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Molecule viewer tools

Software tools and databases to view molecules.

POLYVIEW-MM
Web

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.

CheS-Mapper
Web
Desktop

CheS-Mapper Chemical Space Mapper

Allows 3D visualization of chemical datasets with small compounds. CheS-Mapper…

Allows 3D visualization of chemical datasets with small compounds. CheS-Mapper can be used to analyze the relationship between the structure of chemical compounds, their physico-chemical properties,…

KiNG
Desktop

KiNG Kinemage Next Generation

Allows visualization of scientific data. KiNG is a modular, extensible…

Allows visualization of scientific data. KiNG is a modular, extensible scientific visualization tool used primarily for macromolecular visualization, which has evolved into more than just a…

PUMA
Web

PUMA Platform for Unified Molecular Analysis

Allows comprehensive diversity analysis of compound databases. PUMA computes…

Allows comprehensive diversity analysis of compound databases. PUMA computes six molecular properties of pharmaceutical relevance: molecular weight (MW), hydrogen bond donors (nHBDon), hydrogen bond…

NGL Viewer
Web

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…

Molmil
Web

Molmil

Permits to view molecules. Molmil has been integrated into several services…

Permits to view molecules. Molmil has been integrated into several services offered by Protein Data Bank (PDB) Japan and can be easily extended with new functionality by third party developers. It…

VEGA ZZ
Desktop

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.

Bodil
Desktop

Bodil

Helps to identify key features of proteins critical to molecular recognition in…

Helps to identify key features of proteins critical to molecular recognition in drug discovery applications and to understand the structural basis for function. Bodil incorporates state-of-the-art…

RasMol
Desktop

RasMol

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

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

Cn3D
Web

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.

ChemBioServer
Web

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…

3Dmol.js
Desktop

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…

BALLView
Desktop

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…

ChemGPS-NP
Web

ChemGPS-NP

Allows users to make compound selection. ChemGPS-NP assists user in exploration…

Allows users to make compound selection. ChemGPS-NP assists user in exploration of regions of chemical space most likely to enclose compounds with biologically relevant functions and activities. It…

UTOPIA Tools
Desktop

UTOPIA Tools User-friendly Tools for OPerating Informatics Applications

Allows protein analysis applications. UTOPIA aims to reduce the amount of…

Allows protein analysis applications. UTOPIA aims to reduce the amount of unnecessary technical detail presented to the working biologist. It provides a suite of widgets, ranging from low-level…

YASARA
Desktop
Mobile

YASARA

Allows molecular-graphics, modeling and simulation. YASARA is a molecular…

Allows molecular-graphics, modeling and simulation. YASARA is a molecular modeling program divided into different stages: a free software and three other stages. Each stage contains the features of…

BioBlender
Desktop

BioBlender

Allows the display of molecular surfaces of moving (or still) proteins, putting…

Allows the display of molecular surfaces of moving (or still) proteins, putting special emphasis on their electrical and lipophilic properties. BioBlender is an extension of Blender. The software…

CoLibri
Desktop

CoLibri

Let’s users transform their collective know how into a chemistry space.…

Let’s users transform their collective know how into a chemistry space. CoLibri offers a large chemistry space formed of huge number of virtual but synthetically accessible compounds.

StructureMate
Mobile

StructureMate

Aims to bring chemical dataset analysis and visualization to a much wider range…

Aims to bring chemical dataset analysis and visualization to a much wider range of devices. StructureMate is a portable chemical dataset viewer. This software can be used for browsing SAR reports,…

TexMol
Desktop

TexMol Texture Molecular Viewer

Performs a wide range of structural and volumetric rendering concurrently,…

Performs a wide range of structural and volumetric rendering concurrently, combined with its aggressive use of programmable graphics hardware, distinguish it from existing molecular visualizers.…

chemfig
Desktop

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…

LeView
Desktop

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…

Viewmol
Desktop

Viewmol

A graphical front end for computational chemistry programs.

A graphical front end for computational chemistry programs.

POLYVIEW-2D
Web

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.

BRAGI
Desktop

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.

ModView
Desktop

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.

ePMV
Desktop

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…

CmME
Desktop

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.

Swiss-PdbViewer
Desktop

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.

POLYVIEW-3D
Web

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.

ghemical
Desktop

ghemical

Computes energy and gradient using quantum mechanical methods and molecular…

Computes energy and gradient using quantum mechanical methods and molecular mechanics methods. ghemical is a computational chemistry package that provides options for studying a molecular system…

Garlic
Desktop

Garlic

Identifies transmembrane segments. Garlic is an open source molecular…

Identifies transmembrane segments. Garlic is an open source molecular visualization program designed for visualization and analysis of membrane proteins. It visualizes any type of molecules and…

GAMGI
Desktop

GAMGI General Atomistic Modelling Graphic Interface

Constructs, views and analyses atomic structures. GAMGI is an atomistic…

Constructs, views and analyses atomic structures. GAMGI is an atomistic application that (i) determines any point group of symmetry, (ii) builds crystals for any space group of symmetry, and (iii)…

DensityServer
Desktop

DensityServer

Allows accession of subsets of volumetric density data. DensityServer is able…

Allows accession of subsets of volumetric density data. DensityServer is able to downsample the data depending on the volume of the requested region. It provides near-instant access to even the…

CoordinateServe…
Web

CoordinateServer

Delivers a subset of mmCIF coordinate data. CoordinateServer returns the…

Delivers a subset of mmCIF coordinate data. CoordinateServer returns the specific portions of the structure that are relevant, as specified in your query. It reduces the time needed to transmit and…

LiteMol
Web
Desktop

LiteMol

Handles three-dimensional macromolecular data. LiteMol allows users to…

Handles three-dimensional macromolecular data. LiteMol allows users to visualize molecules and other related data. It can be implemented in web pages to offer rich interaction with data. This tool…

iCn3D Structure Viewer
Web

iCn3D Structure Viewer “I see in 3D” Structure Viewer

Shows the aligned 3D structures by providing two protein data bank (PDB) IDs or…

Shows the aligned 3D structures by providing two protein data bank (PDB) IDs or molecular modeling database (MMDB) IDs, whose alignment has been pre-calculated at NCBI. The iCn3D Structure Viewer is…

NDKmol
Mobile

NDKmol

Permits to view three dimensional (3D) structures of proteins, nucleic acids…

Permits to view three dimensional (3D) structures of proteins, nucleic acids and small molecules. NDKmol is a molecular viewer for Android. It supports most of common representations for molecules,…

ESmol
Mobile

ESmol

Permits to view three dimensional structures of proteins and small molecules on…

Permits to view three dimensional structures of proteins and small molecules on Android phone/tablet. ESmol is an open-source molecular viewers for Android. It supports most of common representations…

GLmol
Desktop

GLmol

Developed to embed molecular models in Web pages without using Java or plugins.…

Developed to embed molecular models in Web pages without using Java or plugins. GLmol is a 3D molecular viewer based on WebGL and Javascript. This application displays biological assembly, displays…

CMol
Mobile

CMol

Allows to open and view Protein Data Bank (PDB) files with complete control…

Allows to open and view Protein Data Bank (PDB) files with complete control over the representations and colours used for individual chains, residues and atoms. CMOL provides cartoon and ribbon view,…

Molecule…
Mobile

Molecule Viewer 3D

Permits to Open the most common 3D molecule file formats saved on a SD card.…

Permits to Open the most common 3D molecule file formats saved on a SD card. Molecule viewer 3D offers a molecule library that include 243 molecules. It offers a browser to find a molecule or a way…

mmView
Web
Desktop

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…

Molsketch
Desktop

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…

ProteinVis
Desktop

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…

QuteMol
Desktop

QuteMol

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

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

Zeus
Desktop

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.

Molecule World
Desktop
Mobile

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…

Molecules
Desktop

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.

MolScript
Desktop

MolScript

Allows visualization of molecular 3D structures. MolScript is a program that…

Allows visualization of molecular 3D structures. MolScript is a program that generates plots of protein structures and allows several kinds of representations, including the basic wire-drawing,…

PMV
Desktop

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.

ZMM
Desktop

ZMM

Allows molecular modeling to theoretically study systems. ZMM is a program that…

Allows molecular modeling to theoretically study systems. ZMM is a program that permits users to model various systems, such as peptides, proteins, nucleic acid, or ligand-receptor complexes. The…

CrystalMaker
Desktop

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.

iMol
Desktop

iMol

Allows molecular visualization. iMol is an application, working on MAC OS X,…

Allows molecular visualization. iMol is an application, working on MAC OS X, that supports several formats including PDB, XYZ, MOL2, HIN, CAR, ALC and BIO. The software allows chemists and molecular…

Molekel
Desktop

Molekel

Allows molecular visualization. Molekel provides several features such as…

Allows molecular visualization. Molekel provides several features such as reading molecular data from different file formats, displaying molecules with different styles, animating atoms, molecule…

Raster3D
Desktop

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.

RasTop
Desktop

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…

SCHAKAL
Desktop

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.

CheVi
Desktop

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.

ChemSymphony
Desktop

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.

ICM-Browser
Desktop

ICM-Browser

Allows 3D molecular visualization. ICM-Browser can assist researchers and…

Allows 3D molecular visualization. ICM-Browser can assist researchers and biologists in communicating their data, studying biological structures, such as Protein Data Bank (PDB) structures,…

OpenAstexViewer
Desktop

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.

Flex
Desktop

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.

PocketMol
Desktop

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.

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