Bioinformatics Vol. 16 no. 9 2000
Pages 815-824
© 2000 Oxford University Press
BALL—rapid software prototyping in computational molecular biology
1 Max-Planck-Institut für Informatik, Im Stadtwald, 66123 Saarbrücken, Germany
Received on December 3, 1999
; revised on April 22, 2000
; accepted on June 18, 2000
Motivation: Rapid software prototyping can significantly reduce development times in the field of computational molecular biology and molecular modeling. Biochemical Algorithms Library (BALL) is an application framework in C++that has been specifically designed for this purpose.
Results: BALL provides an extensive set of data structures as well as classes for molecular mechanics, advanced solvation methods, comparison and analysis of protein structures, file import/export, and visualization. BALL has been carefully designed to be robust, easy to use, and open to extensions. Especially its extensibility which results from an object-oriented and generic programming approach distinguishes it from other software packages. BALL is well suited to serve as a public repository for reliable data structures and algorithms. We show in an example that the implementation of complex methods is greatly simplified when using the data structures and functionality provided by BALL.
Availability: BALL is available via internet from http://www.mpi-sb.mpg.de/BALL/. It may be used free of charge for research and teaching. Commercial licenses are available upon request.
Contact: O.Kohlbacher, oliver{at}mpi-sb.mpg.de
To whom correspondence should be addressed.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  V. Pulim, J. Bienkowska, and B. Berger LTHREADER: Prediction of extracellular ligand-receptor interactions in cytokines using localized threading Protein Sci., February 1, 2008; 17(2): 279 - 292. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Hildebrandt, R. Blossey, S. Rjasanow, O. Kohlbacher, and H.-P. Lenhof Electrostatic potentials of proteins in water: a structured continuum approach Bioinformatics, January 15, 2007; 23(2): e99 - e103. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. K. Gerega and K. M. Downard PROXIMO--a new docking algorithm to model protein complexes using data from radical probe mass spectrometry (RP-MS) Bioinformatics, July 15, 2006; 22(14): 1702 - 1709. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Moll, A. Hildebrandt, H.-P. Lenhof, and O. Kohlbacher BALLView: a tool for research and education in molecular modeling Bioinformatics, February 1, 2006; 22(3): 365 - 366. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
W. Xie and N. V. Sahinidis Residue-rotamer-reduction algorithm for the protein side-chain conformation problem Bioinformatics, January 15, 2006; 22(2): 188 - 194. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Rausch, T. Weber, O. Kohlbacher, W. Wohlleben, and D. H. Huson Specificity prediction of adenylation domains in nonribosomal peptide synthetases (NRPS) using transductive support vector machines (TSVMs) Nucleic Acids Res., October 12, 2005; 33(18): 5799 - 5808. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. L. Kingsford, B. Chazelle, and M. Singh Solving and analyzing side-chain positioning problems using linear and integer programming Bioinformatics, April 1, 2005; 21(7): 1028 - 1039. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. Chazelle, C. Kingsford, and M. Singh A Semidefinite Programming Approach to Side Chain Positioning with New Rounding Strategies INFORMS Journal on Computing, January 1, 2004; 16(4): 380 - 392. [Abstract] [PDF]
|
|