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.