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.
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.
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.