NGL is a fast & interactive web-based tool for 3D visualization of large structures.
For X-ray structures, crystallographic unit cells can be displayed, as well as "supercells" comprising a set of adjacent unit cells.
PDB ID: 4HHB
PDB ID: 5IRE
PDB ID: 3PQR
options for display and analysis. Launch the viewer from any entry's Structure Summary page or by entering an ID below. The Jmol
Applet remains available from the 3D View page, and will continue to work in most browsers. Learn more
PDB ID: 1STP
PDB ID: 4EAR
PV is an alternative to JSmol that while not as feature-rich, uses WebGL and to enables hardware-accelerated graphics in modern web and mobile browsers.
Two of PV's unique features include "out of the browser" views. The "Detached" option launches a standalone viewer window that can be resized and the "Full Screen" option launches a full screen view.
RCSB PDB created these Java Web Start applications for 3D visualization.
Launch the specific viewer from each entry's Structure Summary.
Launch each viewer for Hemoglobin (4HHB) below.
Simple Viewer for 4HHB
Simple Viewer can rotate a structure, zoom in and out, and then save the view of the biological unit as an image file.
Protein Workshop for 4HHB
Protein Workshop can quickly and easily select structural elements to change the coloring, labeling, and representation style to highlight conformation type, hydrophobicity, residue type, and more.
This Java Web Start program from RCSB PDB visualizes macromolecular-ligand interactions in 3D.
Ligand Explorer has options to turn on the display of interactions including hydrogen bonds, hydrophobic contacts, water mediated hydrogen bonds, and metal interactions.
It can be launched from an entry's Structure Summary.
PoseView images are 2D diagrams that show a ligand and interacting residues.
Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions.
Access PoseView images in the Ligand Chemical Component section on an entry's Structure Summary.
Learn more about PoseView.
Provides a graphical summary of a full-length protein sequence from UniProt and how it corresponds to PDB entries. It also loads annotations from external databases (such as Pfam) and homology models information from the Protein Model Portal.
Annotations visualizing predicted regions of protein disorder and hydrophobic regions are displayed.
Learn more about Protein Feature View.
Breast Cancer Type 1 Protein,
Gag-Pol Polyprotein, and
Hemoglobin Alpha (shown image).
This feature is available from the Molecular Description widget on Structure Summary pages and by entering a UniProt ID below.
Illustrates the correspondences between the human genome and 3D structure.
All human genes have been mapped to representative PDB structure protein chains
(selected from sequence clusters at 40% sequence identity) to show which regions
of a gene are available in PDB coordinates.
Learn more about Gene View.
Breast Cancer 1 (early onset) and
Hemoglobin, Alpha 1 (shown image).
This feature is available from the Molecular Description widget on Structure Summary pages and by entering an HGNC Human Gene Symbol below (examples).
Explore metabolic pathways maps that identify pathway components with PDB structures and homology models.
Maps can be accessed from Structure Summary pages (see example 3MOS), Protein View (see example P29401), and the main Pathway View page.
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National Science Foundation, the
National Institutes of Health, and the
US Department of Energy.