PyPDB 1.0 – a Python API for the Protein Data Bank

PyPDB 1.0

:: DESCRIPTION

PyPDB is a Python 3 toolkit for performing searches with the RCSB Protein Data Bank (PDB) using its XML-based API.

::DEVELOPER

William Gilpin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • Python

:: DOWNLOAD

 PyPDB

:: MORE INFORMATION

Citation

PyPDB: a Python API for the Protein Data Bank.
Gilpin W.
Bioinformatics. 2015 Sep 14. pii: btv543

IMAAAGINE – Search Hypothetical 3D Protein Arrangement in Protein Data Bank

IMAAAGINE

:: DESCRIPTION

The IMAAAGINE (IMagine An Amino Acid 3D pattern search enGINE) program allows users to search for hypothetical amino acid 3D arrangement query to be searched against the PDB. Users design their own motif with specific residue types and distances between residues, with a flexible distance tolerance.

::DEVELOPER

The Molecular Function Regulation Lab (M. Firdaus Raih research group)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nurul Nadzirin, Peter Willett, Peter J. Artymiuk, Mohd Firdaus-Raih. 2013.
IMAAAGINE: a webserver for searching hypothetical 3D amino acid side chain arrangements in the Protein Data Bank.
Nucleic Acids Res. 41 (W1): W432-W440

ExSer 1.0 – Mine Protein Data Bank (PDB) for Secondary Structural Elements

ExSer 1.0

:: DESCRIPTION

ExSer facilitates an automated extraction of the amino acid sequence that encode for the secondary structural regions of a protein from the protein data bank (PDB) file.

::DEVELOPER

Dr. L. Arul (arulsra@gmail.com )

:: SCREENSHOTS

ExSer

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 ExSer

:: MORE INFORMATION

Citation

Vignesh D, Daniel P, Raja N, Balasubramanian P, Arul L.
ExSer: A standalone tool to mine protein data bank (PDB) for secondary structural elements.
Bioinformation. 2010 Mar 31; 4(9):390-1. PMID: 20975886; PMCID: PMC2951642

PDB Editor 090203 – PDB (Protein Data Bank) File Editor

PDB Editor 090203

:: DESCRIPTION

PDB Editor (Protein Data Bank ,PDB, File Editor) is a tool for protein crystallographers to expedite selective edit / data extraction / analysis of their PDB files. It  allows the user to selectively search, select, extract and edit information in parallel.

::DEVELOPER

Jonas Lee

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX /  Linux
  • Java

:: DOWNLOAD

PDB Editor

:: MORE INFORMATION

Citation

J. Lee and S.-H. Kim
PDB Editor: a user-friendly Java-based Protein Data Bank file editor with a GUI
Acta Cryst. (2009). D65, 399-402

DashPDB – Mac OS X Dashboard widget to Access to the RCSB Protein Data Bank

DashPDB

:: DESCRIPTION

DashPDB is a Mac OS X Dashboard widget designed to give quick access to the RCSB Protein Data Bank. A single click downloads the PDB file or the biological unit file or opens the RCSB’s webpage on the PDB entry entered.

::DEVELOPER

Dunbrack Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • MacOsX

:: DOWNLOAD

DashPDB

:: MORE INFORMATION

By clicking this link you agree to the BSD-type license here.

WPDB 2.2 – The Protein Data Bank Through Windows

WPDB 2.2

:: DESCRIPTION

WPDB is a Microsoft Windows based program for browsing and interrogating native and derived structural features of biological macromolecules using data obtained from the Protein Data Bank (PDB). Major features of WPDB are a 20-fold compression of PDB files and query and analysis tools. The latter permit the geometric and sequence properties of structures to be analyzed individually or through comparative analysis. The object oriented software design provides a high level of interaction between display windows which facilitates information discovery.

WPDB is useful for detailed analysis of a single structure or comparative analysis of two or more structures. It comes with a variety of databases. Alternatively, you can build your own database from PDB files with the WPDB Loader (WPDBL).

WPDBL Used to build a WPDB database from PDB files for access by the WPDB program. Prebuilt databases of a complete PDB distribution are available already built in the ../ directory.

::DEVELOPER

Ilya Shindyalov and Phil Bourne

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

WPDB ; WPDBL

:: MORE INFORMATION

Those using WPDB should cite:
I.N.Shindyalov and P.E.Bourne J. App. Cryst. 1995, 28(6) 847-852. WPDB A PC-based Tool for Analyzing Protein Structure. [Postscript]