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] OCAŠ 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.
[University College London] This service provides summaries and structural analyses of PDB data files.