List of molecular graphics systems - AbsoluteAstronomy.com

This is a list of software systems that are used for visualizing macromolecules .

The tables below indicates which types of data can be visualized in each system:
EM = Electron microscopy;
HM = Homology modelling;
MD = Molecular Dynamics

Molecular dynamics

Molecular dynamics is a computer simulation of physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a period of time, giving a view of the motion of the atoms...

;
MM = Molecular modelling

Molecular modelling

Molecular modelling encompasses all theoretical methods and computational techniques used to model or mimic the behaviour of molecules. The techniques are used in the fields of computational chemistry, computational biology and materials science for studying molecular systems ranging from small...

and molecular orbital

Molecular orbital

In chemistry, a molecular orbital is a mathematical function describing the wave-like behavior of an electron in a molecule. This function can be used to calculate chemical and physical properties such as the probability of finding an electron in any specific region. The term "orbital" was first...

visualization;
MRI = Magnetic resonance imaging

Magnetic resonance imaging

Magnetic resonance imaging , nuclear magnetic resonance imaging , or magnetic resonance tomography is a medical imaging technique used in radiology to visualize detailed internal structures...

;
NA = Nucleic Acids;
NMR = nuclear magnetic resonance

Protein nuclear magnetic resonance spectroscopy

Nuclear magnetic resonance spectroscopy of proteins is a field of structural biology in which NMR spectroscopy is used to obtain information about the structure and dynamics of proteins. The field was pioneered by Richard R. Ernst and Kurt Wüthrich, among others...

;
Optical = Optical microscopy;
SMI = Small molecule interactions;
XRC = X-ray crystallography

X-ray crystallography

X-ray crystallography is a method of determining the arrangement of atoms within a crystal, in which a beam of X-rays strikes a crystal and causes the beam of light to spread into many specific directions. From the angles and intensities of these diffracted beams, a crystallographer can produce a...

data such as electron density

Electron density

Electron density is the measure of the probability of an electron being present at a specific location.In molecules, regions of electron density are usually found around the atom, and its bonds...

Stand-alone systems

Name	Data	License	Technology	Citation	Comments
Ascalaph Graphics	MM Molecular modelling Molecular modelling encompasses all theoretical methods and computational techniques used to model or mimic the behaviour of molecules. The techniques are used in the fields of computational chemistry, computational biology and materials science for studying molecular systems ranging from small... MD Molecular dynamics Molecular dynamics is a computer simulation of physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a period of time, giving a view of the motion of the atoms...	free	C++ C++ C++ is a statically typed, free-form, multi-paradigm, compiled, general-purpose programming language. It is regarded as an intermediate-level language, as it comprises a combination of both high-level and low-level language features. It was developed by Bjarne Stroustrup starting in 1979 at Bell...
Avizo Avizo (software) Avizo is a general-purpose commercial software application for scientific and industrial data visualization and analysis....	EM MM Molecular modelling Molecular modelling encompasses all theoretical methods and computational techniques used to model or mimic the behaviour of molecules. The techniques are used in the fields of computational chemistry, computational biology and materials science for studying molecular systems ranging from small... MRI Magnetic resonance imaging Magnetic resonance imaging , nuclear magnetic resonance imaging , or magnetic resonance tomography is a medical imaging technique used in radiology to visualize detailed internal structures... Optical XRC X-ray crystallography X-ray crystallography is a method of determining the arrangement of atoms within a crystal, in which a beam of X-rays strikes a crystal and causes the beam of light to spread into many specific directions. From the angles and intensities of these diffracted beams, a crystallographer can produce a...	commercial	Windows, Linux, Mac
Avogadro	MM Molecular modelling Molecular modelling encompasses all theoretical methods and computational techniques used to model or mimic the behaviour of molecules. The techniques are used in the fields of computational chemistry, computational biology and materials science for studying molecular systems ranging from small... XRC X-ray crystallography X-ray crystallography is a method of determining the arrangement of atoms within a crystal, in which a beam of X-rays strikes a crystal and causes the beam of light to spread into many specific directions. From the angles and intensities of these diffracted beams, a crystallographer can produce a... MD Molecular dynamics Molecular dynamics is a computer simulation of physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a period of time, giving a view of the motion of the atoms...	free and open-source	C++ C++ C++ is a statically typed, free-form, multi-paradigm, compiled, general-purpose programming language. It is regarded as an intermediate-level language, as it comprises a combination of both high-level and low-level language features. It was developed by Bjarne Stroustrup starting in 1979 at Bell... /Qt, can be extended with Python Python (programming language) Python is a general-purpose, high-level programming language whose design philosophy emphasizes code readability. Python claims to "[combine] remarkable power with very clear syntax", and its standard library is large and comprehensive... modules
BALLView	MM Molecular modelling Molecular modelling encompasses all theoretical methods and computational techniques used to model or mimic the behaviour of molecules. The techniques are used in the fields of computational chemistry, computational biology and materials science for studying molecular systems ranging from small... Nucleic Acids XRC X-ray crystallography X-ray crystallography is a method of determining the arrangement of atoms within a crystal, in which a beam of X-rays strikes a crystal and causes the beam of light to spread into many specific directions. From the angles and intensities of these diffracted beams, a crystallographer can produce a... SMI	free and open-source, GPL	C++ C++ C++ is a statically typed, free-form, multi-paradigm, compiled, general-purpose programming language. It is regarded as an intermediate-level language, as it comprises a combination of both high-level and low-level language features. It was developed by Bjarne Stroustrup starting in 1979 at Bell... and Python Python (programming language) Python is a general-purpose, high-level programming language whose design philosophy emphasizes code readability. Python claims to "[combine] remarkable power with very clear syntax", and its standard library is large and comprehensive... ; Windows Microsoft Windows Microsoft Windows is a series of operating systems produced by Microsoft.Microsoft introduced an operating environment named Windows on November 20, 1985 as an add-on to MS-DOS in response to the growing interest in graphical user interfaces . Microsoft Windows came to dominate the world's personal... , Linux Linux Linux is a Unix-like computer operating system assembled under the model of free and open source software development and distribution. The defining component of any Linux system is the Linux kernel, an operating system kernel first released October 5, 1991 by Linus Torvalds... , Solaris, and MacOS X Mac OS X Mac OS X is a series of Unix-based operating systems and graphical user interfaces developed, marketed, and sold by Apple Inc. Since 2002, has been included with all new Macintosh computer systems...	BALL project	BALLView uses OpenGL and the real time ray tracer RTFact as render backends. For both renderers, BALLView offers stereoscopic visualization in several different modes.
Cn3D Cn3D Cn3D is a Windows, Macintosh and Unix-based software from the United States National Library of Medicine that acts as a helper application for web browsers to view three-dimensional structures from The National Center for Biotechnology Information's Entrez retrieval service...		free	stand-alone Stand-alone Standalone software can mean:* Computer software that can work offline, i.e. does not necessarily require network connection to function* Software that is not a part of some software bundle... application
CheVi	SMI	free	stand-alone Stand-alone Standalone software can mean:* Computer software that can work offline, i.e. does not necessarily require network connection to function* Software that is not a part of some software bundle... application
chemkit	MM Molecular modelling Molecular modelling encompasses all theoretical methods and computational techniques used to model or mimic the behaviour of molecules. The techniques are used in the fields of computational chemistry, computational biology and materials science for studying molecular systems ranging from small... MD Molecular dynamics Molecular dynamics is a computer simulation of physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a period of time, giving a view of the motion of the atoms...	free and open-source	C++ C++ C++ is a statically typed, free-form, multi-paradigm, compiled, general-purpose programming language. It is regarded as an intermediate-level language, as it comprises a combination of both high-level and low-level language features. It was developed by Bjarne Stroustrup starting in 1979 at Bell...		Software library for cheminformatics, molecular modelling and visualization.
Coot		free
Crystal Studio	MM Molecular modelling Molecular modelling encompasses all theoretical methods and computational techniques used to model or mimic the behaviour of molecules. The techniques are used in the fields of computational chemistry, computational biology and materials science for studying molecular systems ranging from small... XRC X-ray crystallography X-ray crystallography is a method of determining the arrangement of atoms within a crystal, in which a beam of X-rays strikes a crystal and causes the beam of light to spread into many specific directions. From the angles and intensities of these diffracted beams, a crystallographer can produce a...	commercial	Windows		Various Models: Ball & Stick, Stick, Space Filling, Ribbon etc. Plot XRD and Neutron Powder Patterns
CueMol	MM Molecular modelling Molecular modelling encompasses all theoretical methods and computational techniques used to model or mimic the behaviour of molecules. The techniques are used in the fields of computational chemistry, computational biology and materials science for studying molecular systems ranging from small... XRC X-ray crystallography X-ray crystallography is a method of determining the arrangement of atoms within a crystal, in which a beam of X-rays strikes a crystal and causes the beam of light to spread into many specific directions. From the angles and intensities of these diffracted beams, a crystallographer can produce a...	free and open-source	Windows, MacOS X, and Linux application based on OpenGL OpenGL OpenGL is a standard specification defining a cross-language, cross-platform API for writing applications that produce 2D and 3D computer graphics. The interface consists of over 250 different function calls which can be used to draw complex three-dimensional scenes from simple primitives. OpenGL... and Mozilla XULRunner XULRunner XULRunner is a runtime environment developed by the Mozilla Foundation to provide a common back-end for XUL-based applications. It replaced the Gecko Runtime Environment, a stalled project with a similar purpose.... .
Friend	MM Molecular modelling Molecular modelling encompasses all theoretical methods and computational techniques used to model or mimic the behaviour of molecules. The techniques are used in the fields of computational chemistry, computational biology and materials science for studying molecular systems ranging from small... SA Structural alignment Structural alignment attempts to establish homology between two or more polymer structures based on their shape and three-dimensional conformation. This process is usually applied to protein tertiary structures but can also be used for large RNA molecules... MSA Multiple sequence alignment A multiple sequence alignment is a sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In many cases, the input set of query sequences are assumed to have an evolutionary relationship by which they share a lineage and are descended from a common ancestor...	free	Win, Linux		Fast, can work with hundreds of structures and thousands of sequences; millions of atoms. Crosstalk between sequence and structure modules. Sequence module based on Jalview. Accurate Structural alignment by TOPOFIT method. Also available as applet to interface sequence/structure databases.
Gabedit Gabedit Gabedit is a Graphical User Interface to GAMESS , GAUSSIAN, MOLCAS, MOLPRO, MPQC, OpenMopac, PC GAMESS, and Q-Chem computational chemistry packages.- Major features :* builds molecules by atom, ring, group, amino acid and nucleoside....	XRC X-ray crystallography X-ray crystallography is a method of determining the arrangement of atoms within a crystal, in which a beam of X-rays strikes a crystal and causes the beam of light to spread into many specific directions. From the angles and intensities of these diffracted beams, a crystallographer can produce a... MM Molecular modelling Molecular modelling encompasses all theoretical methods and computational techniques used to model or mimic the behaviour of molecules. The techniques are used in the fields of computational chemistry, computational biology and materials science for studying molecular systems ranging from small...	free and open-source	C
g0penMol	MD Molecular dynamics Molecular dynamics is a computer simulation of physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a period of time, giving a view of the motion of the atoms... MM Molecular modelling Molecular modelling encompasses all theoretical methods and computational techniques used to model or mimic the behaviour of molecules. The techniques are used in the fields of computational chemistry, computational biology and materials science for studying molecular systems ranging from small...	free
ICM-Browser ICM-Browser ICM-Browser is a free product of Molsoft, and provides access to structural biology data and protein families. It reads PDB or alignment files directly from online databases and provides a molecular graphics environment with various representations of proteins, DNA and RNA, and multiple sequence...		free	Windows,Mac,Linux, fast C++ graphics, free plugin and activeICM for Web delivery		multiple objects, symmerty, 3D wavefront, alignments, chemistry, tables, plots
Jmol Jmol Jmol is an open-source Java viewer for chemical structures in 3D,that does not require 3D acceleration plugins.Jmol returns a 3D representation of a molecule that may be used as a teaching tool, or for research e.g...		free and open-source	Java applet Applet In computing, an applet is any small application that performs one specific task that runs within the scope of a larger program, often as a plug-in. An applet typically also refers to Java applets, i.e., programs written in the Java programming language that are included in a web page... or stand-alone Stand-alone Standalone software can mean:* Computer software that can work offline, i.e. does not necessarily require network connection to function* Software that is not a part of some software bundle... application		Supports advanced capabilities such as loading multiple molecules with independent movement, surfaces and molecular orbitals, cavity visualization, crystal symmetry
MDL Chime MDL Chime MDL Chime is a free plugin used by web browsers to display the three dimensional structures of molecules. It is part of the ISIS product line acquired by Symyx Technologies from scientific publisher Elsevier in October 2007. It is based on the RasMol code.Chime is used by a wide range of...		free for noncommercial use, proprietary	C++ C++ C++ is a statically typed, free-form, multi-paradigm, compiled, general-purpose programming language. It is regarded as an intermediate-level language, as it comprises a combination of both high-level and low-level language features. It was developed by Bjarne Stroustrup starting in 1979 at Bell... browser plugin for Windows Microsoft Windows Microsoft Windows is a series of operating systems produced by Microsoft.Microsoft introduced an operating environment named Windows on November 20, 1985 as an add-on to MS-DOS in response to the growing interest in graphical user interfaces . Microsoft Windows came to dominate the world's personal... only		Calculates molecular surfaces coloured by electrostatic or hydrophobic potential. Originally based on RasMol RasMol RasMol is a computer program written for molecular graphics visualization intended and used primarily for the depiction and exploration of biological macromolecule structures, such as those found in the Protein Data Bank... .
Molden Molden Molden is a general molecular and electronic structure processing program.- Major features :* Reads output from the ab initio packages GAMESS , Gaussian, MOLPRO and from semi-empirical packages such as MOPAC, and supports a number of other formats....	MM Molecular modelling Molecular modelling encompasses all theoretical methods and computational techniques used to model or mimic the behaviour of molecules. The techniques are used in the fields of computational chemistry, computational biology and materials science for studying molecular systems ranging from small... XRC X-ray crystallography X-ray crystallography is a method of determining the arrangement of atoms within a crystal, in which a beam of X-rays strikes a crystal and causes the beam of light to spread into many specific directions. From the angles and intensities of these diffracted beams, a crystallographer can produce a...
MOE Chemical Computing Group Chemical Computing Group is a software company specializing in research software for computational chemistry, bioinformatics, cheminformatics, docking, pharmacophore searching and molecular simulation. The company's main customer base consists of pharmaceutical and biotechnology companies, as well...	MM Molecular modelling Molecular modelling encompasses all theoretical methods and computational techniques used to model or mimic the behaviour of molecules. The techniques are used in the fields of computational chemistry, computational biology and materials science for studying molecular systems ranging from small... XRC X-ray crystallography X-ray crystallography is a method of determining the arrangement of atoms within a crystal, in which a beam of X-rays strikes a crystal and causes the beam of light to spread into many specific directions. From the angles and intensities of these diffracted beams, a crystallographer can produce a...	commercial		Molecular Operating Environment (MOE) Chemical Computing Group Chemical Computing Group is a software company specializing in research software for computational chemistry, bioinformatics, cheminformatics, docking, pharmacophore searching and molecular simulation. The company's main customer base consists of pharmaceutical and biotechnology companies, as well...
Molekel Molekel Molekel is a free software multiplatform molecular visualization program. It was originally developed at the University of Geneva by Peter F. Flükiger in the 1990s for Silicon Graphics Computers. In 1998, Stefan Portmann took over responsibility and released Version 3.0. Version 4.0 was a nearly...	MM Molecular modelling Molecular modelling encompasses all theoretical methods and computational techniques used to model or mimic the behaviour of molecules. The techniques are used in the fields of computational chemistry, computational biology and materials science for studying molecular systems ranging from small... XRC X-ray crystallography X-ray crystallography is a method of determining the arrangement of atoms within a crystal, in which a beam of X-rays strikes a crystal and causes the beam of light to spread into many specific directions. From the angles and intensities of these diffracted beams, a crystallographer can produce a...	free and open-source	Java3D applet Applet In computing, an applet is any small application that performs one specific task that runs within the scope of a larger program, often as a plug-in. An applet typically also refers to Java applets, i.e., programs written in the Java programming language that are included in a web page... or stand-alone Stand-alone Standalone software can mean:* Computer software that can work offline, i.e. does not necessarily require network connection to function* Software that is not a part of some software bundle... application
NOCH NOCH NOCH - is a free and open source molecular explorer for protein structure visualization. It allows for import of molecular structures described in the Protein Data Bank file format....		free and open-source
O O O is the fifteenth letter and a vowel in the basic modern Latin alphabet.The letter was derived from the Semitic `Ayin , which represented a consonant, probably , the sound represented by the Arabic letter ع called `Ayn. This Semitic letter in its original form seems to have been inspired by a...		free for noncommercial use			see also
Procreate		free	C# stand-alone Stand-alone Standalone software can mean:* Computer software that can work offline, i.e. does not necessarily require network connection to function* Software that is not a part of some software bundle... application		Currently views SEQ and PDB files. Programmed in pure managed .NET using advanced DirectX rendering and effects
PyMOL PyMOL PyMOL is an open-source, user-sponsored, molecular visualization system created by Warren Lyford DeLano and commercialized by DeLano Scientific LLC, which is a private software company dedicated to creating useful tools that become universally accessible to scientific and educational communities...	XRC X-ray crystallography X-ray crystallography is a method of determining the arrangement of atoms within a crystal, in which a beam of X-rays strikes a crystal and causes the beam of light to spread into many specific directions. From the angles and intensities of these diffracted beams, a crystallographer can produce a... SMI EM	free for noncommercial use, open-source	Python Python (programming language) Python is a general-purpose, high-level programming language whose design philosophy emphasizes code readability. Python claims to "[combine] remarkable power with very clear syntax", and its standard library is large and comprehensive...		According to the author, almost a quarter of all published images of 3D protein structures in the scientific literature were made using PyMOL.
Qmol	MM Molecular modelling Molecular modelling encompasses all theoretical methods and computational techniques used to model or mimic the behaviour of molecules. The techniques are used in the fields of computational chemistry, computational biology and materials science for studying molecular systems ranging from small...	free, open-source	C		Provided by DNASTAR DNASTAR DNASTAR is a bioinformatics company headquartered in Madison, WI that provides software for DNA sequence analysis and assembly, gene expression analysis, and genomic visualization.-History:DNASTAR was incorporated in 1984...
RasMol RasMol RasMol is a computer program written for molecular graphics visualization intended and used primarily for the depiction and exploration of biological macromolecule structures, such as those found in the Protein Data Bank...		free and open-source	C stand-alone Stand-alone Standalone software can mean:* Computer software that can work offline, i.e. does not necessarily require network connection to function* Software that is not a part of some software bundle... application
Sirius Sirius visualization software Sirius is a molecular modeling and analysis system developed at San Diego Supercomputer Center. Sirius is designed to support advanced user requirements that go beyond simple display of small molecules and proteins...		free and open-source	Java3D applet Applet In computing, an applet is any small application that performs one specific task that runs within the scope of a larger program, often as a plug-in. An applet typically also refers to Java applets, i.e., programs written in the Java programming language that are included in a web page... or stand-alone Stand-alone Standalone software can mean:* Computer software that can work offline, i.e. does not necessarily require network connection to function* Software that is not a part of some software bundle... application
SPARTAN Spartan (software) SPARTAN is a molecular modeling and computational chemistry application from . It contains code for molecular mechanics, semi-empirical methods, ab initio models, density functional models, post-Hartree-Fock models, and thermochemical recipes including T1....	MM Molecular modelling Molecular modelling encompasses all theoretical methods and computational techniques used to model or mimic the behaviour of molecules. The techniques are used in the fields of computational chemistry, computational biology and materials science for studying molecular systems ranging from small... QM Quantum chemistry computer programs Quantum chemistry computer programs are used in computational chemistry to implement the methods of quantum chemistry. Most include the Hartree–Fock and some post-Hartree–Fock methods. They may also include density functional theory , molecular mechanics or semi-empirical quantum...	commercial	stand-alone Stand-alone Standalone software can mean:* Computer software that can work offline, i.e. does not necessarily require network connection to function* Software that is not a part of some software bundle... application		visualize and edit biomolecules, extract bound ligands from PDB files for further computational analysis, full molecular mechanics and quantum chemical calculations package with streamlined graphical user interface.
SRS3D Viewer	HM Homology modeling Homology modeling, also known as comparative modeling of protein refers to constructing an atomic-resolution model of the "target" protein from its amino acid sequence and an experimental three-dimensional structure of a related homologous protein...	free and open-source	Java3D applet Applet In computing, an applet is any small application that performs one specific task that runs within the scope of a larger program, often as a plug-in. An applet typically also refers to Java applets, i.e., programs written in the Java programming language that are included in a web page... or stand-alone Stand-alone Standalone software can mean:* Computer software that can work offline, i.e. does not necessarily require network connection to function* Software that is not a part of some software bundle... application		Integrates 3D structures with sequence and feature data (domains, SNPs, etc.).
UCSF Chimera UCSF Chimera UCSF Chimera is an extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality and can be created...	XRC X-ray crystallography X-ray crystallography is a method of determining the arrangement of atoms within a crystal, in which a beam of X-rays strikes a crystal and causes the beam of light to spread into many specific directions. From the angles and intensities of these diffracted beams, a crystallographer can produce a... SMI EM MD Molecular dynamics Molecular dynamics is a computer simulation of physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a period of time, giving a view of the motion of the atoms...	free for noncommercial use	Python Python (programming language) Python is a general-purpose, high-level programming language whose design philosophy emphasizes code readability. Python claims to "[combine] remarkable power with very clear syntax", and its standard library is large and comprehensive...		Includes single/multiple sequence viewer, structure-based sequence alignment, automatic sequence-structure crosstalk for integrated analyses.
VMD Visual Molecular Dynamics - External links :* * *...	EM MD Molecular dynamics Molecular dynamics is a computer simulation of physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a period of time, giving a view of the motion of the atoms... MM Molecular modelling Molecular modelling encompasses all theoretical methods and computational techniques used to model or mimic the behaviour of molecules. The techniques are used in the fields of computational chemistry, computational biology and materials science for studying molecular systems ranging from small...	free for noncommercial use	C++ C++ C++ is a statically typed, free-form, multi-paradigm, compiled, general-purpose programming language. It is regarded as an intermediate-level language, as it comprises a combination of both high-level and low-level language features. It was developed by Bjarne Stroustrup starting in 1979 at Bell...
WebMol		free	Java applet and stand-alone		Includes advanced structural analysis features such as packing of secondary structural elements and surface calculations.
WHAT IF WHAT IF software WHAT IF is a computer program used in a wide variety of in silico macromolecular structure research fields such as:* Homology models of protein tertiary structures as well as quaternary structures,...	HM Homology modeling Homology modeling, also known as comparative modeling of protein refers to constructing an atomic-resolution model of the "target" protein from its amino acid sequence and an experimental three-dimensional structure of a related homologous protein... XRC X-ray crystallography X-ray crystallography is a method of determining the arrangement of atoms within a crystal, in which a beam of X-rays strikes a crystal and causes the beam of light to spread into many specific directions. From the angles and intensities of these diffracted beams, a crystallographer can produce a...	shareware for academics	stand-alone		Old-fashioned interface; very good software for the experienced bioinformatician; nearly 2000 protein-structure related options; comes with 500 page writeup.
Yasara Yasara YASARA, Yet Another Scientific Artificial Reality Application, is a molecular visualisation, modelling, and dynamics program that can be used for a series of scientific applications as is expressed by the large number of mentioning this software. The free version of YASARA is well suited for...	HM Homology modeling Homology modeling, also known as comparative modeling of protein refers to constructing an atomic-resolution model of the "target" protein from its amino acid sequence and an experimental three-dimensional structure of a related homologous protein... NMR Protein nuclear magnetic resonance spectroscopy Nuclear magnetic resonance spectroscopy of proteins is a field of structural biology in which NMR spectroscopy is used to obtain information about the structure and dynamics of proteins. The field was pioneered by Richard R. Ernst and Kurt Wüthrich, among others... XRC X-ray crystallography X-ray crystallography is a method of determining the arrangement of atoms within a crystal, in which a beam of X-rays strikes a crystal and causes the beam of light to spread into many specific directions. From the angles and intensities of these diffracted beams, a crystallographer can produce a...	commercial; free version for education and elementary structure work	stand-alone		Very advanced graphics; Best in homology model optimisation in CASP-2008; many drug design options;

Web-based systems

Name	Data	License	Technology	Comments
Relibase	SMI	partly free (full functionality requires a license)	Java Java (programming language) Java is a programming language originally developed by James Gosling at Sun Microsystems and released in 1995 as a core component of Sun Microsystems' Java platform. The language derives much of its syntax from C and C++ but has a simpler object model and fewer low-level facilities... applet Applet In computing, an applet is any small application that performs one specific task that runs within the scope of a larger program, often as a plug-in. An applet typically also refers to Java applets, i.e., programs written in the Java programming language that are included in a web page... integrated into web front-end
WebMol		free	Java applet and stand-alone	Includes advanced structural analysis features such as packing of secondary structural elements and surface calculations.
SRS3D Viewer	HM Homology modeling Homology modeling, also known as comparative modeling of protein refers to constructing an atomic-resolution model of the "target" protein from its amino acid sequence and an experimental three-dimensional structure of a related homologous protein... SMI	free and open-source	Java3D applet Applet In computing, an applet is any small application that performs one specific task that runs within the scope of a larger program, often as a plug-in. An applet typically also refers to Java applets, i.e., programs written in the Java programming language that are included in a web page... or stand-alone Stand-alone Standalone software can mean:* Computer software that can work offline, i.e. does not necessarily require network connection to function* Software that is not a part of some software bundle... application	Integrates 3D structures with sequence and feature data (domains, SNPs, etc.).
Proteopedia	HM Homology modeling Homology modeling, also known as comparative modeling of protein refers to constructing an atomic-resolution model of the "target" protein from its amino acid sequence and an experimental three-dimensional structure of a related homologous protein... SMI	free	Java Java (programming language) Java is a programming language originally developed by James Gosling at Sun Microsystems and released in 1995 as a core component of Sun Microsystems' Java platform. The language derives much of its syntax from C and C++ but has a simpler object model and fewer low-level facilities... applet Applet In computing, an applet is any small application that performs one specific task that runs within the scope of a larger program, often as a plug-in. An applet typically also refers to Java applets, i.e., programs written in the Java programming language that are included in a web page... integrated into web front-end	Integrates 3D structures and different views on those with text descriptions of the structures

External links

A rather detailed, objective, and technical assessment of about 20 tools.

The source of this article is wikipedia, the free encyclopedia. The text of this article is licensed under the GFDL.

Stand-alone systems

Web-based systems

See also

External links