3D Macromolecular Structures

Category Proteomics>Protein Structure/Modeling Systems/Tools

Abstract 3D Macromolecular Structures is a group of interrelated software products that provide tools to examine, analyze, and process three-dimensional structures of biomolecules.

Three-dimensional structures of biomolecules provide a wealth of information on their biological function, on mechanisms linked to the function, and on the evolutionary history of and relationships between macromolecules.

Most 3D-structure data are obtained from X-ray crystallography and NMR-spectroscopy.

3D Macromolecular Structures tools are as follows:

1) Molecular Modeling DataBase (MMDB) --

The Molecular Modeling DataBase (MMDB), also known as “Entrez Structure”, is a database of experimentally determined structures obtained from the Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank (PDB).

MMDB contains 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 - 3D domains are compact structural units within a protein that are identified automatically during MMDB data processing using purely geometric criteria) 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, and then interactively view the sequence-structure relationships, active sites, bound chemicals, journal articles, and more.

2) CBLAST --

CBLAST is a tool that compares a ‘query protein sequence’ against all protein sequences from resolved 3D structures by using protein Basic Local Alignment Search Tool (BLAST) against the PDB data set.

The purpose of this is to find representative 3D structures for the query and/or its homologs, as available.

Each record in the Entrez Protein database has been ‘CBLAST'ed’ and the search results are available as Related Structures in the “Links” menu of Entrez Protein records.

You can also enter a protein query sequence directly into the CBLAST search page in order to find its sequence-similar 3D structure records.

The search results can be viewed in Cn3D (hence the name “CBLAST”), which displays an alignment of the query protein to the related structure’s sequence and allows you to interactively examine the sequence-structure relationship.

3) Cn3D --

Cn3D is a helper application for your web browser that allows you to view three-dimensional structures from NCBI’s Entrez retrieval service.

It was developed as a tool for the visualization of three-dimensional structures with emphasis on interactive examination of sequence-structure relationships and superposition of geometrically similar structures.

Cn3D displays a 3D structure along with its corresponding sequence data and allows you to highlight residues in either the 3D structure or the sequence alignment to see their location in both views, identify the residues within certain distances of bound chemicals, and more.

It can be used to display MMDB structures, superpositions of VAST related structures (see below...), and conserved core motifs identified in conserved domains.

4) IBIS --

IBIS is the National Center for Biotechnology Information (NCBI) Inferred Biomolecular Interaction Server (IBIS), which organizes, analyzes and predicts interaction partners and locations of binding sites in proteins.

IBIS provides annotations for different types of binding partners: Protein, chemical, nucleic acid, peptides and ions.

IBIS reports interactions observed in experimentally determined structural complexes of a given protein, and at the same time infers binding sites/interacting partners by inspecting protein complexes formed by homologous proteins.

Similar binding sites are clustered together based on their sequence and structure conservation.

To emphasize biologically relevant binding sites, several algorithms are used for verification in terms of evolutionary conservation, biological importance of binding partners, size and stability of interfaces, as well as evidence from the published literature.

5) Vector Alignment Search Tool (VAST) --

VAST is a computer algorithm developed at NCBI and used to identify similar protein three-dimensional structures by purely geometric criteria, and to identify distant homologs that cannot be recognized by sequence comparison.

“Related structures” for every structure in MMDB are pre-computed using VAST and accessible via links on the MMDB Structure Summary pages.

The VAST Search page also allows you to compare the coordinates of a newly resolved structure in PDB format against all structures in MMDB to find its neighbors.

System Requirements

Contact manufacturer.


Manufacturer Web Site 3D Macromolecular Structures

Price Contact manufacturer.

G6G Abstract Number 20712

G6G Manufacturer Number 104282