OpenStructure 1.4.0 – Computational Structural Biology Framework

OpenStructure 1.4.0

:: DESCRIPTION

OpenStructure is an open-source computational structural biology framework.This project aims to provide an open-source, modular, flexible, molecular modelling and visualization environment. It is targeted at interested method developers in the field of structural bioinformatics.

::DEVELOPER

The SIB Swiss Institute of Bioinformatics

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OS X

:: DOWNLOAD

 OpenStructure

:: MORE INFORMATION

Citation

M. Biasini, V. Mariani, J. Haas, S. Scheuber, A.D. Schenk, T. Schwede and A. Philippsen
OpenStructure: A flexible software framework for computational structural biology,
Bioinformatics. 2010 Oct 15;26(20):2626-8. doi: 10.1093/bioinformatics/btq481.

Acta Crystallogr D Biol Crystallogr. 2013 May;69(Pt 5):701-9. doi: 10.1107/S0907444913007051. Epub 2013 Apr 19.
OpenStructure: an integrated software framework for computational structural biology.
Biasini M, Schmidt T, Bienert S, Mariani V, Studer G, Haas J, Johner N, Schenk AD, Philippsen A, Schwede T.

StrBio 1.3 – Java Classes for Computational Structural Biology

StrBio 1.3

:: DESCRIPTION

StrBio library is a set of Java classes useful for development of software for computational structural biology research. The StrBio library includes protein format conversion tool, printf-based text formatting, Pred2ary secondary structure prediction, neural net library, Hooke-Jeeves global optimizer, and misc. math & statistics.

::DEVELOPER

John-Marc Chandonia

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

 StrBio

:: MORE INFORMATION

Citation:

Chandonia, JM. 2007.
StrBioLib: a Java library for development of custom computational structural biology applications.
Bioinformatics, May 30, doi: 10.1093/bioinformatics/btm269.

Wattos – Software for Structural Biology and NMR Spectroscopy

Wattos

:: DESCRIPTION

Wattos is a collection of Java programs for structural biology and NMR spectroscopy. It’s programs analyze, annotate, parse, archive, and disseminate experimental NMR data deposited by authors world wide into the PDB and BMRB.

::DEVELOPER

Wattos team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 Wattos

:: MORE INFORMATION

Citation

Doreleijers J.F., Nederveen A.J., Vranken W., Lin J., Bonvin A.M., Kaptein R., Markley J.L., and Ulrich E.L.
BioMagResBank databases DOCR and FRED with converted and filtered sets of experimental NMR restraints and coordinates from over 500 protein PDB structures.
J. Biomol. NMR 32, 1-12 (2005).

DINO 0.9.5 – Structural Biology Data 3D Visualization

DINO 0.9.5

:: DESCRIPTION

DINO is a realtime 3D visualization program for structural biology data. DINO aims to visualize all structural datas in a single program and to allow the user to explore relationships between the data. There are five data-types supported: structure (atomic coordinates and trajectories), surface (molecular surfaces), scalar fields (electron densities and electrostatic potentials), topographs (surface topography scans) and geom (geometric primitives such as lines).

::DEVELOPER

Ansgar Philippsen at the Division of Structural Biology, Biozentrum, University of Basel, Switzerland.

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Linux / IRIX 6.5+ / Digital OSF1 4.0+ / SunOS 5.7+ / MacOSX
  • OpenGL

:: DOWNLOAD

DINO ; Manual

:: MORE INFORMATION

MMTSB toolset – Multiscale Modeling Tools for Structural Biology

MMTSB toolset

:: DESCRIPTION

MMTSB toolset (Multiscale Modeling Tools for Structural Biology) can be used for replica exchange calculations with sander. This package also facilitates other Amber tasks, such as dealing in a consistent way with an ensemble of conformations, massaging PDB files, and carrying out some common types of structural analysis.

::DEVELOPER

NIH Research Resource Center for the Development of Multiscale Modeling Tools for Structural Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Perl

:: DOWNLOAD

MMTSB toolset

:: MORE INFORMATION

Citation:

M Feig, J Karanicolas and CL Brooks, III
MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology
Journal of Molecular Graphics and Modeling, 2004, 22 (5), 377-95.