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.
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.
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.
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.
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 prediction. It provides a method for displaying 3D structure of a substrate allowing the selection of the atoms involved in a given reaction.
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.
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 all the previous stages.
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.
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.
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 connected systems.
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 structural similarity. The program includes a wide range of functionalities including a way to modify algorithm’s parameters; the visualization and inspection of explored space as well as the possibility to export of the generated structures.
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 can be used to load files in various formats from the user’s local hard drive without uploading the data to a server. The tool supports several rendering and colouring modes which can be selected using a point-and-click based menu.
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 and interactions) and aesthetic criteria. LeView generates 2D representations of ligands and their environments and binding interactions for PDB entries.
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 implementation of new visualization techniques. The program is composed of two main modules: a library and a desktop application and allows users to split the visualization task into multiple sub tasks to permit users to consider independently the different parts of the process.
Browses DrugBank in an interactive manner. webDrugCS gives access to a wide range of molecules through a method inspired by 2D-mapplet that uses interactive color-coded 3D-spaces. It aims to assist users in retrieving an information of interest about structural diversity of small molecule drugs. The application allows users to choose between displaying using MQN, SMIfp, APfp, Xfp and Sfp fingerprint 3D-spaces and to submit molecules in SMILES format.
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.
Displays sets of up to 5000 user-defined molecules in 3D chemical spaces. webMolCS replaces the molecules in six different multidimensional-property spaces representing a selection of simple molecular features, computed from the 2D structures of molecules. It integrates composition, shape and pharmacophores, as well as detailed substructures information. This tool enables the visualization of minimum spanning tree representing nearest neighbor relationships.
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.
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 graphics, sequence and structural alignment methods. It aims to eliminate the need for high-priced graphics workstations. The tool permits to see data in several formats simultaneously that allows the user to recognize such relations that cannot be seen in any single view alone.
Displays and investigates molecular structures, density maps, 3D microscopy, and associated data. ChimeraX is applicable on varying resolution on scales ranging from atomic to cellular. It consists of an integrated multiscale modeling environment. This tool can compute solvent-excluded molecular surfaces of atomic models of any size. It groups models into higher-level logical units using a hierarchical representation.
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, ball-and stick and CPK models. An important feature of the software is the atom and residue selection mechanism allowing to give a set of atoms or residues as argument to a command that produces graphical objects. MolScript can also be used for making plots of non-protein structures.
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.
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.
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 purposes but it can also serve as an auxiliary tool for working with biomolecular structures. The standalone version can be installed on the user’s computer.
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.
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 manipulate the data.
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 using geometry optimization, molecular dynamics and conformational searching. OpenGL graphics module permits molecular graphics presentations, molecular editing tools, measurement tools for measuring, visualization options and interactive graphing options.
Offers a building platform for 3D proteins and molecules. Nano-one is a software, delivered with a set of demonstrating samples, that uses virtual reality for permitting users to design structures from organic elements as well as reproduce their interactions. The application allows researchers to annotate their molecules and includes a functionality to take and export their screenshots.
Supplies a graphical interface for molecular building and editing. ViewMol is an utility for displaying, visualizing and drawing of several features including molecular orbitals and inelastic neutron scattering spectra. It also provides features for thermodynamics computing and a module able to produce videos. This application can handle files from more than 10 types including DMol3, Mopac or Vamp, as well as the totality of the files that can be read through OpenBabel.
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 software provides various methods for computational search.