Molecular Modelling

Molecular Modeling Pro  
Molecular Modeling Pro has most of the advanced features available in expensive PC-based molecular modeling programs and more! 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 2,500 atoms and 10 molecules can be displayed on the screen at a time and minimized using the MOLY minimizer. Over 70 physical properties can be calculated instantaneously including molecular weight, volume, length, width, surface area, density, dipole moment, Hansens 3-D solubility parameters, HLB, boiling point, vapor pressure, Log P and connectivity indices. With Molecular Modeling Pro you can perform stoichiometry on reactions, balance equations, and draw reaction mixtures with arrows and conditions.
Submitted: Dec 23, 2000
Crystal Studio  
Crystal Studio is a Windows 95/98/NT software package for crystallography. It is a comprehensive tool for user-friendly creation, 3D graphical design, display and manipulation of crystal structures and for the simulation of diffraction patterns. Empowered with a crystallographic database, Crystal Studio lets you create stunning photo-realistic 3D graphics and diffraction patterns with just a few mouse clicks.
Submitted: Dec 23, 2000
Molecular Graphics  
Molecular Graphics Applications in the Yale Molecular Biophysics Biochemistry Center Structural Biology Core Laboratory.
Submitted: Sep 30, 2000
Atom in a Box  
Real-Time Visualization of Electron in a Quantum Mechanical Hydrogen Atomic Orbital.
Submitted: Jan 04, 2001
PREMIER Biosoft  
PCR primer design, dna microarray, and plasmid vector drawing software.
Submitted: Sep 30, 2000
Turbo Frodo  
Turbo Frodo is a general purpose molecular modelling environnement aimed at people with the need to model de novo macromolecules, polypeptides as well as nucleic acids, to build such macromolecules from experimental 3-D data obtained from X-ray crystallography and NMr, to display the resulting models using various representations including Van der Waals and Connolly's molecular dot surfaces as well as spline surfaces.
Submitted: Dec 22, 2000
Chemistry 4-D Draw  
This next-generation chemistry program combines the most advanced technologies in structure drawing with a proprietary module, NamExpert, that understands IUPAC nomenclature rules. The program allows you to create high-quality structures simply by entering molecular names. It includes a full set of tools for drawing, text and structure editing, and labeling. Features include interactive 3-D rotation, syntax checking, hot-key labeling, multi-step undo, and creating structure templates with user-defined trivial names.
Submitted: Dec 23, 2000
Diamond is an MS Windows application for the exploration and drawing of crystal structures. With its high data capacity, its wide range of functions beginning with the generation of molecules reaching up to the construction of rather complicated inorganic structural frameworks, Diamond is the tool for molecular and solid state chemists as well as for surface and material scientists.
Submitted: Dec 23, 2000
The development of Chimera is funded by the NIH National Center for Research Resources (grant P41-RR01081). The software is available free of charge for academic, govenrment, non-profit, and home use. Chimera runs on SGI, Compaq/DEC Alpha, Linux, and Windows platforms.
Submitted: Dec 17, 2000
Biomolecular Modelling Laboratory  
Biomolecular modelling software: FTDOCK performs rigid-body docking on two biomolecules in order to predict their correct binding geometry. MULTIDOCK provides a method for refining the interface between two proteins at the atomic level given an initial docked complex. PREPI is a Molecular Graphics package for the display of proteins and nucleic acids. PREPI is freely available to non-profit making organisations.
Submitted: Sep 16, 2000
Indigo Instruments  
Molecular models for dna, organic chemistry, crystal lattices, framework structures for teaching, research, promotion and social network analysis.
Submitted: Oct 31, 2000
ZMM Molecular Modeling Software  
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. ·ZMM runs on Windows 95, 98, 2000, XP, UNIX, and Linux ·ZMM can be used via the command-line interface ·ZMM can also be used at Windows via a graphical user interface called MVM (Molecular viewer) which is a freeware
Submitted: Dec 07, 2006
CrystalDesigner is a computer program for building, studying and visualising all kinds of crystal structures. The software has been developed by Crystal Structure Design AS and runs under Macintosh Operating System.
Submitted: Dec 23, 2000
Molecular Images Software for Windows  
Molecular Images is a package of 2 programs, Molw and Showcase, designed for searching, viewing, analyzing, and imaging macromolecular structures from PDB files. It provides a complete molecular modeling solution for Macintosh and Windows.
Submitted: Sep 12, 2000
ACD/Sigma Calculator  
ACD/Sigma Calculator allows you to access directly the electronic substituent constants, s, calculated for your molecular fragment.
Submitted: Dec 23, 2000
Galaxy is a highly integrated and sophisticated molecular modeling and drug design software package for Silicon Graphics and IBM RS-6000 workstations. It is the only package currently available in the industry which is equally good for small molecule based drug discovery projects as well as protein structure based drug design projects. It has several novel approaches for drug design which is unavailable in any of the commercial packages.
Submitted: Jan 06, 2001
Molecular Surface Viewer  
MSV is an OpenGL based viewer for molecular surfaces computed with MSMS.
Submitted: Sep 12, 2000
MOLMOL is a molecular graphics program for displaying, analyzing, and manipulating the three-dimensional structure of biological macromolecules, with special emphasis on the study of protein or DNA structures determined by NMR.
Submitted: Sep 12, 2000
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.
Submitted: Sep 12, 2000
ChemOffice Ultra  
ChemOffice Ultra includes it all, providing ChemDraw Ultra, Chem3D Ultra, and ChemFinder Ultra for a seamlessly integrated suite that fulfills the day to day needs of chemists. Draw reaction mechanisms for publication and visualize 3D molecular surfaces, orbitals and molecular properties. New features include Beilstein’s AutoNom, Connolly surfaces, and ChemFinder for Microsoft Excel 97. And bring your work to the web by utilizing both the ChemDraw and Chem3D browser plugins. For more information on the contents of ChemDraw Ultra, Chem3D Ultra and ChemFinder Ultra, please view those respective product listings below.
Submitted: Dec 23, 2000
Gdis is a GTK based program for the display of molecules. It is in development, but is nonetheless fairly functional. It has the following features: Support for several file types (BIOSYM, XYZ, XTL, MARVIN restart, and GULP), A simple molecular creation and manipulation tool, A dialogue for creating starting configurations for molecular dynamics simulations, Assorted tools for visualization (geometry information, region highlighting etc.), Molecular animation of BIOSYM files (also rendered animations, see below).
Submitted: Dec 22, 2000
Protein Adviser  
Protein Adviser for Windows 1.1 displays and analyses 3D structures of biological molecules such as proteins. Protein Adviser is a powerful tool for visual and numerical investigation of protein molecules and their 3D structures, running on the most popular operating systems: Windows 95 and Windows NT.
Submitted: Sep 30, 2000
CAChe molecular modeling software for experimental chemists uses MOPAC 2000 to enhance productivity in the lab.
Submitted: Dec 23, 2000
Calculates an amino acid distribution by modelling the HPLC-chromatograms by using different density funtction.
Submitted: Sep 07, 2000
The MacroModel® program suite from Schrödinger, Inc. allows the graphical construction of complex chemical structures and the application of molecular mechanics and dynamics techniques in vacuo or in solution.
Submitted: Sep 30, 2000
Protein Explorer  
Protein Explorer is user-friendly freeware for macromolecular visualization.
Submitted: Dec 17, 2000
PyMOL is a molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations. It is fully extensible and available free to everyone via the "Python" license. Although still early in development, PyMOL can already be used to generate molecular images and movies with relative ease.
Submitted: Jan 06, 2001
ACD/Tautomers, provided as a value- added feature within every commercial copy of ACD/ChemSketch, will check and generate the most common tautomeric forms of drawn organic structures.
Submitted: Dec 23, 2000
EyeChem is a set of Explorer modules which support for various areas of molecular modelling. They have been written by Omer Casher at Imperial College.
Submitted: Jan 06, 2001
Flex is a simple, portable molecular graphics program that interactively displays 3D ball-and-stick models on workstations running the Xwindows system. Flex can accept input read from a file or passed over a network socket connection. The latter functionality makes flex ideal for monitoring large-scale simulations as they progress. Flex provides a library of subroutines, netg, to support this function. There are other (earlier) versions of Flex available on the net; this one is supported and includes documentation of the communications library.
Submitted: Oct 08, 2000
gdpc is a program for visualising molecular dynamic simulations, it is a very versatile program and could easily be used for other purposes. gdpc reads xyz input and custom formats and can write out pictures of the frames.
Submitted: Dec 17, 2000
An advanced molecular modeling system that display and manipulate macromolecules such as proteins and nucleic acids.
Submitted: Sep 11, 2000
PDB to MultiGif  
Visualization of chemical 3D structures on the web comes with problems because the web browser cannot display chemical structures without the help of additional software. If you create a page with a 3D structure of a molecule and the visitor of your page does not use this special viewer software for displaying molecules it cannot get the whole information of the page which should be meditated. PDB2MultiGIF takes the 3D structure and generates an animated image which can be displayed using any browser. Thus every visitor of your page can get the whole information.
Submitted: Sep 30, 2000
ProteinScope PDB Viewer  
ProteinScope is a free viewer for RCSB Protein Data Bank files. An integrated desktop application, with hand optimized 3D for fast review of complex molecules. Generate slides and movies in many formats of any PDB.
Submitted: Sep 09, 2002
RAMP is a suite of programs to aid in the modelling of protein three-dimensional structure.
Submitted: Sep 30, 2000
The Atomsmith Molecular Exploration Kit  
Atomsmith is a PC-based program for exploring, building and simulating models of molecules. It combines full-featured molecular visualizaton and simulation technology with innovative curriculum delivery features to make it an ideal tool for introducing molecular modeling into high school and college classrooms.
Submitted: Jul 10, 2003
This program is used to view molecular structures on Netscape.
Submitted: Sep 11, 2000
PREPI is a molecular graphics program which can be used to EASILY produce and interactively manipulate many different types of molecular representations (cartoons) as well as providing quantative information on secondary structural topology. The program is not just limited to proteins, but can also show cartoon representations of NUCLEIC ACIDS. In fact the program is capable of displaying "ANY" object for which cartesian coordinates are available.
Submitted: Oct 18, 2000
SWISS-MODEL is an Automated Protein Modelling Server running at the GlaxoWellcome Experimental Research in Geneva, Switzerland.
Submitted: Oct 18, 2000
Viewmol is an open source graphical front end for computational chemistry programs. It is able to graphically aid in the generation of molecular structures for computations and to visualize their results. Viewmol has originally been developed by Jörg-Rüdiger Hill and Andreas Bleiber in the Quantum Chemistry Group of Humboldt University with contributions by Arne Dummer, Mariann Krossner, Andreas Bünger, and Andries de Man.
Submitted: Dec 17, 2000
Cn3D is a helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez retrieval service. Cn3D runs on Windows, MacOS, and Unix. Cn3D simultaneously displays structure, sequence, and alignment.
Submitted: Sep 11, 2000
DGSOL is a software package for solving large distance geometry problems in macromolecular modeling. DGSOL has been developed for both sequential and parallel architectures.
Submitted: Oct 24, 2000
A graphic tool to build and manipulate nucleic acid structures.
Submitted: Sep 12, 2000
NIH Image  
NIH Image is a public domain image processing and analysis program for the Macintosh.
Submitted: Sep 30, 2000
Noncovalent Bond Finder  
Quickly finds hydrogen bonded atom pairs between chains, between protein and ligand, etc. Requires Chime 2 and Netscape Communicator 4.04 or better.
Submitted: Oct 18, 2000
SnB is a computer program based on Shake-and-Bake, a dual-space direct-methods procedure for determining crystal structures from X-ray diffraction data. This program has been used in a routine fashion to solve difficult structures, containing as many as 1000 unique non-H atoms, that could not be solved by traditional reciprocal-space routines based on the tangent formula alone.
Submitted: Jan 06, 2001
Graphical software for in silico construction of protein mutants and prediction of their activities.
Submitted: Oct 18, 2000
Turbo Frodo Viewer X11  
Turbo Frodo version X (turbox) is a graphic tool that allows to model and manipulate protein and acid nucleic structures. It runs on computers with bitmap display under X version 11 release 4 or higher. Turbox program can be started from a remote or a local machine. When the local machine is overloaded, user running clients can arrange for run turbox on other hosts .
Submitted: Dec 22, 2000
Virus Structure Resource  
This server provides images of virus structures determined by our group in the Structural Biology Programme at EMBL in Heidelberg. It also includes documentation for a number of the program packages used in for the determination of icosahedral structures and the processing of cryo-electron micrographs.
Submitted: Oct 18, 2000

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