:: DESCRIPTION
PDB2CLE is a program that can turn a PDB file to a sequence of structural alphabets. In paricular, each structural alphabet is a discretized set of representatives of the local protein structure.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
MMCIF Dictionary Suite is a collection of tools to parse, validate, manage data dictionaries used by the PDB. Applications are also included, which convert data dictionaries to XML schema, provide HTML browsing, produce mapping information for relational database loaders (Db Loader) and convert data files between related CIF dialects
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
QuickLookPDB is the QuickLook plugin for displaying PDB files and provides two visualisation options. plugin can use pymol to quickly render thumbnail images, while the heart of the plugin lies with the integration of a HTML-5 PDB viewer, Jolecule.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
PDB2PQR is a Python software package that automates many of the common tasks of preparing structures for continuum electrostatics calculations, providing a platform-independent utility for converting protein files in PDB format to PQR format.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Dolinsky TJ, Czodrowski P, Li H, Nielsen JE, Jensen JH, Klebe G, Baker NA.
PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations.
Nucleic Acids Res, 35, W522-5, 2007.
:: DESCRIPTION
XML2RAF is a Perl software to create RAF maps from PDB XML files.The Protein Data Bank provides XML files that include a mapping between the PDB-format records SEQRES (representing the sequence of the molecule used in an experiment) and ATOM (representing the atoms experimentally observed). These XML files (along with the PDB’s chemical dictionary) also provide information on the original identity of most residues prior to any post-translational modifications, including cyclizations.
::DEVELOPER
Computational Genomics Research Group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Chandonia JM, Hon G, Walker NS, Lo Conte L, Koehl P, Levitt M, Brenner SE.
The ASTRAL compendium in 2004.
Nucleic Acids Research 32:D189-D192 (2004).
:: DESCRIPTION
DECOMP repairs and decomposes files from the Protein Data Bank PDB formats.
::DEVELOPER
:: SCREENSHOTS
N/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformation. 2009 Jul 27;3(10):413-4.
DECOMP: a PDB decomposition tool on the web.
Ordog R1, Szabadka Z, Grolmusz V.
:: DESCRIPTION
PAST (PDB Archival Snapshot Toolkit) allows users to create date-stamped mirrors of the current PDB repository, and it maintains all previous archives using an efficient storage mechanism. Although the PDB development team now provides archival copies of the PDB for selected dates, the archives are infrequent (updated yearly) and do not provide an efficient means of storing the redundant data. PAST is based on an efficient indexing technique similar to the ones used by Picasa and iTunes. We only store one physical copy for each unique file. PAST archival snapshots precisely mirror the directory structure and files in the PDB, but all files in the snapshot directory are replaced by links to a minimal set of data to prevent wasteful use of space. PAST has been tested and deployed in our lab to create weekly PDB snapshots corresponding to ASTEROIDS releases.
::DEVELOPER
Degui Zhi and John-Marc Chandonia
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
Super is a web server to rapidly screen superposable oligopeptide fragments from the Protein Data Bank
::DEVELOPER
Laboratory of Computational Biology (LCB), Monash University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
James H. Collier, Arthur M. Lesk, Maria Garcia de la Banda and Arun S. Konagurthu,
Super: A web server to rapidly screen superposable oligopeptide fragments from the Protein Data Bank.
Nucleic Acids Research 40(W1): W334-W339, July 2012.
:: DESCRIPTION
PDB-Explorer is a web application for the interactive visualization of chemical space of RCSB Protein Data Bank (PDB) characterized by protein shape fingerprint (3DP) and shape similarity search for molecules in PDB.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
PDB-Explorer: a web-based interactive map of the protein data bank in shape space.
Jin X, Awale M, Zasso M, Kostro D, Patiny L, Reymond JL.
BMC Bioinformatics. 2015 Oct 23;16(1):339.
:: DESCRIPTION
MolPOV is a PDB to POV file (POV-Ray) converter and molecular visualization tool for MS Windows.The PDB files can be from the Brookhaven PDB itself or from any molecular modeling program that can store structures in the PDB format. A POV setup dialog can be used to edit many of the basic scene features and rendering options. In addition, the program allows launching of the POV program to view the rendering immediately.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION