Cross-indexing terms:   PyMol, PovRay.

AISMIG - An Interactive Server-side Molecule Image Generator

AISMIG is a free web-service that enables molecule visualizion without any additional software like Java or Plug-ins next to a web-browser. You can generate high quality and high resolution images. It is nice alternative to the standart web-based visualizations techniques because the user can see and interact with the structure in any case, independend of the software installed locally. AISMIG is based on PyMol and PovRay.

Authors: Bohne-Lang, Andreas;   Ranzinger, René.   Submitted by: the author. (Entry 70). Submitted on Feb 22, 2005.

Cross-indexing terms:   docking.

Authors: Morris, Garrett M.;   Goodsell, DS;   Huey, R;   Hart, WE;   Halliday, S;   Belew, R;   Olson, AJ.   Submitted by: Martz, Eric. (Entry 13). Submitted on Dec 16, 2000.

Cross-indexing terms:   molecular dynamics;   molecular mechanics;   molecular modeling;   rapid prototyping.

BALLView is an extensible tool for visualizing and modeling bio-molecular structures. It provides a variety of different models for molecular visualization, e.g. ball-and-stick models, molecular surfaces, or ribbon models. In contrast to most existing visualization tools, BALLView also offers rich functionality for molecular modeling and simulation, including molecular mechanics methods (AMBER and CHARMM force fields), continuum electrostatics methods employing a Finite-Difference Poisson Boltzmann solver, and secondary structure calculation. Results of these computations can be exported as publication quality images or as movies. Even unexperienced users have direct access to this functionality through an intuitive graphical user interface, which makes BALLView particularly useful for teaching. For more advanced users, BALLView is extensible in different ways. Owing to its framework design, extension on the level of C++ code is very convenient. In addition, an interface to the scripting language Python allows the interactive rapid prototyping of new methods. BALLView is portable and runs on all major platforms (Windows, MacOS X, Linux, most Unix flavors). It is open source software and available free of charge under the GNU Public License (GPL) from our website.

Authors: Moll, Andreas;   Hildebrandt, A.;   Lenhof, H.P.;   Kohlbacher O..   Submitted by: the author. (Entry 79). Submitted on Dec 20, 2005. Last revised on Dec 22, 2005.

Cross-indexing terms:   annotation;   structure;   graphics;   integration.

Authors: Craig, Paul;   Yang, Peng;   Bourne, Phil;   Goodsell, David.   Submitted by: the author. (Entry 42). Submitted on Apr 5, 2003.

Cross-indexing terms:   pKa;   logP;   logD;   polar surface area (PSA);   charge distribution;   polarizability predictions;   java;   plugin;   Marvin;   JChem;   prediction;   octanol/water partition coefficient;   QSAR;   ionization equilibrium;   apparent logP;   hydrophobicity;   molecular mass;   exact mass;   chemical formula;   elemental composition (w/w%);   drug discovery;   Huckel Analysis;   Hydrogen Bond Donor;   Hydrogen Bond Acceptor;   Major Microspecies;   Refractivity;   Structure Topology;   rotatable bond;   ADME;   TOX.

Calculator Plugins are modules of Marvin and JChem applications which perform calculations based on chemical structures.
Separate Calculator Plugins currently cover a range of calculations and physicochemical predictions. The plugin format is open to third party development, within ChemAxon we have ongoing plugin development, currently available plugins:

• Elemental Analysis
• pKa
• logP
• logD
• Polar Surface Area
• Charge
• Huckel Analysis
• Hydrogen Bond Donor-Acceptor
• Major Microspecies
• Polarizability
• Refractivity
• Topology Analysis

Free for teaching and academic research through ChemAxon's Academic Package. Introduction, terms and application available from http://www.chemaxon.hu/forum/viewpost570.html#570

Author: ChemAxon, Ltd   Submitted by: Allardyce, Alex. (Entry 59). Submitted on Sep 28, 2004. Last revised on Oct 2, 2004.

Cross-indexing terms:   CAChe chemical sample visualization;   orbitals, molecular;   isodensities;   isosurfaces;   Java applet for molecular rendering.

Authors: Purvis, George;   Purvis, John.   Submitted by: the author. (Entry 34). Submitted on May 21, 2002.

Cross-indexing terms:   quantum chemistry;   GAMESS;   Gaussian;   constructing molecules;   geometry, molecular;   orbitals, molecular;   isosurfaces.

Authors: Zhurko, Grigoriy;   Zhurko, Denis..   Submitted by: the author. (Entry 58). Submitted on Aug 6, 2004.

Author: CambridgeSoft, Corp.   Submitted by: Martz, Eric. (Entry 7). Submitted on Dec 2, 2000.

Cross-indexing terms:   safety, chemical.

This site provides access to a chemical and safety relational database developed in 2003 at Nebraska Wesleyan University. The site is designed specifically for local users but access to the database content is not restricted. This database has many features similar to chemfinder.com and the NIST webbook. The major difference is that the content of the database is determined by local interests and needs and is cross indexed to hazard information (specifically NFPA ratings). For example the database presently contains chemical and safety data for materials used in lab experiments in our first and second year chemistry courses.

The database can be searched by CAS numbers, molecular formula, chemical names, or by specific (NFPA) hazards. Included in the database are files of Chime-pdb files [Chime plugin required for viewing], MSDS's, NFPA ratings (graphic view), and 2D graphics of the molecules. In addition local users can cross-index an unlimited number of web-links to other material (such as IR, NMR, UV-vis and MS spectra, experimental data, potential maps, animations, etc) to each molecule in the database.

Authors: Fackler, Nathanael;   Shoemaker, Austin.   Submitted by: the author. (Entry 53). Submitted on Feb 12, 2004.

Cross-indexing terms:   protein-ligand interaction;   publication-quality images;   3D;   Linux;   VTK.

Author: SimBioSys, Inc.   Submitted by: the author. (Entry 87). Submitted on Oct 22, 2006.

Authors: Maffett, Tim;   van Vliet, Bryan;   Adler, Franklin;   Holt, Jean.   Submitted by: Martz, Eric. (Entry 3). Submitted on Nov 30, 2000.

Cross-indexing terms:   ribbons;   surfaces;   sequence-structure association;   hydrogen bonds;   volume data;   Python.

An interactive molecular modeling system developed by the the UCSF Resource for Biocomputing, Visualization, and Informatics. It is free for academic and non-profit use and is available for Windows, Mac OS X, Linux, and other platforms. UCSF Chimera development is funded by the NIH National Center for Research Resources (grant P41-RR01081). Features include:

• Atom-type and hydrogen-bond identification based on detailed geometric criteria
• Display of attributes such as B-factor and hydrophobicity with color, radii, and backbone worms; easy import of arbitrary user-defined attributes
• Display of three-dimensional data sets (electron densities, etc.) as isosurfaces or transparent solids, with interactive threshold adjustment
• Display of sequence alignments (many formats), automatic association of sequences with structures, sequence-structure crosstalk
• Playback of molecular dynamics trajectories (AMBER, CHARMM, GROMACS, GROMOS, MMTK, NAMD, PDB, X-PLOR formats)
• Interface to facilitate screening ligands from DOCK
• Multiscale visualization including low-resolution surfaces
• Generation of publication-quality images
• Movie recorder for saving image frames and assembling them into movie files
• Demo mechanism for scripting and replaying presentations
• Complete and searchable user documentation (HTML) included with download
• Extensibility as a design principle, allowing users to create custom modules without changing Chimera code

Authors: Huang, Conrad;   Couch, Greg;   Pettersen, Eric;   Goddard, Tom;   Greenblatt, Daniel;   Meng, Elaine;   Ferrin, Thomas.   Submitted by: Meng, Elaine. (Entry 45). Submitted on Jun 16, 2003. Last revised on Feb 22, 2007.

Cross-indexing terms:   scoring function for protein-peptide interactions;   drug design;   docking;   free energy;   protein-protein interaction prediction.

Author: Audie, Joseph   Submitted by: the author. (Entry 94). Submitted on Dec 5, 2007.

Author: National Center for Biotechnology Information, National Library of Medicine   Submitted by: Martz, Eric. (Entry 23). Submitted on Aug 16, 2001.

Cross-indexing terms:   drawing software, chemical;   comparison of chemical drawing software;   review of chemical drawing software.

Author: Gunda, Tamas E.   Submitted by: Martz, Eric. (Entry 33). Submitted on May 11, 2002.

Author: Villa, Jordi   Submitted by: the author. (Entry 25). Submitted on Oct 9, 2001.

Cross-indexing terms:   mutation;   evolution;   conservation;   multiple sequence alignment coloring of a protein;   hypervariable residues.

Authors: Glaser, Fabian;   Ben-Tal, Nir;   Pupko, Tal;   Martz, Eric.   Submitted by: Martz, Eric. (Entry 37). Submitted on Jul 1, 2002. Last revised on Oct 9, 2002.

Cross-indexing terms:   Swiss-PDBViewer.

Authors: Guex, Nicolas;   Diemand, Alexandre;   Schwede, Torsten;   Peitsch, Manuel C..   Submitted by: Martz, Eric. (Entry 5). Submitted on Nov 30, 2000. Last revised on Nov 30, 2000.

Cross-indexing terms:   visualization;   molecular surface;   electron density, electrostatic potential;   trajectory;   topograph;   picture generation.

DINO is a realtime 3D visualization program for structural biology data. It runs under X-Windows and uses OpenGL. Supported architectures are IRIX, Linux (i386 and PPC),OSF1 and SunOS. DINO is distributed in binary form only, but is freely available.

DINO aims to visualize the diversity of structural data in a single program and to allow the user to explore relationships between the data. There are five data-types supported: structure (atomic coordinates and trajectories), surface (molecular surfaces), scalar field (electron densities and electrostatic potentials), topograph (surface topography scans) and geom (geometric primitives such as lines).

The number and size of the data the program can handle is only limited by the amount of RAM present in the system. No artifical limits are set.

Supported input file formats are PDB (coordinates), X-PLOR/CNS (coordinates and electron densities), CHARMM (coordinates, trajectories and scalar fields), CCP4 (electron densities), UHBD (electrostatic potentials), DELPHI (electrostatic potentials), GRASP (electrostatic potentials and surfaces) MSMS (surfaces), MSP (surfaces), MEAD (coordinates and electrostatic potentials) and greyscale TIFF (surface topographs).

Output can be written as TIFF, PNG, PostScript or POV-Ray

Author: Philippsen, Ansgar   Submitted by: the author. (Entry 21). Submitted on Apr 28, 2001.

Cross-indexing terms:   visualization;   editing.

• Import/export several file formats for 3D structures, amino acid sequence, and graphics.
• Insert SMILES string as a 3D molecule.
• Manipulate the view of 3D structures.
• Change charges, bonds, hybridization, oxidation state, and stereochemistry.
• Create groups, surfaces, isosurfaces, crystal cells, Catalyst or ISIS query features and labels.
• Monitor distances, angles, torsion, H-bonds, bumps and more.
• Calculate solvent accessibility and RMSD.
• Predict secondary structure.
• Optimize structures using a fast, Dreiding-like forcefield.
• Superimpose by tethers, sequence alignment, residues or matrices.
• Change the display of atoms, proteins, nucleotides, surfaces, sequences, and graphs.
• Perform 3D small molecule sketching, editing and animation.
• Control lighting, depth cueing, and graphical quality.
• Animate.
• Output high-quality graphics to present results to your colleagues.

Author: Accelrys (formerly Molecular Simulations), Inc.   Submitted by: Herraez, Angel. (Entry 83). Submitted on Jun 1, 2006.

Cross-indexing terms:   movie maker;   PyMOL movie maker.

Authors: Hodis, Eran;   Schreiber, Gideon;   Rother, Kristian;   Sussman, Joel L.   Submitted by: the author. (Entry 96). Submitted on May 4, 2008.

Cross-indexing terms:   renumbering;   macros, excel, for PDB files;   PDB file manipulation in Excel;   spreadsheet (excel) macros for PDB files.

Author: Honegger, Annemarie   Submitted by: Martz, Eric. (Entry 66). Submitted on Nov 17, 2004.

Cross-indexing terms:   Jmol;   browser control of Jmol applet;   web browser control of Jmol applet;   java, jmol applet.

Author: Martz, Eric   Submitted by: Foley, Brian. (Entry 82). Submitted on Jun 1, 2006.

Cross-indexing terms:   Java3D.

Authors: Can, Tolga;   Wang, Yujun.   Submitted by: the author. (Entry 43). Submitted on Jun 7, 2003. Last revised on Dec 16, 2005.

Cross-indexing terms:   fragment;   rules;   cleave;   reaction;   molecule;   algorithm;   RECAP;   drug;   design;   virtual;   synthesis.

Fragmenter is the virtual building block creation component of ChemAxon’s Java based chemical software technology.

Fragmenter cleaves molecules to generate fragments which retain their associated cleavage route information.

Using the cleavage route information, the library of fragments generated can be used as building blocks to more easily create small molecule libraries during lead discovery and optimization.

• Customizable fragmentation rules
• Built in RECAP fragmentation module allows "more synthesisable" chemistry
• Rapid fragmentation
• Exhaustive fragmentation can be performed
• Fragmentation information is stored with fragments

Author: ChemAxon, Ltd   Submitted by: Allardyce, Alex. (Entry 62). Submitted on Sep 30, 2004. Last revised on Oct 2, 2004.

Cross-indexing terms:   Rasmol reviewed/compared;   Molmol reviewed/compared;   gOpenmol reviewed/compared;   VMD reviewed/compared;   DINO reviewed/compared;   WebLabViewer reviewed/compared;   SwissPDBViewer reviewed/compared;   O reviewed/compared;   XtalView reviewed/compared;   BioDesigner reviewed/compared;   Chime reviewed/compared;   ICMLite reviewed/compared;   Prepi reviewed/compared;   Pymol reviewed/compared;   Linux-software reviewed/compared;   list with reviews of freeware;   reviews of free software;   comparisons of freeware packages.

Update March 2004 (G Mullier): review seems to have moved - now hung off a blog.

Author: Saric, Marc   Submitted by: Mullier, Graham. (Entry 29). Submitted on Nov 14, 2001. Last revised on Mar 20, 2004.

Cross-indexing terms:   unix;   linux.

Author: Zucic, Damir   Submitted by: the author. (Entry 11). Submitted on Dec 6, 2000. Last revised on Mar 4, 2003.

Cross-indexing terms:   MolMol;   Cn3D;   WebLab Viewer;   MolView;   LinusLite;   WPDB (Windows Protein Database);   MovieMol;   Animation Works;   VMD (Visual Molecular Dynamics);   PDBTools.

Author: Martz, Eric   Submitted by: the author. (Entry 6). Submitted on Nov 30, 2000.

Cross-indexing terms:   structure alignment;   multiple sequence alignment.

Authors: Ilyin, Valentin;   Abyzov, Alex.   Submitted by: the author. (Entry 84). Submitted on Jun 7, 2006.

Cross-indexing terms:   GUI;   computational chemistry packages;   Gamess-US;   Gaussian;   Molcas;   Molpro;   MPQC;   Q-Chem.

Author: ALLOUCHE, Abdul-Rahman   Submitted by: the author. (Entry 91). Submitted on Apr 2, 2007.

Cross-indexing terms:   open source;   GNU GPL;   unix;   linux;   molecular visualization;   garlic;   docking;   create and edit protein structure;   Ramachandran plot;   helical wheel plot;   averaged hydrophobicity plot;   hydrophobic moment plot;   Venn diagram;   sequence comparison.

Author: Zucic, Damir   Submitted by: the author. (Entry 9). Submitted on Dec 4, 2000. Last revised on Mar 4, 2003.

Cross-indexing terms:   quantum-mechanics;   molecular mechanics;   molecular dynamics;   geometry optimization.

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 [1] 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 MOPAC7 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. Ghemical also contains the OpenBabel package for import and export of many different file formats (as well as other tasks).

Authors: Hassinen, Tommi;   Cruz, Mike;   Heikkilä, Ville;   Hutchison, Geoff;   Huuskonen, Jarno;   Rowley, Christopher.   Submitted by: Bizzaro, J.W.. (Entry 73). Submitted on May 2, 2005.

Cross-indexing terms:   molecular dynamics trajectories, visualization;   molecular orbitals;   orbitals, molecular.

Author: Laaksonen, Leif   Submitted by: Martz, Eric. (Entry 28). Submitted on Nov 13, 2001.

Cross-indexing terms:   Molecular Surface;   Grasp;   Chime;   VRML;   Sequence Variability;   Molecular Graphics;   Surface Properties.

Authors: Nayal, Murad;   Hitz, Ben.   Submitted by: the author. (Entry 55). Submitted on Apr 27, 2004.

Cross-indexing terms:   Chemistry;   organic;   SDF;   TPSA;   HBa;   HBd;   ActiveX;   Split;   Merge;   Export;   Browse;   Export;   Hyleos;   Free.

Author: Betton, Christophe   Submitted by: the author. (Entry 69). Submitted on Jan 16, 2005.

Cross-indexing terms:   iMol;   trajectories;   animations;   PDB;   Mac OS X;   OS X, Mac;   OpenGL;   QuickTime.

Author: Rotkiewicz, Piotr   Submitted by: the author. (Entry 52). Submitted on Dec 17, 2003.

Cross-indexing terms:   Interchem;   Presto;   Convert;   Threedom;   Icmech;   Strauss;   Smiles;   Chemspread;   Salford Software;   Fortran-95;   Autobuild;   Interchem-PC;   Presto-PC.

An ever expanding range of 3D structures derived from the 2D structure catalogues of the so-called "diversity suppliers" is being produced. A total of around 1.25 million "drug-like" structures is available now.

The programs are distributed under a cost-free license to academics and other not-for-profit organisations (i.e. charities). Industrial and government organisations are charged a (relatively) small fee (currently 2500 UK pounds) for a perpetual site license. The databases are distributed for no cost to all users.

Author: Bladon, Peter   Submitted by: the author. (Entry 64). Submitted on Oct 19, 2004.

Cross-indexing terms:   java applet;   computational chemistry;   molecular builder;   molecular editor;   gaussian;   gamess, mopac, amber;   vasp;   gromacs;   ADF;   SIESTA;   QChem;   GULP;   VRML;   sftp;   ssh2;   isosurfaces;   molecular orbitals;   electron densities;   frequencies;   animation;   MD trajectory;   interactive charting;   electrostatic potential;   java3d;   picture generation;   BMP;   JPEG;   PNG;   PovRay;   WebStart.

Author: Vassiliev, Vladislav   Submitted by: the author. (Entry 92). Submitted on Apr 11, 2007. Last revised on Nov 21, 2008.

Cross-indexing terms:   java;   jmol;   interactive learning environment for molecular structures;   learning environment;   lesson plans;   authoring tool for educational tutorials.

Authors: Bottomley, Steven;   Chandler, David;   Morgan, Eleanor;   Helmerhorst, Erik.   Submitted by: the author. (Entry 88). Submitted on Jan 10, 2007.

Cross-indexing terms:   structure search;   non structural data;   exact;   substructure;   similarity;   reaction;   search;   database;   Oracle;   cartridge;   Marvin;   API;   2D hashed fingerprint;   pharmacophore;   chemical;   fingerprint;   SQL;   Access;   MySQL;   API;   Java;   SMARTS;   R-Group;   Chemical Terms;   query.

JChem Base is a Java tool for the development of applications that allow for the search of mixed structural and non-structural data. JChem Base can integrate a variety of database systems (Oracle, SQL, Access, etc) with web interfaces and fully supports all ChemAxon technology.

Via the JChem Cartridge many JChem functions, such as structure searching or property predictions are directly available from within Oracle's SQL.

The system includes Marvin, a fast substructure, similarity, and exact search engine using 2D hashed fingerprints. Structures are stored in database tables. Structural and non-structural data can be combined. SDF, SMILES, etc. can be imported and exported. There is API with low and high level classes. Key features:

• Graph based topology search algorithm
• Fingerprint-based database search accelerator technology
• Advanced query features;
  • exact structure and substructure searching
  • similarity searching using chemical and pharmacophore fingerprints
  • generic query atoms
  • SMARTS query property support
  • R-group query expressions
  • reaction queries
  • stereo specific structure and reaction specifications
  • supports Chemical Terms

To find out more please visit this implementation: http://www.jchem.com/index.html?content=examples.html or download and evaluate from our website

Author: ChemAxon, Ltd   Submitted by: Allardyce, Alex. (Entry 60). Submitted on Sep 30, 2004. Last revised on Oct 2, 2004.

Cross-indexing terms:   java applet;   applet;   chime-compatible applet.

Because Jmol is written in Java, Jmol runs on a wide variety of operating systems (Windows, Mac OSX, linux, among others) and in all popular browsers (Internet Explorer, Netscape 4/6/7, Mozilla, Safari, etc.).

Jmol supports the RasMol/Chime scripting language. The Jmol applet provides a migration path for Chime-based web applications. Jmol includes a perl script which will automatically convert many Chime web pages.

The source code and java binaries are available from http://jmol.sourceforge.net and are covered under the GNU Publice Licenses.

Author: Project, Jmol   Submitted by: the author. (Entry 50). Submitted on Dec 14, 2003.

Cross-indexing terms:   molecular modeling;   molecular visualization;   molecular graphics;   computational chemistry;   kinetic simulations;   dynamics;   drug discovery.

Author: Kuznik, Nikodem   Submitted by: the author. (Entry 15). Submitted on Jan 13, 2001.

Cross-indexing terms:   powerpoint;   activex;   visual basic;   presentations.

Author: Perdigao, Luis   Submitted by: the author. (Entry 98). Submitted on Oct 23, 2008.

Cross-indexing terms:   Kinemages;   Java viewers;   presentations;   tutorials.

There is now a capable Java version of Mage which runs on the Web with no plug-ins. The above page (by Martz) comparing Mage and Rasmol is nicely done in general. However, Mage has ribbons, backbone, ball&stick, etc. representations; kinemages are not scripts but are heirarchical, commented, 3D display lists; and making a simple kinemage is extremely easy, and its exploration is just as open-ended as in RasMol - it's only if you want to make a custom-crafted presentation that it gets "technical". Also, an important use of Mage now is to show all-atom contacts made by Probe (in real time, on Unix).

Author: Richardson, David C.   Submitted by: Richardson, Jane S.. (Entry 2). Submitted on Nov 30, 2000. Last revised on May 16, 2001.

Cross-indexing terms:   applet;   JavaBeans;   chemical database;   Windows;   Unix;   Mac;   IE;   Netscape;   Mozilla;   Molfile;   SDfile;   RDfile;   Rgfile;   Rxnfile;   SMILES;   SMARTS;   XYZ;   PDB;   CML;   JPG;   PNG;   SVG;   POV-Ray;   stereochemistry;   query atoms;   query bonds;   R-groups;   R-logic;   reaction, atom-mapping;   2D;   3D;   wireframe;   sticks;   ball-and-stick;   clean;   animation;   table of structures;   reactions;   E/Z double bonds;   R/S chirality;   ABS/OR/AND enhanced stereo;   query stereo configuration;   prediction;   plugin;   pKa;   logP;   logD;   polar surface area (PSA);   charge distribution;   polarizability prediction;   H-bond aceptor/donor;   major microspecies;   reactivity;   refractivity;   elemental analysis;   topology analysis.

• maximum portability (Windows, Unix, Mac, several browsers, like IE, Netscape, Mozilla)
• several import/export formats (Molfile, SDfile, RDfile, Rgfile, Rxnfile, SMILES, SMARTS, XYZ, PDB, CML, etc.)
• image export (JPG, PNG, SVG, POV-Ray, etc.)
• chemical calculation plugin tools: pKa, logP, logD, polar surface area (PSA), charge distribution, polarizability prediction, H-bond aceptor/donor, major microspecies, reactivity, refractivity, elemental analysis, topology analysis, etc
• Advanced stereochemistry, E/Z double bonds, R/S chirality, ABS/OR/AND enhanced stereo, query stereo configuration
• query atoms and bonds
• R-groups and R-logic
• reactions, atom-mapping; several 3D models (wireframe, sticks, ball-and-stick, etc.), Various 2D and 3D cleaning options
• coordinate calculation; animation
• tables of structures with labels, buttons, check boxes, edit boxes,
• text and graphics input
• displaying and editing files containing molecule lists (SDfiles, SMILES)
• custom coloring
• copy and paste
• printing

Author: ChemAxon, Ltd   Submitted by: Allardyce, Alex. (Entry 38). Submitted on Aug 22, 2002. Last revised on Oct 2, 2004.

Cross-indexing terms:   AutoDock;   surfaces, molecular;   Python;   OpenGL.

	AutoDockTools (ADT) AutoDockTools is graphical front-end for setting up and running AutoDock - an automated docking software designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.
	Python Molecular Viewer (PMV) PMV is a powerful molecular viewer that has a number of customizable features and comes with many pluggable commands ranging from displaying molecular surface to running molecular dynamics simulation and energy minimization calculations.
	Vision Vision is a visual-programming environment in which a user can interactively build networks describing novel combinations of computational methods, and yielding new visualizations of their data without actually writing code.

Authors: Sanner, Michel;   Chris Carrillo;   Kevin Chan;   Sophie Coon;   Sargis Dallakyan;   Alex Gillet;   Sowjanya Karnati;   William (Lindy) Lindstrom;   Garrett M. Morris;   Brian Norledge;   Anna Omelchenko;   Daniel Stoffler;   Vincenzo Tschinke;   Guillaume Vareille;   Yong Zhao.   Submitted by: Dallakyan, Sargis. (Entry 86). Submitted on Sep 27, 2006. Last revised on Nov 5, 2008.

Cross-indexing terms:   tinker;   mechanics, molecular;   semi-empirical quantum-mechanics;   mopac;   gamess;   modeling, molecular.

Author: McArdle, Patrick   Submitted by: the author. (Entry 54). Submitted on Mar 30, 2004. Last revised on Apr 8, 2004.

Cross-indexing terms:   dynamics, molecular.

Author: Xie, Charles   Submitted by: the author. (Entry 72). Submitted on Mar 30, 2005.

Cross-indexing terms:   MICE;   collaborative;   interactive;   molecular visualization;   VRML.

The Molecular Interactive Collaborative Environment (MICE) is a Java/Java3D based molecular structure viewer. As a pure Java application, MICE will run without modification on any platform for which Java version 2 and Java3D are available. We have successfully run MICE on Windows 98/NT4.0, Solaris and Linux.

Using a simple form interface, users can users can create custom representations of any molecule in the Protein Databank (PDB), via a network-based scene generator (MSG) that uses MolScript to create VRML representations of the molecule of interest. Once loaded into MICE, the custom view can then be viewed interactively and queried using rudimentary scene interrogation tools.

As well as allowing a user to manipulate and examine a molecule locally, MICE can also share views of molecules across a network. In a collaborative session, multiple users at different geographical locations can view the same representation of the molecule of interest. Any user can take control of the session and alter the view of the molecule, with these changes being seen by all members of the collaboration.

Authors: Moreland, John;   Tate, John;   Gramada, Apostol;   Bourne, Phil.   Submitted by: the author. (Entry 12). Submitted on Dec 6, 2000.

Cross-indexing terms:   structural alignment;   ball-and-stick;   Linux;   Mac OS X;   Windows;   molecular surface;   OpenGL;   PDB;   SDF;   Mol2;   protein superposition;   surfaces, molecular.

MMV main user interface.

Features at a glance

• Share and view results from Molegro Virtual Docker docking runs.
• Imports and exports PDB, SDF, Mol2, and MVDML files.
• Automatic preparation of molecules.
• Molecular surface and backbone visualization.
• Labels, sequence viewer, and biomolecule generator.
• Cropping of molecules and clipping planes.
• Structural protein alignment.
• Cross-platform: Windows, Linux, and Mac OS X is supported.

Authors: Thomsen, Rene;   Christensen, Mikael H..   Submitted by: the author. (Entry 95). Submitted on Jan 21, 2008. Last revised on Jan 22, 2008.

Cross-indexing terms:   NMR multiple-model visualization and violations of constraints;   schematic renderings;   presentation capability;   hydrogen bond identification.

MolMol has been cited by over 500 scientific journal articles (search for "molmol" at highwire.stanford.edu). It ranks among the most popular free visualization programs, including RasMol (>700) and KineMages (>450).

Authors: Koradi, Reto;   Billeter, Martin;   Wuethrich, Kurt;   et al..   Submitted by: Martz, Eric. (Entry 46). Submitted on Jun 26, 2003.

Cross-indexing terms:   Ray-tracing;   PDB;   POV-Ray.

Author: Richardson, David E   Submitted by: the author. (Entry 44). Submitted on Jun 7, 2003. Last revised on Jun 9, 2003.

Cross-indexing terms:   Publication-quality images.

Author: Kraulis, Per   Submitted by: Martz, Eric. (Entry 22). Submitted on Jun 5, 2001. Last revised on May 10, 2002.

Cross-indexing terms:   protein explorer, simplified;   surfaces;   sequence to structure;   comparison of 2 molecules;   French.

MolUSc est un programme de manipulation de molecules base sur le plug-in Chime (MolUSc signifie modelisation de Molecules pour un Usage Scolaire). L'objectif de MolUSc est de donner l'acces aux eleves a toutes les possibilites de Chime, au travers d'une interface conviviale, sans avoir a taper d'instructions de commande. MolUSc permet d'afficher des surfaces, de faire des selections a partir des sequences, de comparer deux molecules,... MolUSc fonctionne avec Netscape Navigator mais aussi avec Internet Explorer (meme mieux). MolUSc peut etre telecharge, et utilise librement dans un but educatif et non commercial uniquement.

Author: Pillot, Paul   Submitted by: the author. (Entry 30). Submitted on Dec 14, 2001. Last revised on Jan 29, 2003.

Cross-indexing terms:   Macintosh;   OSX;   alignments;   neighbors, atomic;   hydropathy plots.

Author: Smith, Thomas   Submitted by: the author. (Entry 56). Submitted on Apr 29, 2004.

Cross-indexing terms:   protein;   nucleic acid;   drug design;   ion channel;   antifreeze proteins;   enzymes;   protease;   internal coordinate molecular mechanics;   docking..

Author: Tikhonov, Denis   Submitted by: Yang, Daniel. (Entry 67). Submitted on Nov 27, 2004.

Cross-indexing terms:   inorganic crystals;   jmol;   organic compounds;   small compounds.

Author: Moeck, Peter   Submitted by: the author. (Entry 77). Submitted on Nov 25, 2005.

Author: Chen, Mengen   Submitted by: the author. (Entry 71). Submitted on Feb 22, 2005.

Cross-indexing terms:   RasMol;   RasWin;   RasMac;   RasTop;   OpenRasMol;   Open Source;   PDB;   CIF.

Authors: Bernstein, Herbert J.;   Sayle, Roger;   Mueller, Arne;   Grossman, Gary;   Molinaro, Marco;   Valadon, P.;   and many others.   Submitted by: the author. (Entry 10). Submitted on Dec 4, 2000.

Cross-indexing terms:   screensaver, molecular;   Gaussian cube file screensaver.

Author: Oeffner, Robert   Submitted by: the author. (Entry 75). Submitted on Jun 27, 2005. Last revised on Feb 19, 2007.

Cross-indexing terms:   Web-Tool;   Animated image (GIF) construction, automatic;   GIF, animated, automatic construction;   Image, animated GIF, automatic construction;   Multi-GIF, automatic construction.

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. It has many controls including size, number of frames, speed and axis of rotation, and if you wish, you can supply your own view as a RasMol script.
Bohne A. PDB2MultiGIF: a web Tool to Create Animated Images of Molecules J. Mol. Model. 4 (1998) 344-34

Author: Bohne, Andreas   Submitted by: the author. (Entry 14). Submitted on Jan 10, 2001.

Cross-indexing terms:   raytracing;   pov-ray.

Author: POV, Team   Submitted by: the author. (Entry 31). Submitted on Apr 8, 2002. Last revised on Oct 9, 2002.

Cross-indexing terms:   amino acid sequence profile;   profile, amino acid sequence;   protein structure prediction visualization;   prediction of protein structure, visualization;   interface recognition.

POLYVIEW - all-in-one for protein sequence/structure analysis

POLYVIEW is a protein structure visualization web server that can be used to generate schematic representations of secondary structures and relative solvent accessibilities, allowing one to highlight selected residues, e.g. polymorphic or involved in protein-protein interactions.

2D schemes are dynamically generated and can be easily customized in order to facilitate the visual analysis of patterns of amino acid physico-chemical properties, secondary structure states, relative solvent accessibilities, and trans-membrane domains, all together.

Beside the PDB deposited proteins, one can get a custom visualization of a protein structure submitted in the PDB format, or results from protein structure prediction servers in the CASP format, as well as arbitrary sequence profiles. Once submitted together, profiles can be aligned for a comparative analysis.

PDB SABLE PSIPRED

Additional services of POLYVIEW provide user with an automatic interface recognition within a given protein complex, calculation of position specific amino acid conservation scores and generation of 3D animated images, which are ready for presentations and publications.

No plug-ins required! For details and examples, please refer to the POLYVIEW documentation.

Authors: Porollo, Aleksey;   Meller, Jaroslaw.   Submitted by: the author. (Entry 78). Submitted on Dec 3, 2005. Last revised on Aug 8, 2006.

Cross-indexing terms:   directx.

• Highly optimised 3D rendering engine using DirectX
• Suite of display modes including space fill, ball & stick, sticks, cartoon, wireframe, backbone and more
• Suite of colouring modes including element, group, structure, ordinal, chain, electrostatic and more
• Suite of post-process effects to alter the appearance of the scene such as depth of field, depth visualisation and more
• Ability to combine display modes for individual atoms/bonds in the protein
• Processing framework to modify the protein's structure
• Powerful API for writing extensions

Author: Gale, Louis   Submitted by: the author. (Entry 101). Submitted on Feb 11, 2009.

Author: Mishchenko, Mikhail   Submitted by: the author. (Entry 99). Submitted on Feb 4, 2009.

Cross-indexing terms:   conservation/mutation, coloring 3D protein by in "one click";   multiple protein sequence alignment coloring of a 3D protein in "one click";   sequence alignment coloring of a 3D protein in "one click";   contact surfaces showing noncovalent bonding between any two moieties in one click;   noncovalent bonds between any two moieties, visualize in one click;   cation-pi interactions in one click;   salt bridges in one click;   visualization for novices;   novice visualization;   easiest visualization for novices;   animate conformational changes, morphs, NMR ensembles;   conformational changes, animate;   morphing proteins.

Protein Explorer is free software for visualizing the three-dimensional structures of protein, DNA, and RNA macromolecules, and their interactions and binding of ligands, inhibitors, and drugs. It is arguably the easiest-to-use software of its kind. It is suitable for high school and college students (ages 16 years and older), yet it is also widely used by graduate students and researchers. More about what Protein Explorer does. Protein Explorer makes the power of Chime accessible, offering extensive features both for novices and advanced features for protein structure specialists. Much easier to use, and much more powerful than RasMol. Extensive built-in context-sensitive help, QuickTour, Tutorials. For details, see Snapshots of Protein Explorer in Action, and Protein Explorer for Novices/Protein Explorer, Advanced.

Author: Martz, Eric   Submitted by: the author. (Entry 4). Submitted on Nov 30, 2000. Last revised on Apr 30, 2003.

Cross-indexing terms:   halftoning, real-time;   Java;   Swing GUI;   OpenGL Shading Language;   Java Bindings for OpenGL;   open source;   GNU General Public License;   PNG;   JPEG;   Shading.

ProteinsShader is a molecular visualization program that uses information from Protein Data Bank files to produce illustrative renderings of proteins that approximate what an artist might create using pen and ink. This free platform-independent open-source program is written primarily in Java, but also makes extensive use of the OpenGL Shading Language to modify the graphics pipeline. A graphics card supporting at least OpenGL 2.0 is required (OpenGL 2.0 was finalized on October 22, 2004).

Author: Weber, Joe   Submitted by: the author. (Entry 97). Submitted on Jul 16, 2008. Last revised on Sep 1, 2008.

Authors: Crivelli, Silvia;   Kreylos, Oliver;   Max, Nelson;   Bethel, Wes;   Lu, Ting-Cheng;   Crawford, Clark.   Submitted by: the author. (Entry 76). Submitted on Sep 30, 2005.

Cross-indexing terms:   DirectX;   Trajectory;   Interactive;   Animations of molecular dynamics;   molecular dynamics trajectories.

This viewer is also an experiment in using DirectX for scientific visualization, which restricts it to computers running Windows 95 and higher. (NT 4.0, Linux, Macintosh will not work; Windows 98, Me, 2000 will work. The current version is limited to PDB files with a single protein chain.).

Authors: Suits, Frank;   Gresh, Donna.   Submitted by: the author. (Entry 27). Submitted on Oct 20, 2001. Last revised on Nov 13, 2001.

Cross-indexing terms:   modelling;   animation;   editing;   ray-tracing;   open-source;   ribbons;   Python;   Molscript;   OpenGL.

Authors: DeLano, Warren;   Grosse-Kunstleve, Ralf W..   Submitted by: the author. (Entry 24). Submitted on Aug 31, 2001.

Cross-indexing terms:   docking.

We have been using Python as a scripting framework to assemble basic components at a high-level. This approach enables the rapid development of custom applications for the visualization and manipulation of molecular data and provides an excellent level of code re-use. Besides being a very powerful "glue" language, its object-oriented nature makes it an appropriate language for the development of components. We have developed a number of Python extensions, also called packages, to deal with different aspects of structural biology. In this course, we will present some of these components and explain how they have been combined to create applications such as PMV: the Python Molecule Viewer and ADT: the AutoDockTools suite. Time permitting , we will also survey other Python-based applications such as MMTK and Chimera.

Full Description.

Author: Sanner, Michel   Submitted by: Foley, Brian. (Entry 40). Submitted on Mar 12, 2003.

Cross-indexing terms:   movies, AVI, generating;   AVI movies, generating;   DCD file format, animate molecular trajectories from;   animate molecular trajectories from DCD file format, PDB, ribbon.

• Display wire frame, stick figure, ball and stick, point, space-filling, ribbon, tube and spline molecular structures from a PDB file.
• Assign secondary structure via STRIDE
• Animate molecular trajectories stored in the DCD file format (both big- and little-endian).
• Kabsch rotate all structures in a trajectory against the initial structure.
• Interactively measure bond lengths, bond angles and torsion angles.
• Dynamically adjust user selected torsion angles.
• Display atom labels.
• Display coordinate axis.
• Dynamic modification of the color scheme (including color-by-element, color-by-atom-number, color-by-temperature and color-by-occupancy).
• Dynamic lighting.
• Adjust atomic radii (including radii-by-temperature and radii-by-occupancy).
• Print to any Windows supported printer and copy images to the Windows clip board.
• Generate AVI movies from a molecular trajectory.
• Directly query the PDB.

Author: Gans, Jason   Submitted by: the author. (Entry 19). Submitted on Mar 15, 2001. Last revised on Jul 17, 2001.

Cross-indexing terms:   Publication-quality images;   OpenGL.

A typical realtime rendering of QuteMol with ambient occlusion and a sophisticated edge cueing effect added.

The 3D shape of very large molecules is difficult to be uderstood without ambient occlusion. Also this example (the 58k atom 1AON) is shown interactively.

Even for small molecules, our ambient-occlusion adds to the clarity.

Yet another QuteMol rendering featuring a fat liquorice mode and ambient occlusion.

Authors: Tarini, Marco;   Cignoni, Paolo.   Submitted by: Cignoni, Paolo. (Entry 81). Submitted on Apr 23, 2006. Last revised on Aug 25, 2006.

Cross-indexing terms:   Ramachandran plot.

Author: Ho, Bosco   Submitted by: the author. (Entry 51). Submitted on Dec 16, 2003. Last revised on Sep 18, 2006.

Cross-indexing terms:   openrasmol.

• The Home Page for RasMol and OpenRasMol is actively maintained by Herb Bernstein. It offers the latest version of RasMol (2.7 or later) with a number of enhancements documented in an updated reference manual. This site does not duplicate most of the extensive help for beginners and usage guides offered at the UMass RasMol site. RasMol 2.7's license requires that all derivatives be free with open source code.

• The RasMol Home Page at UMass, started in 1995 by Eric Martz, provides extensive help for beginners as well as reference materials and guides for advanced users. This site offers RasMol 2.6; its documents pertain to version 2.6 and largely stopped being updated in 1999, when Martz changed his focus to Protein Explorer and other Chime-based resources. This site does not document enhancements in RasMol 2.7, available from the OpenRasMol site. RasMol 2.6 and its source code are in the public domain due to the generosity of its author, Roger Sayle.

Authors: Martz, Eric;   Bernstein, Herb.   Submitted by: the author. (Entry 49). Submitted on Nov 7, 2003. Last revised on Nov 7, 2003.

• RasMol Quick Start! and RasMol Tutorials
• Origin of RasMol
• History of Molecular Visualization
• RasMol 2.6 Downloads for Windows, Macintosh, and other platforms
• RasMol 2.6 Reference Manual
• FAQ for RasMol and Chime including public domain status, literature citation, stereo viewing, printing in high resolution, showing double bonds, and control of covalent and noncovalent bond displays.
• Educational Molecular Visualization
• Guides to Select Commands, Coloring, and van der Waals radii and Covalent Bond Assignment Mechanisms.
• And more (see Contents)