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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,…

VEGA ZZ
Desktop

VEGA ZZ

Assists in collecting, classifying, and analyzing metabolic reactions. VEGA ZZ…

Assists in collecting, classifying, and analyzing metabolic reactions. VEGA ZZ is a program representing a versatile engine to develop in-house targeted applications for metabolism analysis and…

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…

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.

NGLview
Desktop

NGLview

Gathers interactive molecular graphics within Jupyter or IPython notebooks.…

Gathers interactive molecular graphics within Jupyter or IPython notebooks. NGLview offers interactive features for the visualization of molecular structures as well as trajectories from molecular…

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…

Molpher
Desktop

Molpher

Provides a platform dedicated to molecules exploration. Molpher is an open…

Provides a platform dedicated to molecules exploration. Molpher is an open source molecular morphing client-server application that allows users to determine molecules common neighborhood based on…

CoLibri
Desktop

CoLibri

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

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.

ViFrame
Desktop

ViFrame

Offers a platform for 2D molecules visualization. ViFrame also provides an…

Offers a platform for 2D molecules visualization. ViFrame also provides an application for developing and testing new visualization algorithms and focuses on supplying methods to facilitate the…

PV
Desktop

PV Protein Viewer

Provides a default protein-viewer available in SWISS-MODEL. PV is a JavaScript…

Provides a default protein-viewer available in SWISS-MODEL. PV is a JavaScript viewer that permits to visualize protein structures directly in any browser. It uses WebGL for rendering. It has been…

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.

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