- Insight II is a 3D graphical environment for molecular modeling. Its powerful user interface enables
the seamless flow of data between a wide range of scientific applications. The Insight II
environment integrates builder modules, development tools, force fields, simulation and
visualization tools with tools specifically developed for applications in the life and materials
sciences.
See comments by Gert Vriend.
- Submitted by: Martz, Eric. (Entry 9).
- QUANTA provides a powerful and comprehensive modeling environment for 2D
and 3D modeling, simulation, and analysis of macromolecules and small
organics.
See comments by Gert Vriend.
- Submitted by: Martz, Eric. (Entry 10).
- CMD bioscience specializes in the use of novel proprietary computational methods to model and engineer clinically important protein-protein and protein-peptide interactions. Our "Affinity" algorithm is designed to predict protein-protein / protein-peptide binding affinities; it is fast enough for use as a scoring function and is available for licensing.
- Submitted by: the author. (Entry 28).
Together with Amira 2.3 , an object-oriented interactive system for 3D data visualization, the new extension AmiraMol has been released.
AmiraMol combines Amira's strong capabilities for 3D data visualization like hardware accelerated volume rendering with specific tools for molecular visualization and data analysis. Visualization modules like wireframe, bondangle and secondary-structure view are being supplemented by computational methods like Molecular surfaces, sequence alignment or configuration density computation.
AmiraMol is available for Windows, Linux, IRIX, HP-UX, and SunOS
To get more information or to download a free trial version of Amira please visit:
http://www.amiravis.com/mol/- Co-authors: Schmidt-Ehrenberg, Johannes. Submitted by: the author. (Entry 3).
- 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.
A trial version is available free-of-charge and can be downloaded from http://www.crystalimpact.com/diamond/download.htm.
- Co-authors: Brandenburg, Klaus; Putz, Holger. Submitted by: the author. (Entry 13).
- The INTERCHEM is a molecular modelling system written for SGI-IRIX systems.
It includes:
INTERCHEM (the modelling program itself) which handles visualization and structural analysis of both small molecules and biomolecules.
PRESTO, a program for handling sets of protein sequences. It has facilities for editing and aligning sequences, as well as facilities for characterising aligned stes.
CHEMSPREAD, a spreadsheet type programs for multivariate statistical analysis of sets of compounds
THREEDOM, one of group of programs for performing 3Dcomparisons and overlaying of structures using the icoshedral matching algorithm.
CONVERT, a utility for handling format conversions between the more popularly used schemes.
AUTOBUILD, a utility for generating libraries of small molecular structures.
PROTEINS, a utility for searching a local version of the PDB.
STRAUSS, a program for generating 3D structures from SMILES strings. This program allows for specification of conformation and stereochemical information.
ICMECH, a molecular mechsnics program. Versions are built into INTERCHEM and STRAUSS, but this standalone program is provided.
INTERCHEM-PC, a version of INTERCHEM for Windows (TM) systems
PRESTO-PC, a version of PRESTO for Windows (TM) system. This version has very fast sequence alignment algorithms.
The INTERCHEM system license gives access to the source code of all the programs.
The INTERCHEM system is provided without charge to academic and charitable organisations.
- Submitted by: the author. (Entry 17).
- Apollonius is a windows-based software for molecular visualization, specialized for drawing atoms as spheres. A unique feature is the ability
to export semi-transparent images, which is very useful for publishing in the web or for presentations. Other features are a stereo mode, different coloring modes, and a good control over the various rendering parameters.
- Submitted by: the author. (Entry 24).
Marvin Applets and JavaBeans can be applied in web or stand-alone applications for sketching or viewing structures, queries and reactions. Marvin Applets are free for free web sites. MarvinSketch and MarvinView applications are free for academic/home users or for anyone if accessed at the ChemAxon web site. These Java tools are useful in the front end of chemical database systems.
A list of features:- 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
- Submitted by: Allardyce, Alex. (Entry 15).
- 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
To find out more or download JChem to evaluate the Screen tools, please visit the Screen page
- Submitted by: Allardyce, Alex. (Entry 19).
- Pharmacophore Analysis;
-
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.
- Submitted by: Allardyce, Alex. (Entry 20).
-
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
- Submitted by: Allardyce, Alex. (Entry 21).
-
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 unlimited structure based prediction implemetation here: http://www.chemaxon.com/demos/try_marvin.html- Submitted by: Allardyce, Alex. (Entry 22).
-
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
- Submitted by: Allardyce, Alex. (Entry 25).
- Atomsmith is an easy-to-use, interactive, Windows-based computer program for exploring, building and simulating models of molecules. Atomsmith combines sophisticated molecular visualization and simulation techniques with innovative curriculum-delivery tools to bring discovery of the molecular world to the classroom.
- Submitted by: the author. (Entry 18).
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.
Several utilities are also included. For example: support for PDB Fat, Rasmol/Chime and PDBQ subformats - merge and split modes for multiple files - checking of peptide backbone geometry - removing of alternative locations - NMR: adding of CH2 and CH3 centroids - renumbering of molecules by several options - adding of hydrogen bonds - calculating pyramidalities, ring puckerings - support for CA-atom-only or MODEL files - calculation of Gasteiger-Marsili charges, and many more.
POV-Ray: Improved color support - include files - perspectivity and color perspectivity - delocalized rings - shaded planar rings - separated rendering of selected part of the molecule - coloring by models, chains, residues or helix/sheet/turn info - support for 2D molfiles with atom labels.
Improved adding of hydrogens: in the case of PDB files residue, chain and modul informations will be preserved - mimic pH feature for protonating acidic/basic groups of proteins.
Shareware and 30 day unrestricted trial versions.- Submitted by: the author. (Entry 4).
- This review compares five chemical drawing programs, ISIS/Draw, ChemDraw, DrawIt/ChemWindow, ChemSketch and Chemistry 4-D Draw. ISIS/Draw and ChemSketch have free versions; the others are commercial applications. This review is extensive and detailed, with helpful supplementary information (such as why to use gif rather than jpeg files for the web), and sample outputs from all 5 programs. Several other web or linux applications are also briefly described (Marvin, JME editor, ChemPen, XDrawChem, WinPlt etc.)
- Submitted by: the author. (Entry 5).
- Popular with crystallographers for constructing protein models from electron density maps and other modeling operations, O is available free or on a sliding scale to academics. Commercial users must negotiate a license. Available for Irix, unix, linux, Sun, Mac OSX, and Windows.
- Co-authors: Kjeldgaard, Morten. Submitted by: Martz, Eric. (Entry 7).
- Molecular Mechanics, Dynamics, and MoreCHARMm (Chemistry at HARvard Macromolecular
Mechanics) is a highly regarded and widely used simulation package. CHARMm combines
standard minimization and dynamics capabilities with expert features including normal mode
calculations, correlation analysis, and combined quantum and molecular mechanics (QM/MM)
methods. Simulations provide information concerning molecular-level structure, interactions, and
energetics. Originally developed in the laboratory of Professor Martin Karplus at Harvard
University, this program allows you to perform classical empirical energy calculations on a
variety of small and large molecular systems, including proteins, nucleic acids, and carbohydrates.
Using the latest algorithms and methodology, you can explore in detail the dynamics and
thermodynamics of your system of interest, providing insight into your current experiments and
suggesting new directions for future efforts.
- Co-authors: Accelrys, Inc. (formerly MSI). Submitted by: Martz, Eric. (Entry 8).
- See description in the freeware category. (Licensing fee for commercial use.)
- Submitted by: Martz, Eric. (Entry 2).
- Powerful PDB visualization application for Windows and Linux. Select from standard visualization and coloring modes. Instantly render to JPEG, PNG, BMP or TIFF 2D formats. Optionally, export to the most powerful high-end 3D graphics applications currently available (Discreet 3dsmax and Alias|Wavefront Maya) to produce renderings and animations that simply can't be matched by any Molecular Visualization software.
- Submitted by: the author. (Entry 23).
Ascalaph Molecular Modelling Suite
- Molecular Design
- Molecular mechanics simulations
- Quantum calculations
- Force Field development
Ascalaph Graphics provides a graphical interface of the system.
Ascalaph Designer provides methods to construct molecular models.
Ascalaph Quantum provides an interface for the quantum mechanical program PC GAMESS.- Submitted by: the author. (Entry 29).
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.
- Submitted by: the author. (Entry 27).
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.
- Submitted by: the author. (Entry 30).
- Prochemist is a molecular modelling software for the benchemist.
It includes Molecular modelling,Logp,pka..calcs,qsar and data_mining.
The molecule web viewer is a free java applet(prochemist.class). The
applet can be combined with Xml tree viewer applet and xml database.
Some example are given on the site.
- Submitted by: the author. (Entry 12).
MDL Sculpt employs interactive, real-time molecular mechanics to achieve low energy conformations of molecules, including macromolecules. Regions of the molecule can be frozen during minimizations. Conformational adjustments can be directed by simply dragging on an atom (which attaches a "spring" to it), or connecting two atoms with a "spring". In the animated multi-GIF shown, the inhibitor was pulled out of the HIV protease, and PDB files were saved at various stages. (For more about this simulation, see Animations in Protein Explorer.) [This description was written by Eric Martz and has not been edited by MDL staff.]
- Submitted by: Martz, Eric. (Entry 16).
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.
- Submitted by: the author. (Entry 1).
- SYBYL is a comprehensive computational tool kit
for molecular design and analysis, with a special
focus on the creation of new chemical entities.
SYBYL provides essential construction and analysis
tools for both organic and inorganic molecular
structures, and much, much more.
See comments by Gert Vriend.
- Submitted by: Martz, Eric. (Entry 11).
- WHAT IF is a versatile protein structure analysis program that can be used for mutant prediction, structure verification, molecular graphics, etc. A free WHAT IF course is offered periodically. An Overview of the capabilities of WHAT IF is available, as well as a full manual, FAQ, etc.
- Submitted by: Martz, Eric. (Entry 6).
- 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.
ZMM includes a Graphical User Interface (MVM) that is as easy to use as
RASMOL or PYMOL.
FREE DOWNLOAD!
- Submitted by: Yang, Daniel. (Entry 26).
- SPROUT is an effective tool for the design of drug-like, biologically active molecules. It is an interactive system that can assist in several stages of the structure-based rational drug design process. The system is modularized and offers automatic methods for solving a number of problems in drug design (e.g. detection of the active sites, docking, designing novel molecules, scoring, clustering etc.). Powerfully, the user maintains control and is able to guide and modify each module for maximum versatility. The system has been validated with a large number of real-life examples.
- Co-authors: University of Leeds, UK. Submitted by: the author. (Entry 14).
24 total first authors.