p3d 0.4.3 – Python module for Structural Bioinformatics

p3d 0.4.3

:: DESCRIPTION

p3d is an object oriented Python module that adds a simple yet powerful interface to the Python interpreter to process and analyse three dimensional protein structure files (PDB files).

::DEVELOPER

CELLULAR AND MOLECULAR FUNCTIONS OF REACTIVE OXYGEN SPECIES

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Python

:: DOWNLOAD

  p3d

:: MORE INFORMATION

Citation

Christian Fufezan and Michael Specht
p3d – Python module for structural bioinformatics
BMC Bioinformatics 2009, 10:258 doi:10.1186/1471-2105-10-258

Tuftsviewer / Molli 0.99 – Cross Platform Open Source PDB Viewer

Tuftsviewer / Molli 0.99

:: DESCRIPTION

TuftsViewer is an open source program that allows the visualization, rotation and coordinated viewing of multiple 3D protein molecules on the 2D screen.

TuftsViewer has been renamed to Molli. Molli is an open source cross-platform protein structure viewer based on the OpenGL and wxWidgets libraries.

::DEVELOPER

Cowen Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux/MacOsX

:: DOWNLOAD

 Molli

:: MORE INFORMATION

Citation:

Matt Menke, Sara Su, Connor Gramazio, Caitlin Crumm, Daniela Extrum-Fernandez and Lenore Cowen,
TuftsViewer: An Intuitive Interface for viewing 3D Protein Structures,
Proceedings of ISMB 3DSIG, p. 24.

pdb-tools 0.2.1 – Editing and Performing Calculations on wwPDB Files

pdb-tools 0.2.1

:: DESCRIPTION

pdbTools is a set of command line python scripts that manipulate wwPDB protein and nucleic acid structure files. There are many programs, both open source and proprietary, that perform similar tasks; however, most of these tools are buried within programs of larger functionality.

::DEVELOPER

Harms Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • Python

:: DOWNLOAD

  pdb-tools

:: MORE INFORMATION

Reconstruct 1.0 – Reconstructing 3D Structures from Contact Maps

Reconstruct 1.0

:: DESCRIPTION

RECONSTRUCT is a command line program for reconstruction of protein contact maps that uses the distgeom program of the TINKER package.

::DEVELOPER

Reconstruct team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java
  • Tinker

:: DOWNLOAD

 Reconstruct

:: MORE INFORMATION

Citation

Optimal contact definition for reconstruction of Contact Maps.
Jose M Duarte, Rajagopal Sathyapriya, Henning Stehr, Ioannis Filippis and Michael Lappe.
BMC Bioinformatics 2010, 11:283.

CMView 1.1.1 – Protein Contact Map Visualization and Analysis

CMView 1.1.1

:: DESCRIPTION

CMView is an intervative contact map visualization and analysis tool. The tool provides functions for contact map calculation from structure, basic editing, visualization in contact map and 3D space and structural comparison with different built-in alignment methods.

::DEVELOPER

CMView team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 CMView

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jun 1;27(11):1573-4. Epub 2011 Apr 5.
CMView: interactive contact map visualization and analysis.
Vehlow C, Stehr H, Winkelmann M, Duarte JM, Petzold L, Dinse J, Lappe M.

Hollow 1.3 – Illustration software for Proteins

Hollow 1.3

:: DESCRIPTION

HOLLOW facilitates the production of surface images of proteins. Hollow generates fake atoms that identifies voids, pockets, channels and depressions in a protein structure specified in the PDB format.

::DEVELOPER

Hollow team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • Python

:: DOWNLOAD

Hollow

:: MORE INFORMATION

Bosco K. Ho and Franz Gruswitz
HOLLOW: Generating Accurate Representations of Channel and Interior Surfaces in Molecular Structures (2008)
BMC Structural Biology 8:49

CafeMol 3.2.1 – Biomolecular Modeling and Simulation Software

CafeMol 3.2.1

:: DESCRIPTION

CafeMol is a general-purpose coarse-grained(CG) biomolecular modeling and simulation software.It can simulate proteins,nucleic acids,lipids and their mixture with various CG models.

::DEVELOPER

Takada Lab ,Kyoto University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Fortran90/95
  •  C compiler

:: DOWNLOAD

 CafeMol

:: MORE INFORMATION

Citation

Hiroo Kenzaki, Nobuyasu Koga, Naoto Hori, Ryo Kanada, Wenfei Li, Kei-ichi Okazaki, Xin-Qiu Yao, and Shoji Takada ,
CafeMol: A coarse-grained biomolecular simulator for simulating proteins at work,
Journal of Chemical Theory and Computation , 7: 1979-1989, 2011

QuickLookPDB – QuickLook plugin for Displaying PDB Files

QuickLookPDB

:: 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

Ben Porebski

:: SCREENSHOTS

:: REQUIREMENTS

  • Mac OsX

:: DOWNLOAD

 QuickLookPDB

:: MORE INFORMATION

RedMD 2.3 – Perform Molecular Dynamics Simulations for Coarse-grained Models

RedMD 2.3

:: DESCRIPTION

RedMD (Reduced Molecular Dynamics) is a an open source software to perform molecular dynamics simulations for coarse-grained models of proteins, nucleic acids and their complexes. Simulations can be carried out in the microcanonical ensemble, with Berendsen and Langevin thermostats, as well as with Brownian dynamics.

::DEVELOPER

Biomolecular Machines Laboratory 

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 RedMD

:: MORE INFORMATION

Citation

Adam Gorecki, Marcin Szypowski, Maciej Dlugosz, Joanna Trylska,
RedMD – reduced molecular dynamics package,
J. Comput. Chem., 30:2364-2373, 2009

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