Visualization tools and commercial tools

 

  • Moleditor - From Ambinter, to look at compounds, create a database in Smiles, SDF... - online
  • GMine - Genomics Data Miner Tutorial - online
  • Cociter - Text mining - online
  • IGB - Fast, free, and highly customizable genome browser you can use to view and explore big genomic datasets. IGB runs on your desktop and can load data from your local files and also from the internet - database
  • RLetters - A Web-Based Application for Text Analysis of Journal Articles - online
  • Text - Text mining - online
  • TEES - Turku Event Extraction System - online
  • Beegle - From literature mining to disease-gene discovery - online
  • Phenolyzer - Phenotype-based prioritization of candidate genes for human diseases - online
  • VennDiagramWeb - A web application for the generation of highly customizable Venn and Euler diagrams - online
  • LeView - Ligand Environment Viewer - standalone
  • MI bundle - The MI bundle: enabling network and structural biology in genome visualization tools - standalone
  • TVNViewer - An Interactive Visualization Tool for Exploring Networks that Change over Time or Space - online
  • CellDesigner - A diagram editor for drawing gene-regulatory and biochemical networks - standalone
  • NodeXL - Free, open-source template for Microsoft Excel 2007, 2010, 2013 and 2016 that makes it easy to explore network graphs - standalone
  • MESHABLE - Searching PubMed abstracts by utilizing MeSH and MeSH-derived topical terms (data mining) - online
  • VPLG - Visualization of Protein-Ligand Graphs. Computes and visualizes protein graphs for protein structure analysis - standalone
  • DrugQuest - Text mining tool for knowledge discovery: it is designed to cluster DrugBank records based on text attributes in order to find new associations between drugs (data mining) - online
  • Bio3D-web - Online interactive analysis of protein structure ensembles with Bio3D-web - online
  • BioTextQuest - a knowledge integration platform for literature mining and concept discovery (text mining) - online
  • PSAT - Protein Sequence Annotation Tool: a centralized web-based meta-server for high-throughput sequence annotations - online
  • Facio - Facio is a free GUI for computational chemistry softwares (TINKER, MSMS, Firefly, Gamess, MOPAC and Gaussian) - online
  • RING 2.0 - The RING 2.0 web server for high quality residue interaction networks. Residue interaction networks (RINs) are an alternative way of representing protein structures (identification of covalent and non-covalent bonds in protein structures, including pi-pi stacking and pi-cation interactions) - online
  • RapidMiner - Data Science, Reimagined, data mining - standalone
  • SWIFT-Review - Text mining - standalone
  • Text mining - Laurence Anthony Text mining tools, several packages, run also on Mac - standalone
  • Heatmapper - Web-enabled heat mapping for all (2016) - online
  • ePlatton - Ligand-protein clusters - online
  • NAPS - Network Analysis of Protein Structures - online
  • KeyPathwayMinerWeb - Online multi-omics network enrichment - online
  • ALVIS - Sequence Bundles is a new method for visualising sequence alignments - online
  • PHYLOViZ - Web-based tool for visualization, phylogenetic inference, analysis and sharing of minimum spanning trees - online
  • Evolview - Version 2. Online visualization and management tool for customized and annotated phylogenetic trees - online
  • ICM - A web server for integrated clustering of multi-dimensional biomedical data - online
  • ProViz - Web-based visualization tool to investigate the functional and evolutionary features of protein sequences - online
  • POLYVIEW - POLYVIEW 2D and 3D: protein annotation, visualization - online
  • ptgl - The new protein topology graph library web server - online
  • IBS - An illustrator for the presentation and visualization of biological sequences - online and standalone
  • Genome3D - It is a model-view framework for displaying genomic and epigenomic data within a three-dimensional physical model of the human genome (2015) - online
  • 3D Genome - A low-latency, big database system and browser for storage, querying and visualization of 3D genomic data - online
  • Epigenome - the WashU Epigenome Browser - online
  • VNL - Virtual NanoLab works as a graphical user interface for Atomistix ToolKit (ATK) - standalone
  • cellPACK - cellPACK is a software program that extends autoPACK with biologically relevant packing algorithms and a database of molecular recipes to construct models of whole cells or viruses - standalone
  • IMP - A multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks (2015) - online
  • ClustVis - A web tool for visualizing clustering of multivariate data using Principal Component Analysis (PCA) and heatmap (2015) - online
  • VAST+ - Tracking structural similarities between macromolecular complexes - online
  • PLIP - Fully automated protein–ligand interaction profiler (2015) - online
  • PathWhiz - Look at pathways with PathWhiz (2015) - online
  • Skylign - A tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models. Profile can be found via Pfam and or generated with HMMER - online
  • NGL Viewer - A web application for molecular visualization - online
  • structureViz2 - structureViz2: Linking Cytoscape and Chimera - standalone
  • PDBest - PDBest is a freely available platform for manipulating, filtering and normalizing biomolecules in Protein Data Bank (PDB) and mmCIF structure files - standalone
  • DataWarrior - A very nice free tool for Chemistry Aware Data Visualization and Analysis (openmolecules.org). Numerous features from filtering compounds, to data analysis and computation of descriptors (eg, binned log P, log S, druglikeness score, rotatable bonds...automatic SAR, activity cliff, cluster compounds, find similar compounds...search fragments..look all your compounds, 2D, 3D, see physchem parameters...) (for Mac, Windows and Linux) - standalone
  • ContPro - A web tool for calculating amino acid contact distances in protein from 3D ‐structures at different distance threshold - online
  • TOPO2 - Transmembrane Protein Display - online
  • Protter - Visualization of proteoforms and interactive integration of annotated and predicted sequence features - online
  • TMRPres2D - TransMembrane protein Re-Presentation in 2 Dimensions tool, automates the creation of uniform, two-dimensional, high analysis graphical images/models of alpha-helical or beta-barrel transmembrane proteins - online
  • Scratch Protein Predictor - Scratch Protein Predictor programs include: ACCpro: the relative solvent accessibility of protein residues; CMAPpro: Prediction of amino acid contact maps; COBEpro: Prediction of continuous B-cell epitopes; CONpro: predicts whether the number of contacts of each residue in a protein is above or below the average for that residue; DIpro: Prediction of disulphide bridges; DISpro: Prediction of disordered regions; DOMpro: Prediction of domains; SSpro: Prediction of protein secondary structure; SVMcon: Prediction of amino acid contact maps using Support Vector Machines; and, 3Dpro: Prediction of protein tertiary structure (Ab Initio) - online
  • GIANT - GIANT: A Cytoscape Plugin for Modular Networks - standalone
  • Sirius - Sirius is a component-based visualization framework designed for application in molecular modeling, drug discovery, protein structure analysis, as well as database mining and sequence-based work. It is equally suited for protein and small molecule construction and visualization - standalone
  • CDvist - A webserver for identification and visualization of conserved domains in protein sequences - online
  • RRDistMaps - A UCSF Chimera tool for viewing and comparing protein distance maps - standalone
  • PdbViewer - DeepView - Swiss-PdbViewer - standalone
  • PDBsum - Website providing numerous pictorial analyses of each entry in the Protein Data Bank - online
  • iMol EyeMol - Interactively display a set of molecules. Classify, browse and select molecules of interest. - standalone
  • ViewMotions Rainbow - A new method to illustrate molecular motions in proteins. The ViewMotions Web Server is here to automatically generate such diagrams Protein Data Bank files or files from the Macromolecular Movements database (http://molmovdb.org) - online
  • iView - An interactive WebGL visualizer for protein-ligand complex - online
  • rinalyzer - Protein visualization - standalone
  • RING - Networking interacting residues, evolutionary information and energetics in protein structures. Representation of proteins based on residue interaction networks (RINs) - online
  • Pro-origami - It is a system for automatically generating protein structure cartoons - online
  • ConSurf - Protein visualization - online
  • Vanno - A visualization-aided variant annotation tool (2014) - online
  • MuPIT interactive - Webserver for mapping variant positions to annotated, interactive 3D structures - online
  • VERMONT - Visualizing mutations and their effects on protein physicochemical and topological property conservation - online
  • DIVE - A data intensive visualization engine - standalone
  • ChemDoodle - ChemDoodle Web Components, a pure JavaScript chemical graphics and cheminformatics library, presents 2D and 3D graphics and animations for chemical structures - standalone
  • FEATURE - FEATURE is a suite of automated tools that examine biological structures and produce useful representations of the key biophysical and biochemical features of these structures that are critical for understanding function - online
  • Link - The University of California, Santa Cruz (UCSC) Interaction Browser is an online tool for biologists to view high-throughput data sets simultaneously for the analysis of functional relationships between biological entities - online
  • Link - OpenStructure aims to provide an open-source, modular, flexible, molecular modelling and visualization environment. It is targeted at interested method developers in the field of structural bioinformatics - standalone
  • ePMV - The open-source uPy plugin, embedded Python Molecular Viewer (ePMV) runs molecular-modeling software directly in several professional 3D animation applications Cinema4D, Blender, Maya, 3ds Max - standalone
  • Link - NOC is a free molecular explorer for protein structure visualization, validation and analysis - standalone
  • Link - Coot is for macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data. Coot displays maps and models and allows model manipulations such as idealization, real space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers, Ramachandran plots, skeletonization, non-crystallographic symmetry and more. Can be used to analyze ligand-binding pocket - standalone
  • Link - BiologicalNetworks backend database (IntegromeDB) integrates >1000 curated data sources (from the NAR list) for thousands of eukaryotic, prokaryotic and viral organisms and millions of public biomedical, biochemical, drug, disease and health related web resources, molecules in 3D... - standalone
  • Link - Gabedit is a graphical user interface to computational chemistry packages like Gamess-US, Gaussian, Molcas, Molpro, MPQC, OpenMopac, Orca, PCGamess and Q-Chem - standalone
  • Link - Chemcraft : Graphical program for visualization of quantum chemistry calculations - standalone
  • Link - Friend is a bioinformatics application designed for simultaneous analysis and visualization of multiple structures and sequences of proteins and/or DNA/RNA. The application provides basic functionalities such as: structure visualization with different rendering and coloring, sequence alignment, and simple phylogeny analysis, along with a number of extended features to perform more complex analyses of sequence structure relationships, including: structural alignment of proteins, investigation of specific interaction motifs, studies of protein-protein and protein-DNA interactions, and protein super-families. Friend is also useful for the functional annotation of proteins, protein modeling, and protein folding studies - standalone
  • Link - JSME is a conversion of the popular JME applet to JavaScript (B. Bienfait and P. Ertl). JSME supports drawing and editing of molecules and reactions on desktop computer. The applet can also serve as a query input tool for searching molecular databases by supporting creation of complex substructure queries, which are automatically translated into SMARTS - standalone and online
  • Link - Arena3D Visualizing biological networks in 3D - standalone
  • Link - orange: Open source data visualization and analysis for novice and experts - Data Mining Software - standalone
  • Link - BioLayout Express3D is a powerful tool for the visualization and analysis of network graphs - standalone
  • Link - PATIKAweb: a Web interface for analyzing biological pathways through advanced querying and visualization - online
  • Link - Ondex Data integration and visualisation - standalone
  • Link - Osprey Network Visualization System - standalone
  • Link - Gephi The Open Graph Viz Platform - standalone
  • Link - VisANT, visual analysis tool for biological networks and pathways - online and standalone
  • Link - Graphviz - Graph Visualization Software - standalone
  • Link - MQN-Mapplet: Visualization of Chemical Space with Interactive Maps of DrugBank, ChEMBL, PubChem, GDB-11, and GDB-13 - online and standalone
  • Link - UnityMol:  Using the Unity3D game engine to create a molecular viewer and serious games - standalone
  • Link - VAST, short for Vector Alignment Search Tool, is a computer algorithm developed at NCBI and used to identify similar protein 3-dimensional structures by purely geometric criteria, and to identify distant homologs that cannot be recognized by sequence comparison - online
  • Link - The Human Protein Atlas (HPA) is a powerful repository of protein expression patterns in human anatomical structures in normal and diseased tissues, accessible over the Web - online
  • Link - FirstGlance in Jmol:A simple tool for macromolecular visualization online - online
  • Link - DAVID, the Database for Annotation, Visualization And Integrated Discovery system, is a free, publicly-accessible web-based suite of tools for analyzing microarray gene expression results using the metadata properties (i.e., annotations) of a list of genes and their cognate proteins - online
  • Link - CDTree is an integrated suite of software tools for analyzing sequences from protein domains curated in NCBI's Conserved Domains Database (CDD) in the context of domain family hierarchies - online
  • Link - Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data. A lot of plugins are available for various kinds of problem domains, including bioinformatics, social network analysis, and semantic web - standalone
  • Link - IntAct provides a freely available, open source database system and analysis tools for molecular interaction data. All interactions are derived from literature curation or direct user submissions and are freely available - online
  • Link - VisANT 4.0: Integrative network platform to connect genes, drugs, diseases and therapies - online
  • Link - GeneMANIA is a flexible, user-friendly web interface for generating hypotheses about gene function, analyzing gene lists and prioritizing genes for functional assays - online
  • Link - FLink is a tool that enables you to traverse from a group of records in a source database (e.g., Proteins) to a ranked list of associated records in a destination database (e.g., BioSystems) - online
  • Link - MovieMaker - online
  • Link - JKlustor - small molecules
  • Link - Molprime - small molecules - Phone app
  • Link - JChemPaint - small molecules
  • Link - Bkchem - small molecules
  • Link - Molinspiration - small molecules
  • Link - Xdrawchem - small molecules
  • Link - iMoledraw - small molecules - Phone
  • Link - Sketchel - small molecules
  • Link - Chemtool - small molecules
  • Link - Bioclipse - small molecules
  • Link - ketcher - small molecules
  • Link - chemwriter - small molecules
  • Link - molinspiration - small molecules
  • Link - chemaxon - small molecules
  • Link - chemicalize chemaxon - online
  • Link - The SMARTSviewer generates a visualization of a SMARTS string       - online
  • Link - Jamberoo - cross platform molecular editor       - .
  • Link - The CARLSBAD database: a confederated database of chemical bioactivities - Database
  • Link - The PubChem chemical structure sketcher, get SMILES and SMARTS       - online
  • Link - OSRA (Optical Structure Recognition Application) is a utility designed to convert graphical representations of chemical structures and reactions, as they appear in journal articles, patent documents, textbooks, trade magazines etc. - standalone
  • Link - OSRA online (Optical Structure Recognition Application) - Images to SMILES, online
  • Link - OSRA: Optical Structure Recognition, take the 2D drawing of a compound and get the SMILES - Images to SMILES
  • Link - MolviZ.Org To display and rotate macromolecules and small molecules in a single internet browser - Molecular graphics
  • Link - Cn3D: displays structures of macromolecules and performs sequence alignments - Molecular graphics
  • Link - DisMol: Java applet viewer for macromolecules and small molecules - .
  • Link - MolScript - .
  • Link - Colorado3D web server for the visual analysis of protein structures - online
  • Link - Pymol - standalone
  • Link - LigAlign: The same ligand is likely to bind different proteins in similar, instructive ways. This tool automates comparisons of such active sites. This is a PyMOL-based structure visualization tool which utilizes ligand-based active site alignment. - standalone
  • Link - BioJS: an open source JavaScript framework for biological data visualization - standalone
  • Link - NAViGaTOR - Network Analysis, Visualization, & Graphing TORonto is a software package for visualizing and analyzing protein-protein interaction networks - .
  • Link - VMD - Molecular graphics, structural analysis
  • Link - MolWorks: graphic tool for drawing and sketching molecules - .
  • Link - ChemSpotlight: metadata importer pluging for Mac OS X, which reads common chemical file formats (PDB, Mol2, SDF...) - .
  • Link - ICM browser - Molecular graphics
  • Link - OpenEye Vida - Molecular graphics
  • Link - PovChem is a chemical visualization and illustration program - Molecular graphics, structural analysis
  • Link - KMovisto is a 3D molecule viewer essentially for Linux - Molecular graphics
  • Link - YASARA - Molecular graphics and modeling
  • Link - UCSF Chimera - .
  • Link - Open source molecule viewer Jmol - .
  • Link - Links to protein crystallography tools such as CCP4, etc - .
  • Link - Xemistry Web Sketcher Demonstration - online
  • Link - Molecular graphics - Astex - .
  • Link - The PSI3 suite of quantum chemical programs - ab initio quantum chemistry package
  • Link - Protein movie generator - online
  • Link - Vega ZZ - .
  • Link - Avogadro - .
  • Link - Rasmol - .
  • Link - Cosmos - .
  • Link - BINANA - (BINding ANAlyzer). Python-implemented algorithm for analyzing ligand binding
  • Link - Yet Another extended Huckel Molecular Orbital Package (YAeHMOP), freely available extended Huckel calculation and visualization package - standalone
  • Link - IMPACT-F Predicting human oral bioavailability of future drug candidates - commercial
  • Link - Accelrys software: structural bioinformatics, drug design and related (e.g., Pipeline) - commercial
  • Link - Molecular Discovery - commercial
  • Link - Schrodinger software: structural bioinformatics, drug design and related (e.g, Glide) - commercial
  • Link - MOE software: structural bioinformatics, drug design and related - commercial
  • Link - Inte:Ligand drug design and related - commercial
  • Link - Biosolveit software: structural bioinformatics, drug design and related - commercial
  • Link - OpenEye software: drug design - commercial
  • Link - Stardrop software (Optibrium): drug design - commercial
  • Link - GUSAR is a tool to create and use models on quantitative structure-activity relationships (QSAR) Windows - commercial
  • Link - hint is a novel empirical molecular modeling system with new methods for de novo drug design and protein or nucleic acid structural analysis - standalone
  • Link - Cresset software: drug design - commercial
  • Link - Medit software: drug design - commercial
  • Link - Molsoft: software, structural bioinformatics, drug design and related - commercial
  • Link - Tripos software: structural bioinformatics, drug design and related - commercial
  • Link - Molinspiration software: drug design - commercial
  • Link - Daylight software: drug design - commercial
  • Link - Chemaxon software: drug design - commercial
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© Bruno Villoutreix. A first version of this Website was launched in 2006. Thank to Natacha Oliveira