Cross-indexing terms:   Molecular Visualization;   Molecular Surface;   Alignment.

Authors: Baum, Daniel;   Schmidt-Ehrenberg, Johannes.   Submitted by: the author. (Entry 3). Submitted on Aug 27, 2001. Last revised on Aug 29, 2001.

Cross-indexing terms:   PNG;   Windows;   XYZ.

Author: Bonner, Thomas   Submitted by: the author. (Entry 24). Submitted on Jun 15, 2004.

Cross-indexing terms:   modeling, molecular;   design, molecular;   construction, molecular;   mechanic;   dynamic;   builder;   simulation;   quantum.

Ascalaph Molecular Modelling Suite

• Molecular Design
• Molecular mechanics simulations
• Quantum calculations
• Force Field development
• GPU accelerated calculations (with NVIDIA CUDA)

Ascalaph Graphics provides a graphical interface of the system.
Ascalaph Quantum provides an interface for the quantum mechanical programs PC GAMESS, NWChem and CP2K
Ascalaph Designer provides methods to construct molecular models, molecular mechanics and quantum chemistry.

Author: Nikitin, Alexey   Submitted by: the author. (Entry 29). Submitted on Feb 28, 2008. Last revised on Feb 2, 2010.

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;   ADMETOX.

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

Author: ChemAxon, Ltd   Submitted by: Allardyce, Alex. (Entry 22). Submitted on Dec 23, 2003. Last revised on Sep 30, 2004.

Cross-indexing terms:   modeling, protein;   dynamics, molecular;   mechanics, molecular.

Authors: Karplus, Martin;   Accelrys, Inc. (formerly MSI).   Submitted by: Martz, Eric. (Entry 8). Submitted on May 24, 2002.

Cross-indexing terms:   scoring function;   drug design;   free energy;   docking;   protein-protein.

Author: Audie, Joseph   Submitted by: the author. (Entry 28). Submitted on Dec 5, 2007.

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

Author: Gunda, Tamas E.   Submitted by: the author. (Entry 5). Submitted on May 11, 2002. Last revised on Nov 18, 2006.

Cross-indexing terms:   CrystalDiffract;   SingleCrystal;   crystal structures visualization software;   diffraction simulation;   TEM diffraction;   x-ray powder diffraction;   stereographic projections.

This is the home page for CrystalMaker Software Ltd: authors of the award-winning CrystalMaker program for crystal and molecular structures visualization, measurement, animation and movie building.

CrystalMaker is an elegant, easy-to-use application available for both Mac and Windows computers. Featuring a seamless drag-and-drop workflow, CrystalMaker lets you load over 15 different file formats, with automatic format recognition and instant display. Multi-structure sequences can be assembled and edited, with the option of full-screen animation, slideshows or movie output.

CrystalDiffract and SingleCrystal (Apple Design Award 2007) are helper applications, for understanding diffraction patterns from powders and single crystals, respectively. Both programs are designed to work with CrystalMaker, so you can visualize a structure in one window, and work with its simulated diffraction pattern in another window.

The CrystalMaker website contains free software downloads (e.g., CrystalMaker Demo can be used as a free viewer application), plus thousands of crystal structures files, movies and graphics.

Author: Palmer, David   Submitted by: the author. (Entry 30). Submitted on Oct 30, 2008.

Cross-indexing terms:   crystal structure;   inorganics;   minerals;   surfaces;   proteins;   coordination polyhedra;   thermal ellipsoids;   VRML.

Authors: Berndt, Michael;   Brandenburg, Klaus;   Putz, Holger.   Submitted by: the author. (Entry 13). Submitted on Jul 31, 2002.

Cross-indexing terms:   fragmenter;   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 25). Submitted on Sep 30, 2004. Last revised on Oct 2, 2004.

Cross-indexing terms:   fragmenter;   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 25). Submitted on Sep 30, 2004. Last revised on Oct 2, 2004.

Cross-indexing terms:   modeling, server-based, small molecule;   energy minimization, small molecules;   ionization potential, small molecules.

Authors: Ricci, Davide;   Rod, Thomas.   Submitted by: the author. (Entry 31). Submitted on Dec 2, 2009.

Cross-indexing terms:   modeling, protein.

Author: Accelrys, Inc. (formerly MSI)   Submitted by: Martz, Eric. (Entry 9). Submitted on May 24, 2002. Last revised on May 24, 2002.

Cross-indexing terms:   Molecular modelling;   biolmolecules;   molecular mechanics;   SMILES.

Author: Bladon, Peter   Submitted by: the author. (Entry 17). Submitted on Feb 10, 2003.

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;   pharmacophore fingerprint.

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 21). Submitted on Dec 23, 2003. Last revised on Oct 2, 2004.

Cross-indexing terms:   Windows;   Linux.

Author: Muscat, Andre   Submitted by: the author. (Entry 23). Submitted on Mar 10, 2004.

Cross-indexing terms:   applet;   JavaBeans;   Java;   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 15). Submitted on Sep 25, 2002. Last revised on Oct 2, 2004.

Cross-indexing terms:   conversion between atomic coordinate file formats;   PDB subformats;   molecule files;   calculation of geometrical data;   POVRAY.

Mol2Mol manipulates and interconverts about 50 different types of molecule files (incl. subtypes). Capturing of coordinates from Gaussian and Gamess etc. output files. By entering a format string practically every Cartesian or MOPAC type Z matrix formats can be in/outputted (even in polar coordinates). Support added for Jmol java applet: MDL mol, XMOL xyz and HyperChem hin files can be written as a javascript variable for using them as inline molecules in html files.

Author: Gunda, Tamas   Submitted by: the author. (Entry 4). Submitted on Nov 26, 2001. Last revised on Nov 18, 2006.

Cross-indexing terms:   Publication-quality images.

Author: Kraulis, Per   Submitted by: Martz, Eric. (Entry 2). Submitted on Jun 5, 2001.

Cross-indexing terms:   modeling, protein.

Authors: Jones, Alwyn;   Kjeldgaard, Morten.   Submitted by: Martz, Eric. (Entry 7). Submitted on May 24, 2002.

Cross-indexing terms:   povchem;   raytracer;   publication-quality images;   services.

PovChem is a chemical visualization and illustration program with a new graphic interface using OpenGL rendering. It takes molecules in the PDB format, lets one interactively set up a picture with fine control over details of the illustration - colors, atom and bond radii, view orientation, etc. It will calculate bonds and display hydrogen bonds. PovChem exports the picture in POV-Ray format, which allows rendering of the image with a state-of-the-art raytracer. This is provides a quick and easy route to quality images at any resolution, for anything from web page thumbnails to publication-quality high-resolution images for journal covers, advertisements, posters, etc. PovChem is designed for small molecules, showing individual "real" atoms and bonds. While it can render proteins, it does not have schematic backbone or surface displays of more specialized protein visualization applications. A 30-day free trial is available, after which the cost for registration is currently $20 (individual, non-profit). Windows, Macintosh, linux, and SGI Irix are supported. The author also provides a Custom Chemical Graphics service, for those wishing to purchase customized images of any molecule(s). See http://www.ChemicalGraphics.com/Custom for more information.

Author: Thiessen, Paul   Submitted by: the author. (Entry 1). Submitted on Jan 11, 2001. Last revised on Jan 13, 2001.

Cross-indexing terms:   povchem;   raytracer;   publication-quality images;   services.

PovChem is a chemical visualization and illustration program with a new graphic interface using OpenGL rendering. It takes molecules in the PDB format, lets one interactively set up a picture with fine control over details of the illustration - colors, atom and bond radii, view orientation, etc. It will calculate bonds and display hydrogen bonds. PovChem exports the picture in POV-Ray format, which allows rendering of the image with a state-of-the-art raytracer. This is provides a quick and easy route to quality images at any resolution, for anything from web page thumbnails to publication-quality high-resolution images for journal covers, advertisements, posters, etc. PovChem is designed for small molecules, showing individual "real" atoms and bonds. While it can render proteins, it does not have schematic backbone or surface displays of more specialized protein visualization applications. A 30-day free trial is available, after which the cost for registration is currently $20 (individual, non-profit). Windows, Macintosh, linux, and SGI Irix are supported. The author also provides a Custom Chemical Graphics service, for those wishing to purchase customized images of any molecule(s). See http://www.ChemicalGraphics.com/Custom for more information.

Author: Thiessen, Paul   Submitted by: the author. (Entry 1). Submitted on Jan 11, 2001. Last revised on Jan 13, 2001.

Cross-indexing terms:   modeling software;   QSAR;   pKa calculation.

Author: patrick ,Urbaniak   Submitted by: the author. (Entry 12). Submitted on Jul 17, 2002.

Cross-indexing terms:   modeling, protein.

Author: Accelrys, Inc. (formerly MSI)   Submitted by: Martz, Eric. (Entry 10). Submitted on May 24, 2002. Last revised on May 24, 2002.

Cross-indexing terms:   virtual synthesis;   reaction engine;   combinatorial chemistry;   JChem;   chemically feasible;   multi-step.

Reactor is the virtual reaction engine of Chemaxon's JChem technology. It supports "smart" reactions (generic reaction equations combined with reaction rules) generating chemically feasible products even in batch mode. The professional version of the tool includes support for multi-step virtual synthesis and filtering of chemically feasible molecules which are not of interest.

Key features:

• chemoselectivity (advanced reaction site and functional group recognition)
• regioselectivity (directing rules, main product detection)
• stereoselectivity (inversion/retention)
• reverse reaction processing
• random synthesis for lead discovery
• exhaustive synthesis for metabolism applications
• intramolecular reactions
• sequential and combinatorial modes
• memory, file and database operation modes
• synthesis tree generation
• synthesis rules for each synthetic step (for on-the-fly filtering of intermediers)
• graphical user interface for browsing the synthesis database
• colored visualization of the original building blocks in the generated library
  
• wide range of file formats supported (MOL, RXN, RDF, SMILES, SMARTS
• rapid execution

To find out more about Reactor please visit our public implementation or download JChem Base (containing Reactor) from our web site.

Author: ChemAxon, Ltd   Submitted by: Allardyce, Alex. (Entry 20). Submitted on Dec 23, 2003. Last revised on Oct 2, 2004.

Cross-indexing terms:   virtual screening;   molecular descriptors;   fingerprint;   pharmacophores;   java;   chemical database;   focused library;   scaling-fingerprint;   scaffold hopping;   topological fingerprint;   topological cross-correlation histogram;   enrichment;   drug discovery.

• Pharmacophore Analysis;
  • customizable pharmacophore definition framework (fragment- and calculation-based solutions)
  • integration of physico-chemical prediction plugins; pKa, logP, logD, charge distribution, and polarizability predictions.
  • supporting Chemical Terms
• Configurable Molecule Descriptor Generation;
• chemical topology fingerprints
• pharmacophore topology fingerprints
• BCUT
• plug-and-play custom and third party fingerprints
• hypothesis calculation
• fuzzy smoothing
• Virtual Screening;
• dissimilarity metrics (Euclidean, Tanimoto)
• variable metric modifiers (normalization, scaling, weighting, directing)
• enrichment enhancement by selectivity optimizer
• screening performance statistics

Author: ChemAxon, Ltd   Submitted by: Allardyce, Alex. (Entry 19). Submitted on Oct 15, 2003. Last revised on Oct 2, 2004.

Cross-indexing terms:   molecular mechanics;   mechanics, molecular;   MDL;   Interactive Simulations, formerly, now MDL.

Author: Surles, Mark, et al.   Submitted by: Martz, Eric. (Entry 16). Submitted on Dec 1, 2002. Last revised on Sep 12, 2004.

Cross-indexing terms:   drug design;   publication-quality images;   modeling.

Authors: Zsoldos, Zsolt;   University of Leeds, UK.   Submitted by: the author. (Entry 14). Submitted on Aug 14, 2002.

Cross-indexing terms:   drug design.

Author: Tripos, Inc.   Submitted by: Martz, Eric. (Entry 11). Submitted on May 24, 2002.

Cross-indexing terms:   molecular modeling;   educational sofware;   model building;   molecular visualization.

Author: Doherty, David   Submitted by: the author. (Entry 18). Submitted on Aug 5, 2003.

Cross-indexing terms:   python;   publication-quality images;   spreadsheet;   2D;   Windows;   Mac;   Unix;   Linux;   OpenEye.

VIDA is a graphical interface designed to visualize, manage and manipulate large sets of molecular information. It is capable of handling 100,000s of molecules simultaneously. It supports all standard visualization paradigms, including 2D depiction, both hardware and software stereo, surface selection and manipulation, and many other unique facilities.

VIDA is based on OpenEye's OEChem toolkit and as such handles chemistry properly as well as reading and writing a wide range of formats. The primary features include:

• A simple and intuitive interface
• Robust and powerful list manager
• Chemically-oriented, fully functional spreadsheet
• Automatic browsing facilities (slide show)
• List operations
• Substructure searching
• Integrated Python interpreter
• Interactive surface selection/sub-setting, real-time contours
• Concurrent interaction between data in spreadsheet and 2D/3D displays
• Multi-level undo
• Easily save and restore a session
• Single-click visualization of docking, shape overlay, and electrostatic overlay results
• Supported on Windows, Linux, Mac OSX, and IRIX systems

Like all OpenEye software, VIDA is available free of charge for non-commercial use.

Author: OpenEye Scientific Software, Inc   Submitted by: the author. (Entry 27). Submitted on Dec 20, 2005.

Cross-indexing terms:   modeling, protein.

Author: Vriend, Gert   Submitted by: Martz, Eric. (Entry 6). Submitted on May 24, 2002.

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

Author: Zhorov, Boris   Submitted by: Yang, Daniel. (Entry 26). Submitted on Nov 27, 2004. Last revised on Nov 29, 2004.