/Ascalaph_Designer.html

Home Gallery Useful Links Products ... Contacts Ascalaph Designer Molecular models and simulations Features: Molecular graphics Multiple windows Two cameras per model CPK Wire frame Stick Ball and Stick and CPK Wire frame styles Molecular model building Crystal builder Chain Builder Drawing by mouse ... Nanotubes examples Clashes removing Geometry optimization with conjugate gradient methods Molecular dynamics Multiple time step integration Fourth order integration Supercomputer calculations with aid of MDynaMix Flexible SPC water model Implicit water model Quantum chemistry with aid of and PC GAMESS/Firefly Energy Optimization Potential Derived Charges ... Table of contents

90. Journal Of Molecular Modeling Molecular, protein, peptide and drug design, computational modeling, molecular mechanics/dynamics in the fields of life sciences and chemistry. http://www.springer.com/chemistry/journal/894

Basket USA Change New User Login Home ... My Springer Manage your Account Change Email or Postal Address Change Password Password Lost? Manage your Alerts Change alert profile Unsubscribe Article Tracking Online Book Review Copies ... Subjects Choose a discipline: Astronomy Biomedical Sciences Chemistry Computer Science ... Services Find all our services for you Authors Booksellers Book Reviews Librarians ... Subscription Agencies We are happy to help you! Manage your Account Online Exam Copies Order process Our Email Services SpringerAlerts Overview SpringerAlerts for Journals SpringerAlerts for Book Series SpringerAlerts for Books ... SpringerAlerts for Booksellers More about: Spektrum Akademischer Verlag Birkhäuser T.M.C. Asser Press Publishers and Imprints with external Websites Apress BioMed Central Codes Rousseau Etrasa ... About us Company Information Mission Statement Management Annual Reports Key Facts ... Locations Worldwide What we do Publishing Fields Springer and Open Access Springer in China Developing Countries Initiative Press Press Releases Springer Select Media Kit and Downloads Career All Job Vacancies Trainee-Programs / Editorial Trainees Internships Vocational Training There are no results matching your search terms.

91. OnScreen DNA™ s and screen shots of the educational software providing an interactive virtual 3D molecular model in a tutorial framework. Lite edition is a free download....... http://www.onscreen-dna.com/

92. Taylor & Francis Journals: Journal Not Found Covers all aspects of original research on receptors and ion channels and the related signalling elements, at the levels of molecular biology and genetics, biochemistry, physical analysis, molecular modelling, immunochemistry, molecular pharmacology and electrophysiology. http://www.tandf.co.uk/journals/titles/10606823.html

93. The Software Page :: Kinemage Website Software and methods source for molecular model visualization, model validation via all-atom contact analysis and utility. Linux, Mac, SGI, Sun, and Windows platforms. http://kinemage.biochem.duke.edu/software/

3D Analysis :: "The Software Page" Home Kinemages RNA Software ... About us The table below lists the popular software packages from RLab. Other software and binaries for other platforms are also available, please see either the individual sofware pages or browse our download section . The "About" link before each program name is linked to that software's download page; there, you'll find a fuller description of the software. The cell at the intersection of program name and platform type contains the current distribution version number and release date. Selecting/clicking the download link in that cell will start the download process (immediately). OS / Platform Software Linux(i386) MacOSX (10.4+) Windows Source About KiNG 2.17, 29-Aug-09 download 2.17, 29-Aug-09 download 2.17, 29-Aug-09 download 2.17, 29-Aug-09 download About Mage 6.44, 06-Jun-06 download 6.47, 15-Mar-07 download 6.44, 06-Jun-06 download 6.44, 06-Jun-06 download About Prekin 6.51, 22-Nov-08 download 6.51, 22-Nov-08 download 6.42, 17-Dec-05 download 6.51, 22-Nov-08 download About Reduce 3.14, 21-Aug-08

94. Polish Journal Of Chemistry Journal with contributions from all fields of pure chemistry (physical, theoretical, inorganic, organic and bioorganic) and as well as medicinal, macromolecular and supramolecular chemistry, and molecular modelling. Published by the Polish Chemical Society. http://malina.ichf.edu.pl/pjch/

About the Journal CONTENTS ABSTRACTS AUTHOR and SUBJECT INDEXES VOLUME 71 (1997) VOLUME 72 (1998) VOLUME 73 (1999) VOLUME 74 (2000) ... VOLUME 83 (2009) The Polish Chemical Society decided to join the consortium ChemPubSoc Europe in order to become one of the founders of the European Journal of Inorganic Chemistry and European Journal of Organic Chemistry ROCZNIKI CHEMII - POLISH JOURNAL OF CHEMISTRY 1921-2009

95. Molecular Informatics - Wiley Online Library Interdisciplinary forum for contributions on molecular modelling and all aspects of computer-assisted design of biologically active compounds as applied to medicinal, agricultural, environmental chemistry and materials sciences. http://www3.interscience.wiley.com/journal/104557877/home

document.documentElement.className = "js_en"; Skip to Main Content Home Help PUBLICATIONS ... ABOUT US LOGIN Enter e-mail address Enter password REMEMBER ME NOT REGISTERED ? FORGOTTEN PASSWORD ? JOURNAL TOOLS Get New Content Alerts Get RSS feed Save to My Profile Get Sample Copy JOURNAL MENU Journal Home FIND ISSUES Current Issue All Issues FIND ARTICLES Early View Most Accessed GET ACCESS Subscribe / Renew FOR CONTRIBUTORS Author Guidelines OnlineOpen Submit an Article ABOUT THIS JOURNAL Editorial Board Contact Overview SPECIAL FEATURES Call for Papers Special Issue: EuroQSAR 2010 Molecular Informatics Online ISSN: Recently Published Issues See all Current Issue: October 11, 2010 Volume 29, Issue 10 September 17, 2010 Volume 29, Issue 8-9 July 12, 2010 Volume 29, Issue 6-7 May 17, 2010 Volume 29, Issue 5 April 12, 2010 Volume 29, Issue 4 New journal in 2010 Molecular Informatics publishes: "Methods Corner" Reviews, that feature important technological concepts and advances. Sample Reviews Communications Full Papers Read the first issue for free Submit your excellent paper now.

96. ChemMedChem - Wiley Online Library Covers medicinal and pharmaceutical sciences, ranging from drug design and discovery to drug development and delivery, from molecular modeling to combinatorial chemistry. http://www3.interscience.wiley.com/journal/110485305/home

document.documentElement.className = "js_en"; Skip to Main Content Home Help PUBLICATIONS ... ABOUT US LOGIN Enter e-mail address Enter password REMEMBER ME NOT REGISTERED ? FORGOTTEN PASSWORD ? JOURNAL TOOLS Get New Content Alerts Get RSS feed Save to My Profile Get Sample Copy JOURNAL MENU Journal Home FIND ISSUES Current Issue All Issues FIND ARTICLES Early View Accepted Articles Most Accessed Most Cited GET ACCESS Subscribe / Renew FOR CONTRIBUTORS Author Guidelines OnlineOpen Submit an Article ABOUT THIS JOURNAL Editorial Board Contact For Journalists News ... Society Information SPECIAL FEATURES Cover Gallery Special Issues Editorials Tag Cloud ... Subscribe ChemMedChem Impact Factor: 3.232 Online ISSN: Associated Title(s): ChemBioChem ChemCatChem ChemPhysChem ChemSusChem Recently Published Issues See all Current Issue: November 8, 2010 Volume 5, Issue 11 Special Issue: HIV Research October 4, 2010 Volume 5, Issue 10 September 3, 2010 Volume 5, Issue 9 August 2, 2010 Volume 5, Issue 8 July 5, 2010 Volume 5, Issue 7 Latest News More News Read the interview now Recently Published Articles Probing Small-Molecule Binding to Cytochrome P450 2D6 and 2C9: An In Silico Protocol for Generating Toxicity Alerts Gianluca Rossato, Beat Ernst, Martin Smiesko, Morena Spreafico and Angelo Vedani

97. Altoris Consultants in chemoinformatics for computer aided drug design. Areas of expertise include design of chemical libraries for high throughput screening, structure guided drug design, molecular modeling, virtual screening, predictive toxicology, and software development. http://www.altoris.com/

7660-H Fay Ave #347, La Jolla, Ca 92037 phone 858.259.8161, fax 858.764.5483, info-at-altoris.com Understanding our work Researchers have become increasingly reliant on Information Technology tools to reduce the costs and boost the productivity of life sciences research and development. That is our focus. We work on our partners to provide chemical information management systems, consulting and services in structure guided design and programming of scientific applications. We service a broad range of needs for a broad range of customers. Our emphaisis is on analytics tools and data mining for the bench scientist...

98. European Journal Of Medicinal Chemistry - Elsevier Monthly publication for original papers, laboratory notes, short communications and invited reviews on organic synthesis, pharmacological activity, molecular modeling, drug design, receptor interactions and QSAR. Archive since 1987 from Elsevier, BV. http://www.elsevier.com/wps/find/journaldescription.cws_home/505813/description

99. Periodic Table Of Computational Chemistry Basic This table lists and describes some well documented and validated parameter sets available for modeling each element by Molecular Mechanics and Quantum Mechanics molecular modeling methods. http://www.chamotlabs.com/Freebies/Table/parameters-table.html

100. Molecular Models For Biochemistry At CMU Pictures of the molecular structure of amino acids. Also features common properties of all amino acids, peptide structures, and a protein structure quiz. http://www.bio.cmu.edu/Courses/BiochemMols/BCMolecules.html

Molecular Models for Biochemistry at CMU The linked pages described here have tutorials and quizzes that are based on Chime and RasMol images of the molecules and macromolecules found in biochemistry. They are intended to complement standard biochemistry texts where more explanation is provided, but where interactive 3-D images of the molecules are not available. Please see viewing suggestions below before choosing a topic. S MALL M OLECULE G ALLERY to Chime displays of some textbook examples used in the Modern Biology (03-121) and Cell Biology (03-240) courses at CMU. Also shown are some protein and lipid bilayer structures. Quizzes (T-F and Chime) on functional groups are linked from the page. Practice Quizzes : A separate listing of the Chime and GIF-based quizzes at this site. A MINO A CID S TRUCTURES are viewed as Chime-generated images. Take an Amino Acid Structure Quiz based on GIFs from the above tutorial. Structures are shown as a collection of Amino Acid GIF images. Amino Acid Identification Quizzes The names, abbreviations, and one-letter codes are tested in three formats:

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