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URLs Display molecules - Visualization of information and main commercial packages Comments
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