Vivaldi – Visualisation, Analysis and Validation of NMR entries

Vivaldi

:: DESCRIPTION

Vivaldi is a web-based service for the analysis, visualization, and validation of NMR structures in the Protein Data Bank (PDB).

::DEVELOPER

Protein Data Bank in Europe

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Vivaldi: visualization and validation of biomacromolecular NMR structures from the PDB.
Hendrickx PM, Gutmanas A, Kleywegt GJ.
Proteins. 2013 Apr;81(4):583-91. doi: 10.1002/prot.24213

PDB2PQR 2.1.1 – Convert Protein files in PDB format to PQR format

PDB2PQR 2.1.1

:: 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

PDB2PQR Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

PDB2PQR

:: 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.

MolPOV 2.1.0 – PDB to POV File Converter & Visualizer

MolPOV 2.1.0

:: 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

Professor David E. Richardson

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

MolPOV

:: MORE INFORMATION

PDB-Explorer – Web-based interactive Map of PDB in Shape Space

PDB-Explorer

:: 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

PDB-Explorer team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: 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.

Super 20130207 – Screen Superposable Oligopeptide Fragments from PDB

Super 20130207

:: 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

  • Linux
  • C Compiler

:: DOWNLOAD

  Super

:: 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.

PAST 1.4 – Store & Archive Multiple Datestamped Snapshots of PDB

PAST 1.4

:: 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

 PAST

:: MORE INFORMATION

DECOMP – PDB Decomposition Tool

DECOMP

:: DESCRIPTION

DECOMP repairs and decomposes files from the Protein Data Bank PDB formats.

::DEVELOPER

PIT Bioinformatics Group

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 DECOMP

:: 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.

XML2RAF 1.02 -Create RAF Maps from PDB XML files

XML2RAF 1.02

:: 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

 XML2RAF

:: 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).

MembraneEditor 2.2.2_1 – Modeling, Visualization and Analysis of PDB-based Membranes

MembraneEditor 2.2.2_1

:: DESCRIPTION

The CELLmicrocosmos MembraneEditor (CmME) interactively generates heterogeneous PDB-based membranes with varying lipid compositions and semi-automatic protein placement. Supports membrane patches and vesicles, microdomains as well as stacking of monolayer and/or bilayer membranes.

::DEVELOPER

the Bioinformatics / Medical Informatics department at Bielefeld University.

:: SCREENSHOTS

MembraneEditor

:: REQUIREMENTS

  •  Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 MembraneEditor

:: MORE INFORMATION

Citation

J Chem Inf Model. 2011 May 23;51(5):1165-82. doi: 10.1021/ci1003619. Epub 2011 Apr 19.
CELLmicrocosmos 2.2 MembraneEditor: a modular interactive shape-based software approach to solve heterogeneous membrane packing problems.
Sommer B1, Dingersen T, Gamroth C, Schneider SE, Rubert S, Krüger J, Dietz KJ.