Searches of PDB
Bioinformatics & Genomics
3-D Structure Prediction
Protein Data Bank (PDB)
Searches of PDB
Secondary Structure Prediction & Assignment
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[Institute of Physical and Chemical Research] “3DInSight is an integrated database and search tool for structure, property, and function of biomolecules, which will help
researchers to get insight into their relationship.”
Culling the PDB
[Fox Chase Cancer Center] This tools allows the user to either download a list of protein chains from the PDB that have been compiled for various parameter sets (resolution, sequence identity, etc.), or to have a list compiled based on user defined parameter sets.
The Live Bench Project is a continuous
benchmarking program. Every week new Protein Data Bank (PDB)
proteins are submitted to all participating
fold recognition servers. The results are
collected and evaluated using automated model
Metalloprotein Database and Browser
[Scripps Reasearch Institute] TSRI’s Metalloprotein site Database and Browser (MDB), is a database that aims to contain quantitative
information on all the metal containing sites available from structures in the PDB distribution, as well as from
in-house (TSRI) structures.
Molecules R US
[NIH] A WWW Forms interface which facilitates access (browsing, searching and retrieval) to the molecular structure data contained within the Brookhaven Protein Data Bank (PDB).
[Weizmann Institute of Science] MutaProt compares PDB files which differ by point mutations. It provides: a full list of file-pairs which differ by one, or two, amino acids; amino acid neighbors, and atomic contacts, of the mutated residue(s) (based on CSU software); 3D visualization of the mutated region(s) using CHIME; information and definitions page.
[Weizmann Institute] OCA� is a browser/database for retrieving rich content annotation on structure and function for proteins found in the Protein Data Bank.
PDB at a Glance
[National Institutes of Health] PDB At A Glance consists of a set of pre-defined biochemically meaningful search contexts (accessed by keyword) that represent the entire territory of the database.
The PDB-ISL (PDBintermediate Sequence Library) is a sensitive and fast search procedure. It is useful for finding sequences in the PDB
protein structure database that are homologous to a sequence of unknown structure. PSI-BLAST, Smith Waterman, and FASTA searches are provided.
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Protein Data Bank 3DB Browser
[PDB] Allows the user to rapidly search through the contents of the entire PDB Archive entries for obeying certain constraints.
Protein Topology Home Page
[EBI] This site offers services devoted to protein structural topology and protein topology cartoons.
Proteins Plus Search
[Nucleic Acid Database Project] A search engine for locating protein structures contained in the Protein Data Bank (PDB).
[Medical Research Council Laboratory of Molecular Biology, Cambridge] The purpose of this server is to provide structural (and hence implied functional) assignments to protein sequences at the Structural Classification of Proteins (SCOP)
superfamily level. SCOP provides a classification of all proteins in the Protein Data Bank (PDB). Whole genome assignment results are also provided.
[San Diego Supercomputing Center] “The PDB through Microsoft Windows, or WPDB for short, is a Microsoft Windows 3.1, Windows95, and Windows NT (client and server) based program to interrogate the 3-dimensional structure of biological macromolecules as found in the Protein Data Bank (PDB) using query and display tools like those shown above. ”