Tag: PDB

pdb_extract 3.11 – Prepare Data for Submission to the PDB

pdb_extract 3.11

:: DESCRIPTION

The pdb_extract Program Suite contains tools and examples for extracting mmCIF data from structure determination applications.

pdb_extract Online Version

::DEVELOPER

RCSB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX with darwin
  • C/C++ compilers

:: DOWNLOAD

 pdb_extract

:: MORE INFORMATION

Citation

Acta Crystallogr D Biol Crystallogr. 2004 Oct;60(Pt 10):1833-9. Epub 2004 Sep 23.
Automated and accurate deposition of structures solved by X-ray diffraction to the Protein Data Bank.
Yang H, Guranovic V, Dutta S, Feng Z, Berman HM, Westbrook JD.

QuickPDB 20021101 – Java Applet for quickly viewing PROTEIN PDB Structure

QuickPDB 20021101

:: DESCRIPTION

QuickPDB permits you to find and quickly review a macromolecular structure looking at interactions between sequence and structure. Typically, once you have located structure(s) of interest you would download then for further analysis using local programs. QuickPDB is also available from the View Structure section of the Structure Explorer page for any entry in the Protein Data Bank .

::DEVELOPER

the Bourne Laboratory

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux/MacOsX.
  • Java

:: DOWNLOAD

  QuickPDB

:: MORE INFORMATION

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

PDBCNS 2.0 – Interconvert Atom Names between PDB & CNS formats

PDBCNS 2.0

:: DESCRIPTION

PDBCNS is a perl script to convert atom names for common amino acids and nucleic acid bases from PDB format to CNS (or XPLOR) style atom names.

::DEVELOPER

Richardson Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

:: DOWNLOAD

PDBCNS

:: MORE INFORMATION

PDBCNS is free software available under the terms of its own BSD-style license.

ANTHEPROT 3D 1.0.162- Molecule Viewer to look at PDB files

ANTHEPROT 3D 1.0.162

:: DESCRIPTION

Antheprot 3D is a molecular graphics program intended for the visualisation of proteins, nucleic acids from RCSB archive. The program is aimed at display, teaching and generation of publication quality images.

The program reads in a molecule coordinate file (PDB format) and interactively displays the molecule on the screen in a variety of color schemes and molecule representations. Currently available representations include wireframes, sticks, spheres, ball and stick, atom labels and distances. PDB files that are available either locally (Ctrl+O or File=>Open) or distantly at “POLE Bioinformatique Lyonnais” (Ctrl+I) or File=> PBIL URL can be loaded directly into AntheProt3D.

The program is made of 3 different windows:

  • A 3D view window which allows the user to interactively move the molecule
  • A group selection panel for group selection
  • A text window for provinding the user the list of clicked atoms, information (F2) and PHI, PSI values

A Ramachandran interactive plot is also available

Features

  • Alpha trace, wireframe, space filled,Balla nd Sticks, Sticks and surface mode.
  • Full support of clipping (“molecule slicing”)
  • Full support of stereo (side by side, anaglyph or quad buffer stereo)
  • Interactive Ramachandran plot
  • Hydrogen addition or removal by reduce
  • Selection of amino acids by group, chain or within a sphere
  • Surface viewer for MSMS files (Sanner, M.F., Spehner, J.-C., and Olson, A.J. (1996).Biopolymers, 38 (3), 305-320.
  • Ribbon or cylinder mode from Molscript program (P. J. Kraulis, (1991) Journal of Applied Crystallography 24, pp 946-950.)
  • Support for Delphi electrostatic potential Rocchia, W.; Alexov, E.; Honig, B. (2001) J Phys. Chem. 105, 6507-6514

::DEVELOPER

Pr Gilbert Deléage at France Institute of Biology and Chemistry of Proteins

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

ANTHEPROT 3D 1.0.162

:: MORE INFORMATION

ANTHEPROT3D album

If you use ANTHEPROT on PC, please cite one of the following references :

Deleage G, Combet C, Blanchet C, Geourjon, C
ANTHEPROT: An integrated protein sequence analysis software with client/server capabilities?
(2001) COMPUTERS IN BIOLOGY AND MEDICINE 31 (4): 259-267