| 3D Macromolecular Structures |
|
|
| |
|
Molecular Modeling Database (MMDB) |
Experimentally resolved structures of proteins, RNA, and DNA, derived from the Protein Data Bank (PDB), with value-added features such as explicit chemical graphs, computationally identified 3D domains (compact substructures) that are used to identify similar 3D structures, as well as links to literature, similar sequences, information about chemicals bound to the structures, and more. These connections make it possible, for example, to find 3D structures for homologs of a protein sequence of interest, then interactively view the sequence-structure relationships, active sites, bound chemicals, journal articles, and more.
|
|
| |
|
iCn3D |
A new WebGL-based viewer for interactive viewing of three-dimensional macromolecular structures on the web, without the need to install a separate application, and enables you to (1) interactively view 3D structures and corresponding sequence data; (2) interactively view superpositions of similar structures; (3) cutomize the display of a structure and generate a URL that allows you to share the link; (4) incorporate iCn3D into your own pages. An example of each is accessible from the "About iCn3D" page.
|
|
| |
|
Cn3D |
A tool for visualization of three-dimensional structures, available for Mac and PC, with emphasis on interactive examination of sequence-structure relationships and superposition of geometrically similar structures. Cn3D can be used to display MMDB structures, superpositions of VAST similar structures, and conserved core motifs identified in conserved domains.
|
|
| |
|
Vector Alignment Search Tool (VAST) |
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. "Similar structures" for every structure in MMDB are pre-computed using VAST and accessible via links on the MMDB Structure Summary pages. The VAST Search web service also allows you to compare the coordinates of a newly resolved structure in PDB file format against all structures in MMDB to find its neighbors.
|
|
| |
|
Vector Alignment Search Tool Plus (VAST+) |
A tool designed to identify macromolecules that have similar 3-dimensional structures, with an emphasis on finding those with similar biological assemblies ("biological units" or "biounits"). The similarities are calculated using purely geometric criteria, and therefore can identify distant homologs that cannot be recognized by sequence comparison. VAST+ is built upon the original Vector Alignment Search Tool (VAST), and expands the capabilities of that program by making it possible to now find macromolecular structures that have similarly shaped biological units, not just those that share similarly shaped individual protein molecules or fragments.
|
|
| |
| |
|
| |
 |
|
|
|
|
