Confocal laser scanning microscopy (CLSM) provides highly detailed 3D structure of biological tissues at cellular and sub-cellular level. In this article we present a data flow which enables the import of CLSM data to sophisticated
animation software, thus enabling the creation of anatomically accurate movies for educational and public engagement purposes. This requires consideration of multimedia and cognitive load theories.
Resources
Encyclopedia of Life
The Encyclopedia of Life aims to contain data on all species in the world. It includes information such as the size, distribution, diet, habitat, ecology and age of species. It can be used as a comparative reference for all species on earth.
WormAtlas
WormAtlas is a database for the behavioral and structural anatomy of C. elegans. This resource contains a comprehensive set of images and videos of C. elegans anatomy and motility.
WormBook
WormBook contains peer-reviewed chapters on the biology of C. elegans.
WormBase
WormBase contains information on proteins and genes.
Morphbank
Morphbank is a repository for microscopy images that can be used for the comparative anatomy of many organisms.
DPDx
DPDx is a database, maintained by the CDC, that contains images of parasites and information on parasitic life cycles in diseases. This resource can be used as a reference for the 3D structure and appearance of parasites and as a starting point for collecting information for a human disease centric bio-visualization.
Mouse Genome Informatics
The Mouse Genome Informatics database contains a wealth of information on the mouse model organism.
Rat Genome Database (RGD)
The rat scientific resource, model organism in medical, psychological, and other research. Molecular, physiological pathways. Phenotypes. Disease Portals: Cancer, Cardiovascular, Diabetes, Immune and Inflammatory, Neurological, Obesity/Metabolic, Renal, Respiratory.
ZFIN
The zebrafish model organism database resource, model organism for embryonic development; esp. regeneration. Anatomy atlases and resources, phenotypes, gene expression etc.
Xenbase
The scientific resource for Xenopus, model organism in vertebrate embryology and development, basic cell and molecular biology, genomics, neurobiology, toxicology, human diseases. Anatomy, organ atlas, cell fate maps, developmental stages, movies; genome, expression data etc.
Gramene
The comparative scientific resource for plants! Gramene is a curated, integrated data resource for crops and model plant species.
The Arabidopsis Information Resource (TAIR)
The scientific resource for Arabidopsis thaliana. Genetic, molecular biology data. Gene expression, proteomics, metabolomics, nomenclature portals.
BeeBase
Comprehensive data source for the bee research community. Model organism for social behavior & global ecology.
VectorBase
The scientific resource for information relevant to invertebrate vectors of human pathogens. Genomes, transcriptomes, proteomes, mitochondrial data, population biology, pathogen transmission etc.
FlyBase
The scientific resource for Drosophila, model organism in genetics and developmental biology, human disease. Visual browsers by organ, life cycle stages, germ layer, tagma. Atlases, images, videos. Various data repositories. Interaction and pathway databases. Human disease Drosophila models & orthologous genes.
dictyBase
The scientific resource for Dictyostelium discoideum, model organism borderline between uni- & multicellularity. Biochemical pathways, phenotypes, videos etc.
PomBase
The scientific resource for fission yeast. PomBase is a comprehensive database for the fission yeast S. pombe, providing structural and functional annotation, literature curation and access to large-scale data sets.
Saccharomyces Genome Database (SGD)
Provides comprehensive integrated biological information for the budding yeast S. cerevisiae along with search and analysis tools to explore these data. Expression, biochemical pathways, phenotypes, interactions etc.
PSORTdb
Database of protein subcellular localizations for bacteria and archaea, determined through laboratory experimentation and computational predictions.
Archaeal Browser
A “window” on the biology of more than 100 microbial species from the domain Archaea.
BsubCyc
Model-organism database for the bacterium Bacillus subtilis. Gram-positive. Model for bacterial chromosome replication and cell differentiation.
EcoCyc
Scientific database for the bacterium Escherichia coli, the most widely studied prokaryotic model organism. Gram-negative.
All the Virology on the WWW
Up to date index site seeks to link and catalog virology pages world-wide.
VirusWorld
Virus structural resources, virus structure tutorials, gallery.
VIPERdb
Database of virus structures, a Virus Particle Explorer. The emphasis of the resource is on providing data from structural and computational analyses, as well as high quality renderings for visual exploration.
Virtual Plants Project
Computational approach to plant development to better understand the complex interaction of physical, physiological and genetic mechanisms that control plant morphogenesis. Aims to build an integrated picture of meristem development at different spatial and temporal scales by bringing together knowledge coming from plant architecture at macroscopic scales and from developmental biology at cellular and molecular scales. Computational models of plant development to understand the physical and biological principles that drive the development of plant branching systems and organs.
Embryology wiki
Movies and visuals of vertebrate embryology. Chicken, Mouse, Human. Various embryology resources, discussions, links to references.
Human Protein Atlas
The Human Protein Atlas is a histology and immunofluorescence tissue based human proteomics database, containing both normal and cancerous human tissue samples. This database contains stained histological tissue samples that show a protein of interest’s location on both the tissue and cellular level. It can be used to determine the most relevant cellular environment for a protein of interest.
Atlas of Microscopic Anatomy
The Atlas of Microscopic Anatomy is a collection of histological cross sections of human tissue. These images can be used to infer the 3D structure of biological tissues.
Keller, Philipp
Dynamics of building plans of animals from single-cell to whole-organism level (fly, zebrafish, mouse). Quantitative high-speed imaging and multiview dynamics of developing embryos. Lab website: movies, links to references.
Stocker, Roman
Microbiology at the interface between fluid mechanics and microbial ecology. Video microscopy and image analysis to capture and quantify microbial behavior. Topics include: bacterial rheotaxis, phytoplakton holographic microscopy, flagella mechanics, bacterial turbulence and collective behavior, bacterial chemotaxis, biofilms. Lab website: movies, links to references.
Moss, Bernard
Dynamic mechanisms used by viruses to infect cells. Topics include: Vaccinia virion movement, dynamic orthopoxvirus inclusion bodies. Lab website: movies, links to references.
Singer, Robert H
Real-time visualization of transcription kinetics, mRNA transport, and degradation in cells (yeast, fly, human). Quantitative fluorescence data, mathematical modeling. Lab website: visuals, links to references.
Gertler, Frank
Signaling and cytoskeleton dynamics during guided cell movement. Topics include: cancer, axon guidance. Lab website: movies, links to references.
Kirchhausen, Tomas
Dynamic processes that mediate movement of membrane proteins throughout cells. Topics include: clathrin, receptor-mediated endocytosis, secretion. Lab website: movies, visuals, links to references.
Cytokinetic Mafia
Cytokinesis. Movies of cytokinesis from various organisms: E.coli, yeast, Dicty, C.elegans, sea urchin, Xenopus, Zebrafish, rat, etc. (a.k.a. havoc from the Ted Salmon lab)
Theriot, Julie
Microbiology and dynamics of bacterial and fungal pathogens. Topics include: Listeria, Shigella, Salmonella, Candida. Lab website: movies, links to references.
The Bacterial Cytoplasm Has Glass-like Properties and Is Fluidized by Metabolic Activity
A primary research article describing the glass-like properties of bacterial cytoplasm than can be used as a reference for modeling the dynamics of molecules in the cytoplasm.
Individual versus collective fibroblast spreading and migration: regulation by matrix composition in 3D culture.
Fibroblast migration in 3D matrix
Cytotoxic T- Cells on Patrol
Nice video footage of cytotoxic t-cell migration than can be used as a reference for cell migration.
The Cell – An Image Library
The Cell – An Image Library is a repository for microscopy images and videos of eukaryotic and bacterial organelles and macromolecular structures. The images can be used as a reference to infer the 3D structure of organelles and macromolecules, and the videos can be used as reference for the dynamic movement of cellular structures.
Nikon Small World Image Gallery
The Nikon Small World Image Gallery contains winning microscopy images from the Nikon Small World Competition, which recognizing excellence in photography with the optical microscope. While it is not a comprehensive source for reference images, the beautiful, high-quality images may be a source of inspiration.
Nikon Fluorescence Microscopy Image Gallery
The Nikon Fluorescence Microscopy Image Gallery contains high quality 2D fluorescence microscopy images of cells and tissues. These images can be used to infer the 3D structure of cellular organelles, macromolecules (including cytoskeletal components) and tissues.
JCB Cell Biology Image Database
JCB Cell Biology Image Database is a repository for images associated with articles published in the Journal of Cell Biology. The database contains a wide variety of high quality images on many topics in cell biology and may be a useful source of reference imagery.
Neurocytology TEM Atlas
The Neurocytology TEM Atlas contains a collection of Electron Microscopy images specifically focusing on the subcellular and tissue level anatomy of neurons and surrounding brain tissue. These images can be used to infer the 3D structure of cellular organelles and tissues in the brain.
Nanoworld Image Gallery
The Nanoworld Image Gallery contains Electron Microscopy images of subcellular organelles, tissues, cells, and small organisms. These images can be used to infer the 3D structure of cellular macromolecules and organelles, or as a reference for the 3D external structure of small organisms, such as fruit flies.
CDC Public Health Image Library
The CDC Public Health Image Library contains a collection of light microscopy, transmission and scanning electron microscopy images pertaining to public health. Reference images of the external structure of bacteria, viruses, and small organisms can be found here.
Electron Microscopic Atlas of Cells, Tissues, and Organs
The Electron Microscopic Atlas of Cells, Tissues, and Organs is a collection of Electron Microscopic Images of tissues, cells and subcellular organelles. These images can be used to deduce the 3D structure of the respective organelles and tissues.
Human Protein Atlas
The Human Protein Atlas is a histology and immunofluorescence tissue based human proteomics database, containing both normal and cancerous human tissue samples. It can be used to determine where a protein of interest can be found in human tissue.
Orientations of Proteins in Membranes (OPM) Database
OPM provides spatial arrangements of membrane proteins with respect to the hydrocarbon core of the lipid bilayer. Archaeal, bacterial (gram±), chloroplast, ER, endosome, eukaryotic PM, Golgi, lysosome, mitochondrial (inner/outer), nuclear (inner/outer), peroxisome, secreted proteins, thylakoid, vacuole, vesicle, viral.
PSORTdb
Database of protein subcellular localizations for bacteria and archaea, determined through laboratory experimentation and computational predictions.
LocDB
The LocDB contains protein subcellular localization data of proteins in Human (Homo sapiens) and Weed (Arabidopsis thaliana). Users can search for lists of proteins present in different cellular organelles, and can be used to populate the environment of a molecular landscape and set context for the protein(s) of interest.
Organelle Database
The Organelle Database contains protein localization data to more than 50 organelles, subcellular structures, and protein complexes from model organisms including yeast and humans. Users can search for lists of proteins present in different cellular organelles and protein complexes, and can be used to populate the environment of a molecular landscape and set context for the protein(s) of interest.
LOCATE
The LOCATE database contains data describing the membrane organization and subcellular localization of human and mouse proteins. This database can be used to query the known location of proteins of interest within a cell. It also provides lists of proteins found in different cellular compartments. The list of proteins are not comprehensive, so other proteins relevant to the environment may be missing. This resource can then be used to populate the environment of a molecular landscape and set context for the protein of interest.
Uniprot
The Uniprot database can be used to find protein sequence and functional information. The information in this database can be combined with 3D structural data to determine the function of the whole protein as well as different domains of the protein. This information can be used to determine, for example, the regions of a membrane protein that are present inside or outside a cell, or the region of a protein that binds to DNA.
Gene Ontology
The Gene Ontology (GO) is a resource that compiles functional information on genes from the experimental evidence reported in peer-reviewed scientific papers. Once a list of genes or proteins of interest is collected for a molecular visualization, the genes and proteins can be queried in GO to learn more about their known functions.
Human Protein Atlas
The Human Protein Atlas is a histology and immunofluorescence tissue based human proteomics database, containing both normal and cancerous human tissue samples. This database contains stained histological tissue samples that show a protein of interest’s location on both the tissue and cellular level. It can be used to determine the most relevant cellular environment for a protein of interest.
PhosphoSitePlus (PSP)
Resource providing comprehensive information and tools for the study of protein post-translational modifications (PTMs) including phosphorylation, ubiquitination, acetylation and methylation.
RESID
Database of Protein Modifications, a comprehensive collection of annotations and structures for protein modifications including amino- terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications.
Glycosciences
Databases and tools for glycobiology and glycomics.
Phospho.ELM
Database of experimentally verified Serine, Threonine and Tyrosine sites in eukaryotic proteins.
PhosphaBase
Database resource for information on protein phosphatases.
PhosphoBase
Information on phosphorylated residues in proteins and peptide phosphorylation data on various protein kinases.
Histone Database
Resource for the analysis of chromatin structure and function focused on histones and histone fold-containing proteins.
Human Epigenome Project (HEP)
Epigenetic resource for human tissues and cell lines.
Epigenie
Databases and tools in epigenetics.
Reactome
Pathways database, manually curated, peer-reviewed database of biomolecular pathways.
KEGG Pathway Maps
KEGG Pathway Maps is a resource for common signaling pathway maps. It can be used as a “first stop” for reviewing a signaling pathway of interest. Signaling pathways are often the basis for telling a story about a molecule (or molecules) of interest in a molecular visualization.
CST pathways
CST pathways is a resource for common signaling pathway maps. It can be used as a “first stop” for reviewing a signaling pathway of interest. Signaling pathways are often the basis for telling a story about a molecule (or molecules) of interest in a molecular visualization.
PathwayLinker
PathwayLinker is a resource for visualizing signaling pathways that integrates data from three signaling pathway databases. The user can query a protein of interest to determine its interaction partners and to view a more complete picture of the signaling pathways the protein is part of. This information can help to create a story for the “life” of the protein in a molecular visualization.
Uniprot
The Uniprot database can be used to find protein sequence and functional information. The information in this database can be combined with 3D structural data to determine the function of the whole protein as well as different domains of the protein. This information can be used to determine, for example, the regions of a membrane protein that are present inside or outside a cell, or the region of a protein that binds to DNA.
Human Protein Interactome
The Human Protein Interactome is a database for human protein-protein interactions. This database can be used to determine what other proteins a protein of interest binds to and interacts with, which hints at the function of that protein. After using abundance data to determining which components to include in the environment of a molecular landscape, this database can be used to determine which components should interact with one another.
Human Protein Atlas
The Human Protein Atlas is a histology and immunofluorescence tissue based human proteomics database, containing both normal and cancerous human tissue samples. This database can be used to determine the abundance of a protein of interest, as well as it’s location on both the tissue and cellular level. It contains information on relative protein abundance in different human tissues and can be used to determine the most relevant cellular environment for a protein of interest.
Yeast GFP fusion localization database
The yeast GFP fusion localization database contains data on the abundance and cellular localization of yeast proteins. This data can be used to populate the molecular environment of a yeast cell.
The Proteomics DB
The Proteomics DB can be used to compare the relative expression of a Human protein of interest between multiple tissue types. It can be used to determine the most relevant cellular environment for a protein of interest and set context for the molecule(s) of interest.
PaxDB
PaxDB is a comprehensive absolute protein abundance database, which contains whole genome protein abundance information for different organisms and tissue types. A list of the most abundant proteins found in a particular organism/tissue, as well as the relative abundance of those proteins, can then be used to populate the environment of a molecular landscape and set context for the molecule(s) of interest.
Yanagida, Toshio
Single molecular imaging, nanometry, 3D single particle tracking. Topics include: diffusional movements of single membrane proteins, 3D tracking of vesicle transport, signal transduction, chemotaxis. Lab website: visuals, methods, links to references.
Ueda, Masahiro
Single-molecule imaging. Topics include: cell migration, chemotaxis, signal transduction, transcription. Lab website: movies, links to references.
van Oijen, Antoine
Novel single molecule biophysics techniques. Topics include: DNA replication, viral fusion, membrane transporters. Lab website: links to references.
Xie, Xiaoliang Sunney
Single molecule spectroscopy, microscopy and enzymology. Topics include: gene expression, single cell genomics / sequencing. Lab website: structure / function analysis, visuals, methods, links to references.
Gonzalez, Ruben
Single-molecule biophysical approaches to investigate the molecular mechanism of protein synthesis. Lab website: visuals, methods, links to references.
Spudich, James
Myosin motor proteins. Lab website: Movies and links to publications about myosin motor proteins.
Block, Steven M
Kinesin motor proteins. Lab website: Movies and analysis of single molecule experiments on kinesins, links to publications.
Croquette, Vincent. Bensimon, David
Single molecule micromanipulation, in vivo single molecule fluorescence, single-cell physiology. Topics include: helicases, topoisomerases, translocases, DNA-protein interactions, chromatin. Lab website: visuals, methods, links to references.
Marriott, Gerard
Optical probes and biosensors in vitro and in vivo, super-resolution imaging. Topics include: cytoskeleton, cell motility. Lab website: visuals, movies, methods, links to references.
Kapanidis, Achillefs N
Mechanisms of gene expression using single-molecule biophysical methods; observation of single biomolecules in real time, both “in vitro” and in living cells. Topics include: DNA Polymerase, RNA Polymerase, DNA recombination, DNA biosensors and nanodevices, super-resolution imaging of bacterial replication and transcription. Lab website: structure / function analysis, visuals, methods, links to references.
Stone, Michael
Single-molecule biophysical methods to probe enzyme structure and dynamics of protein-nucleic acid complexes. Topics include: telomerase dynamics, telomeres, ribonucleoprotein (RNP) complex structure. Lab website: links to references.
Scheuring, Simon
Atomic force microscopy (AFM) based research of membrane phenomena. Topics include: structure, dynamics, diffusion, interaction, mechanics and supramolecular assembly of membrane proteins and other membrane constituents. Lab website: links to references.
Moerner, William E
Super-resolved fluorescence microscopy. Topics include: Nav Channel, GroEL, Lambda-DNA, MreB actin homolog, MHC II. Lab website: movies, links to references.
Elcock, Adrian H
Elcock’s faculty page with links to his literature; topics include: computer simulations of the bacterial cytoplasm, models of macromolecular crowding effects, diffusion / crowding and molecular stability, protein folding, conformational flexibility, etc.
Theoretical and Computational Research, Illinois, Nanotechnology
Various movies of simulations and analysis. DNA origami; deformable material with programmable electrical properties. Coarse-grained model of ssDNA. Sequencing DNA using a nanopore capacitor. Electrostatic tweezers, etc.
Theoretical and Computational Biophysics Group, UIUC, Research
Rich source of MD/CG movies and accompanying analysis in various research categories: Membrane Biology, Mechanobiology, Neurobiology, Nanoengineering, Bioenergetics, Quantum Biology, Steered/Interactive MD, and many others.
CDDB
The Conformational Dynamics Database offers automated prediction of conformational dynamics of high molecular weight protein assemblies based on electron density maps.
ENM
Server provides a spectrum of analyses for the dynamics of an elastic network model (ENM) built from a given macromolecular structure.
elNémo
Web-interface to the Elastic Network Model (ENM), a fast and simple way for computing the low frequency normal modes of a macromolecule. This server can perform calculations for all-atom structures.
Biological Magnetic Resonance Data Bank (BMRB)
Repository for Data from NMR spectroscopy on proteins, peptides, nucleic acids, and other biomolecules.
Protein NMR: A Practical Guide
Descriptions and discussions of NMR experiments. Links to suggested resources for further reading.
NMR Information Server
Information on the basics of NMR, tutorials, references. Links to academic NMR groups. Who’s Who.
Aquaria
Aquaria is a repository for x-ray crystallographic, and nuclear magnetic resonance (NMR) data of large biological molecules and complexes. This resource can be used to find visual representations of a biological molecule of interest. All available structures for a given protein can be viewed at a glance to assist in choosing the most appropriate structure(s) for a given visualization. Once a structure is chosen, users can be directed to the PDB to download coordinate data that can be used with a compatible molecular viewing and manipulation software.
The Uniprot database
The Uniprot database can be used to find protein sequence and functional information. The information in this database can be combined with 3D structural data to determine the function of the whole protein as well as different domains of the protein. This information can be used to determine, for example, the regions of a membrane protein that are present inside or outside a cell, or the region of a protein that binds to DNA.
The Electron Microscopy Data Bank (EMDB)
The Electron Microscopy Data Bank (EMDB) is a repository for electron microscopy density maps of large biological molecules and complexes. This resource can be used to find visual representations of a biological molecule of interest. A 3D representation of the data can be viewed in the browser, or files containing the coordinate data can be downloaded and used with a compatible molecular viewing and manipulation software.
The PDB Molecule of the Month
The PDB Molecule of the Month features select structures from the PDB with introductions by David Goodsell that address structure/function, roles in human health/welfare, and additional resources.
The Protein Data Bank (PDB)
The Protein Data Bank (PDB) is a repository for x-ray crystallographic, and nuclear magnetic resonance (NMR) data of large biological molecules and complexes. This resource can be used to find visual representations of a biological molecule of interest. Various 3D representations of the molecule of interest, including space filling, ball-and-stick, and ribbon models, can be viewed in the browser, or files containing coordinate data can be downloaded to use with compatible molecular viewing and manipulation software (ex. Chimera, mMaya). Other information about the molecule, including sequence length, posttranslational modification locations and common structural motifs, which hint at the functions of different parts of the molecule, can also be found here.
Complex Portal
Manually curated, encyclopaedic resource of macromolecular complexes from a number of key model organisms.
CATH/Gene3D
Hierarchical classification of protein domain structures that clusters proteins at four major levels, Class, Architecture, Topology, and Homologous superfamily. ~26 million protein domains classified into ~2,740 superfamilies.
SCOPe
Structural Classification of Proteins, database of experimentally determined protein structures, divided into domains. Alpha proteins, beta, alpha and beta (a/b, a+b), multi-domain, membrane and cell surface proteins and peptide folds, small proteins, coiled-coil, low resolution, peptides, designed protein folds.
TRANSFAC
Database of eukaryotic transcription factors, their genomic binding sites and DNA-binding profiles.
Eukaryotic Promoter Database
Several databases of experimentally validated promoters from various species; human, mouse, zebrafish, Drosophila, C.elegans, A. thaliana.
ProNIT
Thermodynamic database for protein-nucleic acid interactions.
Nucleic Acid Database (NDB)
Portal for 3D structural information on experimentally-determined nucleic acids and complex assemblies. Use the NDB to perform searches based on annotations relating to sequence, structure and function, and to download, analyze, and learn about nucleic acids.
LipidBank
Database on the biochemistry of lipids. Fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins. More than 6000 unique molecular structures, their lipid names (common name, IUPAC), spectral information (mass, UV, IR, NMR and others), and most importantly, literature information. Expert curated.
SwissLipids
Database for lipid biology
MetaboLights
Metabolomics archive and reference database. Cross-species, cross-application, open-access, open-submission archive and reference database for metabolomics. Covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments.
MEROPS
Database of proteolytic enzymes, their substrates and inhibitors.
Enzyme Portal
Integrated enzyme data from EMBL-EBI resources. Integrated functional, sequence, nomenclature, substrate, product and cofactor data for enzymes.
Rhea
Curated database of enzyme-catalysed reactions.
ChEMBL
Bioactive data for drug discovery. An open data resource of binding, functional and ADMET bioactivity data.
PDBeChem
Dictionary of chemical components referred to in PDB entries and maintained by the wwPDB. Ligands, small molecules and monomers etc.
Chemical Entities of Biological Interest (ChEBI)
Resource for molecular entities, focused on ‘small’ chemical compounds. Reference chemical structures, nomenclature and ontological classification.
Multiple Sequence Alignment (MSA)
Web tools for the alignment of multiple biological sequences (protein or nucleic acid). From the output, homology can be inferred. Visual depictions of the alignment can illustrate events such as point mutations, insertions, deletions, etc. Useful in assessing conservation of domains, tertiary/secondary structures, residues or nucleotides.
BLAST
Web tool for finding regions of similarity between biological sequences; nucleotide/protein, various genomes, complex queries. Useful in identifying any sequences that resemble query sequence.
FlyMove
Site dedicated to movies of Drosophila embryogenesis, organogenesis, morphogenetic movements, cellular processes, etc.
Visible Human Project
The Visible Human Project by the National Institute of Health a complete, anatomically detailed, digital image database of complete human male and female cadavers reconstructed from CT, MRI and cryosections. It can be used as an anatomical reference for the human body.
Virtual Human Body
The Virtual Human Body is an illustrated human anatomy atlas. It can be used as a whole organism structural reference for human body systems including the lymphatic, cardiovascular, and nervous systems.
PRIDE
Repository of proteomics data
Ensembl
Alternative splicing and isoform annotation integrated with the Ensembl genome browser. Minimal set of compatible isoforms derived for each gene.
Alternative Splicing Gallery (ASG)
Splice graphs of human genes.
autoPACK, cellPACK
“pack any recipe of objects into anything”. Tools for assembling large-scale models from molecular building blocks. http://www.autopack.org
Chimera
Interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. Computational capabilities include fitting molecules in maps, morphing between maps, structural superimposition, structure/sequence conservation mapping, surface electrostatics/analysis, H-bond analysis, distance/area/ volumetric analysis etc. etc. PDB format output.
Visual Molecular Dynamics (VMD)
Molecular visualization – displaying/animating and analyzing large biomolecular assemblies using 3-D graphics and scripting. Capable of working with very large structures, long-timescale simulation trajectories to be loaded into physical memory, large volumetric datasets (e.g. The 64 million atom HIV capsid simulation, Nature 2013).
Open Babel
Chemical toolbox designed to speak the many languages of chemical data. Search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. Read, write and convert over 110 chemical file formats. http://openbabel.org/
AliasServer
Tool to handle multiple aliases used to refer to the same protein. “Multiple aliases” is a common obstacle to an efficient workflow.
Ontology Lookup Service (OLS)
Provides a unified interface to multiple ontologies, OBO format, including obsolete terms.
BioPortal
Comprehensive repository of biomedical ontologies. 48 resources. Advanced search and mappings. Visualization.
Gene Ontology
The Gene Ontology project aims to produce an unambiguous, universal language to describe biological phenomena across all species.
Science Viz Lab at U. of Toronto
(Ongoing research on biovis/molecular animation design principles)
Edward Tufte books
- The Visual Display of Quantitative Information
- Envisioning Information
- Visual Explanations
RNAcentral
Unified access to the ncRNA sequence data supplied by the Expert Databases: ENA, Rfam, RefSeq, Vega, gtRNAdb, miRBase, RDP, tmRNA Website, PDBe, snOPY, SRPDB, IncRNAdb.
Entrez Gene
Unified query environment for genes. Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus- specific resources worldwide. Entrez integrates the scientific literature, DNA and protein sequence databases, 3D protein structure and protein domain data, population study datasets, expression data, assemblies of complete genomes, and taxonomic information.