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.

OpenStructure 2.2 – Computational Structural Biology Framework

OpenStructure 2.2

:: 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.

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.