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Molecule visualization software tools | Drug discovery data analysis

Software tools and databases to view molecules.

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UCSF Chimera
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Permits to interactively visualize and analyse molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. UCSF Chimera allows users to incorporate new features. It contains some extensions which permits to visualize large-scale molecular assemblies such as viral coats, and allows researchers to share a Chimera session interactively despite being at separate locales. Other extensions can be used for extend the tool capabilities.
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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 dynamics simulations. It permits customization of the visualization and to add, change and remove representations. This tool can be utilized for displaying individual docking solutions and coloring it.
NGL Viewer
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Permits visualization of proteins and other molecular structures. NGL Viewer provide scalable molecular graphics on the web. The software uses modern browser features, including WebGL and Web Workers for 3D graphics and numerical calculations. It supports common molecular representations, including spacefill, ball & stick, cartoon and surfaces, and can parse and render volumetric data showing electron densities and electrostatic potentials. NGL Viewer enables the visualization and manipulation of large systems.
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 provides compound property description, clustering overview and property interpretation via the principal component analysis (PCA) loading vectors. This tool can be used to review analytical results, as well as to identify and delineate volumes of chemical space in which the confirmed active compounds reside.
mmLib / Macromolecular Library
Provides a toolkit for the analysis and manipulation of macromolecular structural models. mmLib contains several software components such as mmCIF and PDB files parser, a library of atomic elements and monomers, an OpenGL molecular viewer or an object-oriented data structure characterizing biological macromolecules. The data model is designed to facilitate the implementation for macromolecular crystallography, nuclear magnetic resonance (NMR), modeling and visualization.
CheS-Mapper / Chemical Space 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, and biological or toxic effects. CheS-Mapper embeds a dataset into 3D space, such that compounds that have similar feature values are close to each other. It can compute a range of descriptors and supports clustering and 3D alignment. It is an open-source Java application, based on the Java libraries Jmol, CDK, WEKA, and utilizes OpenBabel and R.
Generates high-quality publication-ready molecular graphics images and animations. PyMOL is a molecular graphics system targeted at medium to large biomolecules like proteins. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. It includes visualization of molecules, molecular trajectories and surfaces of crystallography data or orbitals, molecular builder and sculptor, internal raytracer and movie generator.
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 continuum electrostatics models. BALLView is a versatile and extensible tool for research in structural bioinformatics and molecular modelling. The convenient and intuitive graphical user interface offers novice users direct access to the full functionality, rendering it ideal for teaching.
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 compounds along with their properties, (ii) filter chemical compounds for a variety of properties such as steric clashes and toxicity, (iii) apply perfect match substructure search, (iv) cluster compounds according to their physicochemical properties providing representative compounds for each cluster, (v) build custom compound mining pipelines and (vi) quantify through property graphs the top ranking compounds in drug discovery procedures. ChemBioServer allows for pre-processing of compounds prior to an in silico screen, as well as for post-processing of top-ranked molecules resulting from a docking exercise with the aim to increase the efficiency and the quality of compound selection that will pass to the experimental test phase.
PUMA / Platform for Unified Molecular Analysis
Allows comprehensive diversity analysis of compound databases. PUMA computes six molecular properties of pharmaceutical relevance: molecular weight (MW), hydrogen bond donors (nHBDon), hydrogen bond acceptors (nHBAcc), topological polar surface area (TopoPSA), number of rotatable bonds (nRotB), and octanol water partition coefficient (ALogP). This tool is linked to other free online services that analyze global diversity of databases and activity landscape modeling.
KiNG / Kinemage Next Generation
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 visualizer. It offers backrub motions to correct some mistakes, provides tools for switching among different 3D projections of the data, can export high-resolution 2D views in several widely supported picture formats or by direct screen capture and also has a movie-maker function, allowing users to create movies for use in presentations.
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 provides various types of visualization for the analysis of proteins structures: alpha carbon, main chain, main chain and side chains, all atoms (including hydrogens) and molecular surface. It can help to understand the dynamical forces governing intermolecular interactions and thus facilitate new insights and discoveries.
UTOPIA Tools / User-friendly Tools for OPerating Informatics Applications
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 ‘Grid-friendly’ file requestors and resource browsers to higher level 3D-structure viewing panes and sequence alignment widgets. This tool employs object-orientated techniques to expose the functionality in a coherent manner.
TexMol / Texture Molecular Viewer
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. TexMol is a high-performance, interactive molecular exploration tool. It uses a molecular specification file to construct the Flexible Chain Complex (FCC), a robust, dynamic data structure that serves as TexMol’s internal representation for molecular structures.
Supplies a bioinformatics platform to save, manage, develop and combine various bioinformatics tools to avoid obsolescence of software developed by academics. SATurn offers a platform including functionalities dedicated to: (i) the visualization of items such as protein & DNA sequences or compound structures; and (ii) the generation of phylogenetic trees or multiple sequence alignments sequencing files. The application also contains an editor that can be exploited to create or extend plugins or scripts.
GAMGI / General Atomistic Modelling Graphic Interface
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) makes Random Close Packing structures, Voronoi and coordination polyhedra for arbitrary structures. It comes with comprehensive atomic data, including ionic radius and isotopic data. It can be useful for the scientific community who needs a graphic interface to build and analyse atomic structures or to study atomic structures and to prepare images for presentations.
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