Publications

  • A. K. Hildebrandt, D. Stöckel, N. Fischer, L. de la Garza Trevino, J. Krüger, S. Nickels, M. Röttig, C. Schärfe, M. Schumann, P. Thiel, H. Lenhof, O. Kohlbacher, and A. Hildebrandt, "Ballaxy: web services for structural bioinformatics," Bioinformatics, vol. 31, iss. 1, pp. 121-2, 2015.
    [Bibtex]
    @Article{BALLaxyBioinfo,
    author = {Hildebrandt, Anna Katharina and Stöckel, Daniel and Fischer, Nina and de la Garza Trevino, Luis and Krüger, Jens and Nickels, Stefan and Röttig, Marc and Schärfe, Charlotta and Schumann, Marcel and Thiel, Philipp and Lenhof, Hans-Peter and Kohlbacher, Oliver and Hildebrandt, Andreas},
    title = {ballaxy: web services for structural bioinformatics},
    year = {2015},
    abstract = {MOTIVATION: Web-based workflow systems have gained considerable momentum in sequence-oriented bioinformatics. In structural bioinformatics, however, such systems are still relatively rare: while commercial stand-alone workflow applications are common in the pharmaceutical industry, academic researchers often still rely on command-line scripting to glue individual tools together. RESULTS: In this work, we address the problem of building a web-based system for workflows in structural bioinformatics. For the underlying molecular modelling engine, we opted for the BALL framework (Hildebrandt et al., 2010) due to its extensive and well tested functionality in the field of structural bioinformatics. The large number of molecular data structures and algorithms implemented in BALL allows for elegant and sophisticated development of new approaches in the field. We hence connected the versatile BALL library and its visualization and editing frontend BALLView with the Galaxy workflow framework. The result, which we call ballaxy, enables the user to simply and intuitively create sophisticated pipelines for applications in structure-based computational biology, integrated into a standard tool for molecular modelling. AVAILABILITY: ballaxy consists of three parts: some minor modifications to the Galaxy system, a collection of tools, and an integration into the BALL-framework and the BALLView application for molecular modelling. Modifications to Galaxy will be submitted to the Galaxy project, and the BALL and BALLView integrations will be integrated in the next major BALL release. After acceptance of the modifications into the Galaxy project, we will publish all ballaxy tools via the Galaxy toolshed. In the meantime, all three components are available from http://www.ball-project.org/ballaxy. Ballaxy is licensed under the terms of the GPL.},
    journal = {Bioinformatics},
    volume = {31},
    number = {1},
    pages = {121-2},
    url = {http://dx.doi.org/10.1093/bioinformatics/btu574},
    pmid = {25183489}
    }
  • A. Hildebrandt, A. K. Dehof, A. Rurainski, A. Bertsch, M. Schumann, N. C. Toussaint, A. Moll, D. Stöckel, S. Nickels, S. C. Mueller, H. Lenhof, and O. Kohlbacher, "BALL--biochemical algorithms library 1.3.," Bmc bioinformatics, vol. 11, iss. 1, p. 531, 2010.
    [Bibtex]
    @article{Hildebrandt2010,
    abstract = {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.},
    author = {Hildebrandt, Andreas and Dehof, Anna Katharina and Rurainski, Alexander and Bertsch, Andreas and Schumann, Marcel and Toussaint, Nora C and Moll, Andreas and St\"{o}ckel, Daniel and Nickels, Stefan and Mueller, Sabine C and Lenhof, Hans-Peter and Kohlbacher, Oliver},
    file = {:Users/thiel/Library/Application Support/Mendeley Desktop/Downloaded/Hildebrandt et al. - 2010 - BALL--biochemical algorithms library 1.3.pdf:pdf},
    issn = {1471-2105},
    journal = {BMC bioinformatics},
    keywords = {Algorithms,BALL,Computational Biology,Computational Biology: methods,Databases, Factual,Software},
    mendeley-tags = {BALL},
    month = jan,
    number = {1},
    pages = {531},
    title = {{BALL--biochemical algorithms library 1.3.}},
    url = {http://www.biomedcentral.com/1471-2105/11/531},
    volume = {11},
    year = {2010}
    }
  • [DOI] A. Kerzmann, J. Fuhrmann, O. Kohlbacher, and D. Neumann, "BALLDock/SLICK: a new method for protein-carbohydrate docking.," Journal of chemical information and modeling, vol. 48, iss. 8, pp. 1616-25, 2008.
    [Bibtex]
    @article{Kerzmann2008,
    abstract = {Protein-ligand docking is an essential technique in computer-aided drug design. While generally available docking programs work well for most drug classes, carbohydrates and carbohydrate-like compounds are often problematic for docking. We present a new docking method specifically designed to handle docking of carbohydrate-like compounds. BALLDock/SLICK combines an evolutionary docking algorithm for flexible ligands and flexible receptor side chains with carbohydrate-specific scoring and energy functions. The scoring function has been designed to identify accurate ligand poses, while the energy function yields accurate estimates of the binding free energies of these poses. On a test set of known protein-sugar complexes we demonstrate the ability of the approach to generate correct poses for almost all of the structures and achieve very low mean errors for the predicted binding free energies.},
    author = {Kerzmann, Andreas and Fuhrmann, Jan and Kohlbacher, Oliver and Neumann, Dirk},
    doi = {10.1021/ci800103u},
    issn = {1549-9596},
    journal = {Journal of Chemical Information and Modeling},
    keywords = {Algorithms,Binding Sites,Calibration,Carbohydrate Metabolism,Carbohydrates,Carbohydrates: chemistry,Computational Biology,Computational Biology: methods,Dimerization,Models, Molecular,Protein Binding,Protein Structure, Tertiary,Proteins,Proteins: chemistry,Proteins: metabolism,SLICK,Scoring,Software Design},
    mendeley-tags = {SLICK,Scoring},
    month = aug,
    number = {8},
    pages = {1616--25},
    pmid = {18646839},
    publisher = {American Chemical Society},
    title = {{BALLDock/SLICK: a new method for protein-carbohydrate docking.}},
    url = {http://dx.doi.org/10.1021/ci800103u},
    volume = {48},
    year = {2008}
    }
  • O. Kohlbacher and H. P. Lenhof, "BALL--rapid software prototyping in computational molecular biology. Biochemicals Algorithms Library.," Bioinformatics (oxford), vol. 16, iss. 9, pp. 815-24, 2000.
    [Bibtex]
    @article{Kohlbacher2000,
    abstract = {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.},
    author = {Kohlbacher, O and Lenhof, H P},
    issn = {1367-4803},
    journal = {Bioinformatics (Oxford)},
    keywords = {Algorithms,BALL,Computational Biology,Computational Biology: methods,Computer Simulation,Computer Simulation: standards,Databases,Factual,Internet,Protein Binding,Protein Structure,Software,Software Validation,Software: standards,Tertiary,Time Factors,User-Computer Interface},
    mendeley-tags = {BALL},
    month = sep,
    number = {9},
    pages = {815--24},
    pmid = {11108704},
    title = {{BALL--rapid software prototyping in computational molecular biology. Biochemicals Algorithms Library.}},
    url = {http://www.ncbi.nlm.nih.gov/pubmed/11108704},
    volume = {16},
    year = {2000}
    }
  • [DOI] A. Moll, A. Hildebrandt, H. Lenhof, and O. Kohlbacher, "BALLView: an object-oriented molecular visualization and modeling framework.," Journal of computer-aided molecular design, vol. 19, iss. 11, pp. 791-800, 2005.
    [Bibtex]
    @article{Moll2005,
    abstract = {We present BALLView, an extensible tool for visualizing and modeling bio-molecular structures. It provides a variety of different models for bio-molecular visualization, e.g. ball-and-stick models, molecular surfaces, or ribbon models. In contrast to most existing visualization tools, BALLView also offers rich functionality for molecular modeling and simulation, including molecular mechanics methods (AMBER and CHARMM force fields), continuum electrostatics methods employing a Finite-Difference Poisson Boltzmann solver, and secondary structure calculation. Results of these computations can be exported as publication quality images or as movies. Even unexperienced users have direct access to this functionality through an intuitive graphical user interface, which makes BALLView particularly useful for teaching. For more advanced users, BALLView is extensible in different ways. Owing to its framework design, extension on the level of C per thousand+ per thousand per thousand+ code is very convenient. In addition, an interface to the scripting language Python allows the interactive rapid prototyping of new methods. BALLView is portable and runs on all major platforms (Windows, MacOS X, Linux, most Unix flavors). It is available free of charge under the GNU Public License (GPL) from our website http://www.ballview.org.},
    author = {Moll, Andreas and Hildebrandt, Andreas and Lenhof, Hans-Peter and Kohlbacher, Oliver},
    doi = {10.1007/s10822-005-9027-x},
    issn = {0920-654X},
    journal = {Journal of Computer-Aided Molecular Design},
    keywords = {Computer Graphics,Computer Simulation,Models,Molecular,Software,Static Electricity,Thermodynamics},
    month = nov,
    number = {11},
    pages = {791--800},
    pmid = {16470421},
    title = {{BALLView: an object-oriented molecular visualization and modeling framework.}},
    url = {http://www.ncbi.nlm.nih.gov/pubmed/16470421},
    volume = {19},
    year = {2005}
    }
  • [DOI] A. Moll, A. Hildebrandt, H. Lenhof, and O. Kohlbacher, "BALLView: a tool for research and education in molecular modeling.," Bioinformatics (oxford, england), vol. 22, iss. 3, pp. 365-6, 2006.
    [Bibtex]
    @article{Moll2006,
    abstract = {We present BALLView, a molecular viewer and modeling tool. It combines state-of-the-art visualization capabilities with powerful modeling functionality including implementations of force field methods and continuum electrostatics models. BALLView is a versatile and extensible tool for research in structural bioinformatics and molecular modeling. Furthermore, the convenient and intuitive graphical user interface offers novice users direct access to the full functionality, rendering it ideal for teaching. Through an interface to the object-oriented scripting language Python it is easily extensible.},
    author = {Moll, Andreas and Hildebrandt, Andreas and Lenhof, Hans-Peter and Kohlbacher, Oliver},
    doi = {10.1093/bioinformatics/bti818},
    file = {:Users/thiel/Library/Application Support/Mendeley Desktop/Downloaded/Moll et al. - 2006 - BALLView a tool for research and education in molecular modeling.pdf:pdf},
    issn = {1367-4803},
    journal = {Bioinformatics (Oxford, England)},
    keywords = {BALL,Computer Graphics,Computer Simulation,Computer-Assisted Instruction,Computer-Assisted Instruction: methods,Models, Molecular,Molecular Biology,Molecular Biology: education,Molecular Biology: methods,Research Design,Software,User-Computer Interface},
    mendeley-tags = {BALL},
    month = {feb},
    number = {3},
    pages = {365--6},
    pmid = {16332707},
    title = {{BALLView: a tool for research and education in molecular modeling.}},
    url = {http://bioinformatics.oxfordjournals.org/content/22/3/365.abstract},
    volume = {22},
    year = {2006}
    }
  • [DOI] P. Thiel, L. Peltason, C. Ottmann, and O. Kohlbacher, "Deterministic clustering of the available chemical space," Journal of cheminformatics, vol. 5, iss. Suppl 1, p. P53, 2013.
    [Bibtex]
    @article{Thiel2013a,
    author = {Thiel, Philipp and Peltason, Lisa and Ottmann, Christian and Kohlbacher, Oliver},
    doi = {10.1186/1758-2946-5-S1-P53},
    file = {:Users/thiel/Library/Application Support/Mendeley Desktop/Downloaded/Thiel et al. - 2013 - Deterministic clustering of the available chemical space.pdf:pdf},
    issn = {1758-2946},
    journal = {Journal of Cheminformatics},
    keywords = {Clustering},
    mendeley-tags = {Clustering},
    number = {Suppl 1},
    pages = {P53},
    title = {{Deterministic clustering of the available chemical space}},
    url = {http://www.jcheminf.com/content/5/S1/P53},
    volume = {5},
    year = {2013}
    }
  • [DOI] P. Thiel, L. Sach-Peltason, C. Ottmann, and O. Kohlbacher, "Blocked Inverted Indices for Exact Clustering of Large Chemical Spaces.," Journal of chemical information and modeling, vol. 54, pp. 2395-2401, 2014.
    [Bibtex]
    @article{Thiel2014,
    abstract = {The calculation of pairwise compound similarities based on fingerprints is one of the fundamental tasks in chemoinformatics. Methods for efficient calculation of compound similarities are of utmost importance for various applications like similarity searching or library clustering. With the increasing size of public compound databases, exact clustering of these databases is desirable, but often computationally prohibitively expensive. We present an optimized inverted index algorithm for the calculation of all pairwise similarities on 2D fingerprints of a given dataset. In contrast to other algorithms it does neither require GPU computing, nor does it yield a stochastic approximation of the clustering. The algorithm has been designed to work well with multicore architectures and shows excellent parallel speedup. As an application example of this algorithm we implemented a deterministic clustering application, which has been designed to decompose virtual libraries comprising tens of millions of compounds in a short time on current hardware. Our results show, that our implementation achieves more than 400 million Tanimoto similarity calculations per second on a common desktop CPU. Deterministic clustering of the available chemical space thus can be done on modern multicore machines within a few days.},
    author = {Thiel, Philipp and Sach-Peltason, Lisa and Ottmann, Christian and Kohlbacher, Oliver},
    doi = {10.1021/ci500150t},
    file = {:Users/thiel/Documents/Articles/thiel\_2014\_jcim.pdf:pdf},
    issn = {1549-960X},
    journal = {Journal of Chemical Information and Modeling},
    keywords = {MyPub},
    mendeley-tags = {MyPub},
    month = aug,
    pages = {2395--2401},
    pmid = {25136755},
    publisher = {American Chemical Society},
    title = {{Blocked Inverted Indices for Exact Clustering of Large Chemical Spaces.}},
    url = {http://dx.doi.org/10.1021/ci500150t},
    volume = {54},
    year = {2014}
    }