Tyrannosaurus Rex Model
http://www.stanford.edu/group/nmbl/people/Scott_Delp.htm delp@stanford.edu Scott Delp 1:0:1 0 4 - Development with public userbase \N \N \N \N \N \N \N \N \N \N \N \N \N \N \N
2 geZ036e7vpr62POQGK 1138928863 6 0 Amber Force Fields Scripps Research Institute molecular force fields for dynamics simulations Database or Data Source http://amber.scripps.edu/#ff Four new force fields are available: a re-parameterization of an all-atom protein force field (ff03), based on quantum calculations in a continuum solvent environment; a major extension of the General Amber Force Field (gaff), that expands the range of applicable molecules, particularly for conjugated systems; a new version of the "glycam" carbohydrate force field (glycam04) developed in Rob Woods` group; and a "QM/MM" facility by which part of the system can use energies and forces derived from a semiempirical Hamiltonian such as AM1 or PM3.
David A. Case | e-mail: case@scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | WWW:
La Jolla CA 92037 USA | http://www.scripps.edu/case case@scripps.edu David Case 1:0:0 0 6 - Mature \N \N \N \N \N \N \N \N \N \N \N \N \N \N \N
43 6L8tg6WuQZ2MmX8Jmu 1139941618 10 1 ABAQUS Abaqus, Inc. Software Suite for finite element analysis Software: Platform, Development Environment http://www.hks.com/ ABAQUS, Inc. is the world`s leading provider of software for advanced finite element analysis. The ABAQUS software suite has an unsurpassed reputation for technology, quality and reliability. It has been adopted by many major corporations across all engineering disciplines as an integral part of their design process. ABAQUS, Inc. provides superior solutions for linear, non-linear, explicit and multi-body dynamics problems to deliver a unified finite element analysis environment without equal. Our software is a compelling alternative to implementations involving multiple products and vendors. Since our founding in 1978, our continued focus on innovation, quality and outstanding customer support has built a loyal base of satisfied customers. At ABAQUS, Inc., we appreciate the fundamental importance of finite element analysis to the business goals of every single customer, and we remain entirely focused on FEA technology.
http://www.hks.com/contact.html support@abaqus.com Abaqus, Inc. (Company) 1:1:1 0 6 - Mature \N \N \N \N \N \N \N \N \N 3 - Organ / Organism \N \N
21 UwkQhtW18GJAX3DrRU 1138929697 2 0 Rasmol University of Massachusetts Molecular Visualization Software: Support Tool http://www.umass.edu/microbio/rasmol/index2.htm RasMol is a free program which displays molecular structure. It is available for on PC/Windows (RasWin), MacIntosh (RasMac), unix, and VAX VMS (the latter two via X-windows), and also (through ports by users) for NEXTSTEP and for Acorn Archimedes RISC OS. RasMol is a powerful educational tool for showing the structure of DNA, proteins and smaller molecules. It is also a powerful research tool. It is easy to use and produces beautiful, space-filling, colored, 3-dimensional images (see the Gallery!). It is the generous gift to the scientific public of its author, Roger A. Sayle, Ph.D., GlaxoWellcome, and the University of Edinburgh (all in the United Kingdom).
Rasmol has been replaced by Protein Explorer. See website. http://www.umass.edu/molvis/martz/ emartz@microbio.umass.edu Eric Martz 1:1:0 0 0 - Inactive / Retired \N \N \N \N \N \N \N \N \N \N \N \N \N \N \N
5 ma6FFTyyUuzmlGWvoh 1142968754 4 1 Chime Elsevier MDL, Inc. Browser plug-in that renders 2D and 3D molecules directly within a Web page. Software: Support Tool http://www.mdl.com/products/framework/chime/ Chime is a browser plug-in that renders 2D and 3D molecules directly within a Web page. The molecules are "live", meaning they are not just static pictures, but chemical structures that scientists can rotate, reformat, and save in various file formats for use in modeling or database applications.
Chime will be of special interest to organic chemists engaged in pharmaceutical, agrochemical, and biotechnology R&D, in industry and academia. It is a particularly valuable tool for scientists specializing in cheminformatics.
Using Chime, researchers can easily add structures to their projects, tutorials, newsletters, journals, and presentations published across an intranet or the Internet. With knowledge of Rasmol or CSML scripting, you can even create interactive Web pages. http://www.mdl.com/contact/index.jsp
Elsevier MDL
14600 Catalina Street
San Leandro, CA 94577
TEL: +1 (510) 895-1313
FAX: +1 (510) 483-4738
Elsevier MDL (Company) 1:0:0 0 5 - Production/Stable \N \N \N \N \N \N \N \N \N 1 - Atomic / Molecular \N \N
38 2pGjkauNbh9RvGIJei 1142968914 6 0 SIMM MusculoGraphics, Inc. Construction, modeling, animation, and analysis of three-dimensional musculoskeletal systems Software: Platform, Development Environment http://www.musculographics.com/ For health care professionals, scientists, engineers, and animators, the SIMM Biomechanics Software Suite is a powerful tool kit that facilitates the construction, modeling, animation, and analysis of three-dimensional musculoskeletal systems. Unlike traditional animation and mechanical CAD packages, the SIMM software suite- SIMM, Gait Module, and the Dynamics Pipeline - is specifically designed to work with systems that consist of bones, muscles, ligaments, and tendons.
In SIMM, a musculoskeletal model consists of a set of body segments that are connected by joints. The joints are modeled using detailed, accurate kinematic functions, or as simple pin or ball-and-socket joints. The model includes muscle-tendon actuators that span the joints and develop force, thus generating moments about the joints. The SIMM Biomechanics Software Suite is your only choice if you need to quickly create, analyze, edit, and display realistic musculoskeletal models.
http://www.musculographics.com/contactus/contactus.html
MusculoGraphics, Inc.
c/o Motion Analysis Corporation
3617 Westwind Blvd.
Santa Rosa, CA 95403
attn: Rita Maloney rita.maloney@motionanalysis.com Rita Malony 1:1:1 0 4 - Development with public userbase \N \N \N \N \N \N \N \N \N \N \N
51 ar2T5oYCTzk0jdGHf8 1139249187 1 0 NDB - Nucleic Acids Database Rutgers University Repository of three-dimensional structural information about nucleic acids \N Database or Data Source http://ndbserver.rutgers.edu/ The goal of the Nucleic Acid Database Project (NDB) is to assemble and distribute structural information about nucleic acids. The NDB was founded in 1992 by Helen M. Berman, Rutgers University, Wilma K. Olson, Rutgers University, and David Beveridge, Wesleyan University. In addition, Anke Gelblin, Tamas Demeny, S. -H. Hsieh, A.R. Srinivasan, and Bohdan Schneider were members of the original NDB project team. http://ndbserver.rutgers.edu/about_ndb/index.html
The Nucleic Acid Database
Rutgers, the State University
Department of Chemistry and Chemical Biology
Wright-Reiman Laboratories
610 Taylor Road
Piscataway, NJ 08854-8087
Phone: 732.445.0103
Fax: 732.445.4320
ndbadmin@ndbserver.rutgers.edu Helen M. Berman 1:0:1 0 5 - Production/Stable \N \N \N \N \N \N \N \N \N \N \N \N \N \N \N
3 LUr4mFSKuZCndVZqKx 1138930584 8 2 BioSimGrid University of Oxford Sharing results of large-scale computer simulations of biomolecules Web / Online Resource http://www.biosimgrid.org/ The aim of the BioSimGrid project is to make the results of large-scale computer simulations of biomolecules more accessible to the biological community. Such simulations of the motions of proteins are a key component in understanding how the structure of a protein is related to its dynamic function.
This project is funded by BBSRC (Biology and e-Science) and DTI (e-Science Pilot Projects), and supported by the Oxford e-Science Centre and the Southampton Regional e-Science Centre. Additional support is provided by the Worldwide Universities Network. https://www.biosimgrid.org/demo/enquiry.html None 1:0:1 0 4 - Development with public userbase None \N \N \N GNU General Public License (GPL) \N \N \N \N 2003 1 - Atomic / Molecular 2 - Organized User base / Mailing lists http://www.biosimgrid.org/#mailing http://www.biosimgrid.org/docs/ \N
4 PaI5gXl2WGPMRzfMCb 1141671128 18 1 CHARMM Harvard University Program for macromolecular simulations, including energy minimization, molecular dynamics and Monte Carlo simulations Software: Algorithm or Reusable Library http://www.charmm.org/ CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a program for macromolecular simulations, including energy minimization, molecular dynamics and Monte Carlo simulations.
The CHARMM Development Project involves a network of developers in the United States and elsewhere working with Professor Karplus and his group at Harvard to develop and maintain the CHARMM program.
The current released version of CHARMM is version c32b1. If you are running an earlier version, you should consider upgrading. Academic users can obtain CHARMM by contacting The CHARMM Development Project.
Professor Martin Karplus
Department of Chemistry & Chemical Biology
12 Oxford Street
Harvard University
Cambridge, Massachusetts 02138 marci@tammy.harvard.edu Martin Karplus 1:1:1 0 5 - Production/Stable For-profit companies should contact Accelrys Inc. http://www.accelrys.com/ 600 for academic, see website for commerical options. \N Other - not listed here \N \N \N \N \N 1 - Atomic / Molecular \N \N
26 w4GkOnHPniH7uul7ko 1138930263 2 0 VMD University of Indiana displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting Software: Support Tool http://www.ks.uiuc.edu/Research/vmd VMD is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer. http://www.ks.uiuc.edu/Overview/reach.html kschulte@ks.uiuc.edu Klaus Schulten 1:1:1 0 4 - Development with public userbase \N \N \N \N \N \N \N \N \N \N \N \N \N \N \N
71 VacmoRaUSfC7LNj0gW 1143339211 0 0 Clipper University of York Improved Crystallographic Modeling Software: Simulation Application http://www.ysbl.york.ac.uk/~cowtan/clipper/clipper.html The aim of the project is to produce a set of object-oriented libraries for the organisation of crystallographic data and the performance of crystallographic computation. The libraries are designed as a framework for new crystallographic software, which will allow the full power of modern programming techniques to be exploited by the developer. This will lead to greater functionality from simpler code which will be easier to develop and debug. http://www.ysbl.york.ac.uk/~cowtan/ cowtan@ysbl.york.ac.uk Kevin Cowtan 1:0:1 0 5 - Production/Stable \N \N \N \N \N \N \N \N \N 1 - Atomic / Molecular \N \N
49 hnh7qyhLON8OL87JVL 1143339245 4 0 Chimera University of California, San Francisco Extensible, interactive molecular graphics program Software: Support Tool http://www.cgl.ucsf.edu/chimera/ UCSF Chimera is a highly extensible, interactive molecular graphics program. It is the successor to UCSF Midas and MidasPlus; however, it has been completely redesigned to maximize extensibility and leverage advances in hardware. UCSF Chimera can be downloaded free of charge for academic, government, non-profit, and personal use. It includes full user documentation and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix. UCSF Chimera development is funded by the NIH National Center for Research Resources (grant P41-RR01081). http://www.cgl.ucsf.edu/home/tef/ tef@cgl.ucsf.edu Thomas Ferrin 1:1:1 0 5 - Production/Stable \N \N \N \N \N \N \N \N \N 1 - Atomic / Molecular \N \N
7 T7PigM4MFwOeLp2TOO 1143339274 1 1 Folding@Home Distributed Computing Stanford University Distributed Computing to Fold Proteins Web / Online Resource http://folding.stanford.edu Folding@Home is a distributed computing project -- people from through out the world download and run software to band together to make one of the largest supercomputers in the world. Every computer makes the project closer to our goals.
Folding@Home uses novel computational methods coupled to distributed computing, to simulate problems thousands to millions of times more challenging than previously achieved. http://folding.stanford.edu/people/VijayPande.html Vijay Pande 1:0:1 0 5 - Production/Stable \N \N \N \N \N \N \N \N \N \N \N
73 GCF0yjxoP6svHOO5PU 1143339361 0 0 Modeller University of California, San Francisco Homology or comparative modeling of protein three-dimensional structures Software: Simulation Application http://salilab.org/modeller/ MODELLER is used for homology or comparative modeling of protein three-dimensional structures (1). The user provides an alignment of a sequence to be modeled with known related structures and MODELLER automatically calculates a model containing all non-hydrogen atoms. MODELLER implements comparative protein structure modeling by satisfaction of spatial restraints (2, 3), and can perform many additional tasks, including de novo modeling of loops in protein structures, optimization of various models of protein structure with respect to a flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, etc. MODELLER is written in Fortran 90 and runs on Pentium PC`s (Linux and Win XP), Itanium 2 and x86_64 (Linux), Apple Macintosh (OS X) and workstations from Silicon Graphics (IRIX), Sun (Solaris), IBM (AIX), and DEC Alpha (Tru64). http://salilab.org/modeller/contact.html modeller-care@salilab.org Ben Webb 1:1:1 0 4 - Development with public userbase \N \N \N \N \N \N \N \N \N \N \N
64 ZtOlJDx8vQ8lwhrnpC 1143339412 0 0 UMFPACK University of Florida Routines for solving unsymmetric sparse linear systems Software: Algorithm or Reusable Library http://www.cise.ufl.edu/research/sparse/umfpack/ UMFPACK is a set of routines for solving unsymmetric sparse linear systems, Ax=b, using the Unsymmetric MultiFrontal method. Written in ANSI/ISO C, with a MATLAB (Version 6.0 and later) interface. Appears as a built-in routine (for lu, backslash, and forward slash) in MATLAB. Includes a MATLAB interface, a C-callable interfance, and a Fortran-callable interface. http://www.cise.ufl.edu/~davis/ davis@cise.ufl.edu Tim Davis 1:0:1 0 5 - Production/Stable \N \N \N \N \N \N \N \N \N \N \N
23 YunC3eG1BxVZAn6fWS 1143341106 6 0 Simulink MathWorks, Inc. Matlab Toolkit for Simulation and Model-Based Design Software: Platform, Development Environment http://www.mathworks.com/products/simulink/ Simulink is a platform for multidomain simulation and Model-Based Design for dynamic systems. It provides an interactive graphical environment and a customizable set of block libraries, and can be extended for specialized applications. http://www.mathworks.com/company/aboutus/contact_us/ Mathworks, Inc.(Company) 1:0:1 0 5 - Production/Stable \N \N \N \N \N \N \N \N \N \N \N
17 AOtYS9k4uBED6BYlNZ 1143341435 0 0 PDB - Protein Databank Rutgers University Public repository for molecular structures Database or Data Source http://www.rcsb.org/pdb/ The RCSB PDB provides a variety of tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease.
The RCSB is a member of the wwPDB whose mission is to ensure that the PDB archive remains an international resource with uniform data.
This site offers tools for browsing, searching, and reporting that utilize the data resulting from ongoing efforts to create a more consistent and comprehensive archive.
Information about compatible browsers can be found here.
A narrated tutorial illustrates how to search, navigate, browse, generate reports and visualize structures using this http://www.rcsb.org/pdb/static.do?p=general_information/about_pdb/contact/index.html info@rcsb.org General Mailbox 1:0:1 0 6 - Mature \N \N \N \N \N \N \N \N \N \N \N
58 lfpTclIdhjJV9axLfy 1143341466 1 0 Paraview Sandia National Lab -- LLNL -- Kitware, Inc. Parallel visualization application for large datasets Software: Support Tool http://www.paraview.org Welcome to ParaView, an application designed with the need to visualize large data sets in mind. The goals of the ParaView project include the following: