Software tools and databases to view molecules.
Web app
POLYVIEW-MM POLYVIEW-MM

POLYVIEW-MM

Integrates high-quality animation of molecular motion (MM) with structural and…

Integrates high-quality animation of molecular motion (MM) with structural and functional analysis of macromolecules.

Web app
Desktop app
mmView mmView

mmView

A web-based application which allows to comfortably explore the structural data…

A web-based application which allows to comfortably explore the structural data of biomacromolecules stored in the mmCIF format. The mmView software system is primarily intended for educational…

Web app
ChemBioServer ChemBioServer

ChemBioServer

A publicly available web application for effectively mining and filtering…

A publicly available web application for effectively mining and filtering chemical compounds used in drug discovery. ChemBioServer provides researchers with the ability to (i) browse and visualize…

Desktop app
chemfig chemfig

chemfig

A TeX package for drawing molecules. chemfig allows user to draw molecules…

A TeX package for drawing molecules. chemfig allows user to draw molecules using the tikz package. While the diagrams produced are essentially 2-dimensional, the package supports many of the…

Desktop app
Ligand Environment… Ligand Environment Viewer

LeView Ligand Environment Viewer

Generates 2D diagrams of biomacromolecule/ligand interactions. LeView produces…

Generates 2D diagrams of biomacromolecule/ligand interactions. LeView produces customised and high-quality figures, with a good compromise between a faithful representation of the 3D data (structures…

Desktop app
Molecule World Molecule World

Molecule World

An application to explore thousands of biological and chemical structures…

An application to explore thousands of biological and chemical structures easily on an iPad. Molecule World permits to view and manipulate chemical structures, sequences and structures of proteins…

Desktop app
BALLView BALLView

BALLView

A molecular viewer and modelling framework. BALLView combines state-of-the-art…

A molecular viewer and modelling framework. BALLView combines state-of-the-art visualization capabilities with powerful modelling functionality including implementations of force field methods and…

Desktop app
Molsketch Molsketch

Molsketch

A 2D molecular editing tool. Molsketch helps users to draw molecules quickly…

A 2D molecular editing tool. Molsketch helps users to draw molecules quickly and easily. It opens, saves and imports files in all formats supported by the OpenBabel(tm) library. Creations can be…

Desktop app
ProteinVis ProteinVis

ProteinVis

A visualization tool which supports fast rendering of proteins in different…

A visualization tool which supports fast rendering of proteins in different molecular representations. For the primary structure representations, the spherical element is applied to the space-fill…

Web app
NGL Viewer NGL Viewer

NGL Viewer

A web application for the visualization of macromolecular structures. By fully…

A web application for the visualization of macromolecular structures. By fully adopting capabilities of modern web browsers, such as WebGL, for molecular graphics, the viewer can interactively…

Desktop app
3Dmol.js 3Dmol.js

3Dmol.js

A modern, object-oriented JavaScript library that uses the latest web…

A modern, object-oriented JavaScript library that uses the latest web technologies to provide interactive, hardware-accelerated three dimensional representations of molecular data without the need to…

Web app
POLYVIEW-3D POLYVIEW-3D

POLYVIEW-3D

A tool for protein structure analysis, with the focus on annotation and…

A tool for protein structure analysis, with the focus on annotation and visualization of protein complexes.

Desktop app
QuteMol QuteMol

QuteMol

An open source (GPL), interactive, high quality molecular visualization system.

An open source (GPL), interactive, high quality molecular visualization system.

Desktop app
RasMol RasMol

RasMol

An interactive molecular graphics program, for the display of biomolecular…

An interactive molecular graphics program, for the display of biomolecular structures.

Desktop app
YASARA YASARA

YASARA

A molecular graphics, modeling and simulation program.

A molecular graphics, modeling and simulation program.

Desktop app
Zeus Zeus

Zeus

A molecular visualization tool that supports PDB, MOL, MOL2/SYBYL and XYZ file…

A molecular visualization tool that supports PDB, MOL, MOL2/SYBYL and XYZ file formats.

Desktop app
Molecules Molecules

Molecules

An application for the iPhone, iPod touch, and now iPad that allows you to view…

An application for the iPhone, iPod touch, and now iPad that allows you to view three-dimensional renderings of molecules and manipulate them using your fingers.

Desktop app
MolScript MolScript

MolScript

A program for displaying molecular 3D structures, such as proteins, in both…

A program for displaying molecular 3D structures, such as proteins, in both schematic and detailed representations.

Desktop app
PocketMol PocketMol

PocketMol

Allows you to view and manipulate Protein Data Bank (pdb) files on a PocketPC.

Allows you to view and manipulate Protein Data Bank (pdb) files on a PocketPC.

Web app
POLYVIEW-2D POLYVIEW-2D

POLYVIEW-2D

It can be used to generate amino acid sequence annotations, such as secondary…

It can be used to generate amino acid sequence annotations, such as secondary structure, relative solvent accessibility, evolutionary conservation, and physico-chemical property profiles.

Desktop app
Python Molecular… Python Molecular Viewer

PMV Python Molecular Viewer

A powerful molecular viewer that has a number of customizable features and…

A powerful molecular viewer that has a number of customizable features and comes with many pluggable commands ranging from displaying molecular surfaces to advanced volume rendering.

Desktop app
ZMM ZMM

ZMM

A molecular modeling program for theoretical studies of systems of any…

A molecular modeling program for theoretical studies of systems of any complexity: small molecules, peptides, proteins, nucleic acids, and ligand-receptor complexes.

Desktop app
BioBlender BioBlender

BioBlender

A software package built on the open-source 3D modeling software.

A software package built on the open-source 3D modeling software.

Desktop app
BRAGI BRAGI

BRAGI

A package for viewing and modeling of three-dimensional (3D) structures of…

A package for viewing and modeling of three-dimensional (3D) structures of biological macromolecules.

Desktop app
CELLmicrocosmos… CELLmicrocosmos MembraneEditor

CmME CELLmicrocosmos MembraneEditor

Generates heterogeneous PDB-based membranes with varying lipid compositions and…

Generates heterogeneous PDB-based membranes with varying lipid compositions and semi-automatic protein placement.

Desktop app
CrystalMaker CrystalMaker

CrystalMaker

A program for building, displaying, manipulating and animating all kinds of…

A program for building, displaying, manipulating and animating all kinds of crystal & molecular structures.

Desktop app
embedded Python… embedded Python Molecular Viewer

ePMV embedded Python Molecular Viewer

An open-source plug-in that runs molecular modeling software directly inside of…

An open-source plug-in that runs molecular modeling software directly inside of professional 3D animation applications (hosts) to provide simultaneous access to the capabilities of these newly…

Desktop app
iMol iMol

iMol

A free molecular visualization application for Mac OS X operating system.

A free molecular visualization application for Mac OS X operating system.

Desktop app
Molekel Molekel

Molekel

An open-source multi-platform molecular visualization program.

An open-source multi-platform molecular visualization program.

Desktop app
Raster3D Raster3D

Raster3D

A set of tools for generating high quality raster images of proteins or other…

A set of tools for generating high quality raster images of proteins or other molecules.

Desktop app
RasTop RasTop

RasTop

A molecular graphics program intended for the visualisation of proteins,…

A molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules based on the popular Rasmol software. RasTop is aimed at the rapid visualization and…

Desktop app
SCHAKAL SCHAKAL

SCHAKAL

A FORTRAN program for the graphical representation of molecular and solid-state…

A FORTRAN program for the graphical representation of molecular and solid-state structure models.

Desktop app
VEGA ZZ VEGA ZZ

VEGA ZZ

A complete molecular modelling suite that includes several features to make…

A complete molecular modelling suite that includes several features to make your research jobs very easy.

Desktop app
Viewmol Viewmol

Viewmol

A graphical front end for computational chemistry programs.

A graphical front end for computational chemistry programs.

Desktop app
ChemSymphony ChemSymphony

ChemSymphony

A platform-independent set of interactive Java applets that allows 3-D…

A platform-independent set of interactive Java applets that allows 3-D molecular structures to be easily incorporated into HTML documents.

Web app
Cn3D Cn3D

Cn3D

A helper application for your web browser that allows you to view 3-dimensional…

A helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez Structure database.

Desktop app
ICM-Browser ICM-Browser

ICM-Browser

Provides a biologist or a chemist with direct access to the treasures of…

Provides a biologist or a chemist with direct access to the treasures of structural biology and protein families.

Desktop app
ModView ModView

ModView

A program to visualize and analyze multiple biomolecule structures and/or…

A program to visualize and analyze multiple biomolecule structures and/or sequence alignments.

Desktop app
OpenAstexViewer OpenAstexViewer

OpenAstexViewer

A Java molecular graphics program that can be used for visualisation in many…

A Java molecular graphics program that can be used for visualisation in many aspects of structure-based drug design.

Desktop app
Flex Flex

Flex

A simple, portable molecular graphics program that interactively displays 3D…

A simple, portable molecular graphics program that interactively displays 3D ball-and-stick models on workstations running the Xwindows system.

Desktop app
Swiss-PdbViewer Swiss-PdbViewer

Swiss-PdbViewer

An application that provides a user friendly interface allowing to analyze…

An application that provides a user friendly interface allowing to analyze several proteins at the same time.

Desktop app
Chemical Visualizer Chemical Visualizer

CheVi Chemical Visualizer

A chemical visualization package specifically designed to help computational…

A chemical visualization package specifically designed to help computational chemists gain insight in to how ligands and receptors interact.

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