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BALL--biochemical algorithms library 1.3.

Hildebrandt A, Dehof AK, Rurainski A, Bertsch A, Schumann M, Toussaint NC, Moll A, Stöckel D, Nickels S, Mueller SC, Lenhof HP, Kohlbacher O - BMC Bioinformatics (2010)

Bottom Line: Here, we discuss BALL's current functionality and highlight the key additions and improvements: support for additional file formats, molecular edit-functionality, new molecular mechanics force fields, novel energy minimization techniques, docking algorithms, and support for cheminformatics.It is available free of charge under the Lesser GNU Public License (LPGL).Parts of the code are distributed under the GNU Public License (GPL).

View Article: PubMed Central - HTML - PubMed

Affiliation: Center for Bioinformatics Saar, Saarland University, Saarbrücken, Germany. anhi@bioinf.uni-sb.de

ABSTRACT

Background: The Biochemical Algorithms Library (BALL) is a comprehensive rapid application development framework for structural bioinformatics. It provides an extensive C++ class library of data structures and algorithms for molecular modeling and structural bioinformatics. Using BALL as a programming toolbox does not only allow to greatly reduce application development times but also helps in ensuring stability and correctness by avoiding the error-prone reimplementation of complex algorithms and replacing them with calls into the library that has been well-tested by a large number of developers. In the ten years since its original publication, BALL has seen a substantial increase in functionality and numerous other improvements.

Results: Here, we discuss BALL's current functionality and highlight the key additions and improvements: support for additional file formats, molecular edit-functionality, new molecular mechanics force fields, novel energy minimization techniques, docking algorithms, and support for cheminformatics.

Conclusions: BALL is available for all major operating systems, including Linux, Windows, and MacOS X. It is available free of charge under the Lesser GNU Public License (LPGL). Parts of the code are distributed under the GNU Public License (GPL). BALL is available as source code and binary packages from the project web site at http://www.ball-project.org. Recently, it has been accepted into the debian project; integration into further distributions is currently pursued.

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Overview of the structure of BALL. The diagram shows the general layout of the structure of BALL, where every box symbolizes one library or fundamental layer.
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Figure 1: Overview of the structure of BALL. The diagram shows the general layout of the structure of BALL, where every box symbolizes one library or fundamental layer.

Mentions: Several frameworks for structural bioinformatics have been reported in the literature; most of them, however, with a different focus, scope, or intended audience. Hence, comparison with these projects is difficult in general. Among those projects, the most similar in scope and functionality are commercial packages like the suites from Schrödinger [15] or the Chemical Computing Group's Molecular Operating Environment (MOE) [16]. While these packages typically focus on sophisticated graphical user interfaces for concrete modelling tasks, they also provide powerful scripting interfaces aimed at developers. Notable open source projects in the field include Biopython [17], PyMOL [18] (which provides extensive scripting functionality apart from the molecular viewer), CDK [19], MESHI [20], JOELib [21], the EGAD Library [22], and StrBioLib [23]. To the best of our knowledge, BALL offers the widest range of functionality for rapidly and robustly developing applications in structural bioinformatics, it is growing fast and can be easily extended. It addresses users of the implemented techniques as well as designers of completely new approaches. An overview of BALL's design can be found in Figure 1.


BALL--biochemical algorithms library 1.3.

Hildebrandt A, Dehof AK, Rurainski A, Bertsch A, Schumann M, Toussaint NC, Moll A, Stöckel D, Nickels S, Mueller SC, Lenhof HP, Kohlbacher O - BMC Bioinformatics (2010)

Overview of the structure of BALL. The diagram shows the general layout of the structure of BALL, where every box symbolizes one library or fundamental layer.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2984589&req=5

Figure 1: Overview of the structure of BALL. The diagram shows the general layout of the structure of BALL, where every box symbolizes one library or fundamental layer.
Mentions: Several frameworks for structural bioinformatics have been reported in the literature; most of them, however, with a different focus, scope, or intended audience. Hence, comparison with these projects is difficult in general. Among those projects, the most similar in scope and functionality are commercial packages like the suites from Schrödinger [15] or the Chemical Computing Group's Molecular Operating Environment (MOE) [16]. While these packages typically focus on sophisticated graphical user interfaces for concrete modelling tasks, they also provide powerful scripting interfaces aimed at developers. Notable open source projects in the field include Biopython [17], PyMOL [18] (which provides extensive scripting functionality apart from the molecular viewer), CDK [19], MESHI [20], JOELib [21], the EGAD Library [22], and StrBioLib [23]. To the best of our knowledge, BALL offers the widest range of functionality for rapidly and robustly developing applications in structural bioinformatics, it is growing fast and can be easily extended. It addresses users of the implemented techniques as well as designers of completely new approaches. An overview of BALL's design can be found in Figure 1.

Bottom Line: Here, we discuss BALL's current functionality and highlight the key additions and improvements: support for additional file formats, molecular edit-functionality, new molecular mechanics force fields, novel energy minimization techniques, docking algorithms, and support for cheminformatics.It is available free of charge under the Lesser GNU Public License (LPGL).Parts of the code are distributed under the GNU Public License (GPL).

View Article: PubMed Central - HTML - PubMed

Affiliation: Center for Bioinformatics Saar, Saarland University, Saarbrücken, Germany. anhi@bioinf.uni-sb.de

ABSTRACT

Background: The Biochemical Algorithms Library (BALL) is a comprehensive rapid application development framework for structural bioinformatics. It provides an extensive C++ class library of data structures and algorithms for molecular modeling and structural bioinformatics. Using BALL as a programming toolbox does not only allow to greatly reduce application development times but also helps in ensuring stability and correctness by avoiding the error-prone reimplementation of complex algorithms and replacing them with calls into the library that has been well-tested by a large number of developers. In the ten years since its original publication, BALL has seen a substantial increase in functionality and numerous other improvements.

Results: Here, we discuss BALL's current functionality and highlight the key additions and improvements: support for additional file formats, molecular edit-functionality, new molecular mechanics force fields, novel energy minimization techniques, docking algorithms, and support for cheminformatics.

Conclusions: BALL is available for all major operating systems, including Linux, Windows, and MacOS X. It is available free of charge under the Lesser GNU Public License (LPGL). Parts of the code are distributed under the GNU Public License (GPL). BALL is available as source code and binary packages from the project web site at http://www.ball-project.org. Recently, it has been accepted into the debian project; integration into further distributions is currently pursued.

Show MeSH
Related in: MedlinePlus