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Publications

Publications from the Kohlbacher lab, sorted by year and author.

2003

[21] Hildebrandt, A, Kohlbacher, O, Blossey, R, and Lenhof, H (2003).
Using nonlocal electrostatics for solvation free energy computations: ions and small molecules
Preprint at ArXiv.

[20] Sandelin, A, Höglund, A, Lenhard, B, and Wasserman, W (2003).
Integrated analysis of yeast regulatory sequences for biologically linked clusters of genes
Funct Integr Genomics, 3(3):125-134.

2002

[19] Althaus, E, Kohlbacher, O, Lenhof, HP, and Müller, P (2002).
A Combinatorial Approach to Protein Docking with Flexible Side-Chains
J. Comput. Biol., 9(4):597-612.

[18] Dönnes, P and Elofsson, A (2002).
Prediction of MHC class I binding peptides, using SVMHC
BMC Bioinformatics, 3(25).

[17] Neumann, D, Kerzmann, A, and Kohlbacher, O (2002).
Modelling the sugar-lectin interaction by computer simulated docking
In: Abstracts of the 20th Interlec Meeting, ed. by Bog-Hansen, Torkhild, pp. 116, University of Copenhagen, Copenhagen, Denmark.

[16] Neumann, D, Kohlbacher, O, Lenhof, H, and Lehr, C (2002).
Protein-sugar interactions: Calculated versus experimental binding energies
Eur. J. Biochem., 269(5):1518-1524.

[15] Sirava, M, Schäfer, T, Eiglsperger, M, Kaufmann, M, Kohlbacher, O, Bornberg-Bauer, E, and Lenhof, H (2002).
BioMiner - modeling, analysing, and visualizing biochemical pathways and networks
Bioinformatics, 19(10):S219-230.

2001

[14] Kohlbacher, O (2001).
BALL - A Framework for Rapid Application Development in Molecular Modeling
In: Beiträge zum Heinz-Billing-Preis 2000, pp. 13-28, Gesellschaft für wissenschaftliche Datenverarbeitung mbH, Göttingen.

[13] Kohlbacher, O, Burchardt, A, Hildebrandt, A, Moll, A, Bayer, P, and Lenhof, H (2001).
A NMR-spectra-based scoring function for protein docking
In: RECOMB 2001, Proceedings of the Fifth Annual International Conference on Computational Molecular Biology, ed. by David Sankoff and Thomas Lengauer, pp. 169-177, ACM press.

[12] Kohlbacher, O, Burchardt, A, Moll, A, Hildebrandt, A, Bayer, P, and Lenhof, H (2001).
Structure prediction of protein complexes by a NMR-based protein docking algorithm
J. Biomol. NMR, 20:15-21.

[11] Turner, RJ, Chaturvedi, K, Edwards, NJ, Fasulo, D, Halpern, AL, Huson, DH, Remington, KA, Schwartz, R, Walenz, B, Yooseph, S, and Istrail, S (2001).
Visualization Challenges for a New Cyberpharmaceutical Computing Paradigm
In: Proceedings of the IEEE Symposium on Parallel and Large-Data Visualization and Graphics (PVG2001), pp. 7–18, San Diego, USA,.

2000

[10] Althaus, E, Kohlbacher, O, Lenhof, H, and Müller, P (2000).
A Combinatorial Approach to Protein Docking with Flexible Side-Chains
In: RECOMB 2000 – Proceedings of the Fourth Annual International Conference on Computational Molecular Biology, ed. by Ron Shamir and Satoru Miyano and Sorin Istrail and Pavel Pevzner and Michael Waterman, pp. 15–24, ACM press.

[9] Althaus, E, Kohlbacher, O, Lenhof, H, and Müller, P (2000).
A branch and cut algorithm for the optimal solution of the side-chain placement problem
Max-Planck-Institute für Informatik, Stuhlsatzenhausweg 85, 66123 Saarbrücken, Germany.

[8] Boghossian, NP, Kohlbacher, O, and Lenhof, HP (2000).
Rapid software prototyping in molecular modeling using the biochemical algorithms library (BALL)
J. Exp. Algorithmics, 5:16.

[7] Kohlbacher, O and Lenhof, H (2000).
BALL - Rapid Software Prototyping in Computational Molecular Biology
Bioinformatics, 16(9,):815–824.

[6] Neumann, D, Kohlbacher, O, Haltner, E, Lenhof, H, and Lehr, C (2000).
Modeling the Sugar Lectin Interaction by Computational Chemistry Relevant to Drug Design
In: Proc. 3rd World Meeting on Pharmaceutics, Biopharmaceutics and Pharmaceutical Technology, pp. 233.

1999

[5] Adams, CS, Davies, HJ, and Nilse, L (1999).
Synchronous Tuning of Extended Cavity Lasers: The Case for an Optimum Pivot Point
Appl. Opt., 38(3):548-553.

[4] Boghossian, NP, Kohlbacher, O, and Lenhof, H (1999).
BALL: Biochemical Algorithms Library
In: Algorithm Engineering, 3rd International Workshop, WAE'99, Proceedings, ed. by Vitter, J.S. and Zaroliagis, C.D., pp. 330-344, Springer.

[3] Boghossian, NP, Kohlbacher, O, and Lenhof, H (1999).
BALL: Biochemical Algorithms Library
Max-Planck-Institut für Informatik, Saarbrücken, Germany.

[2] Kohlbacher, O and Lenhof, H (1999).
Rapid Software Prototyping in Computational Molecular Biology
In: Proceedings of the German Conference on Bioinformatics (GCB'99).

1998

[1] Neumann, D, Haltner, E, Lehr, C, Kohlbacher, O, and Lenhof, H (1998).
Investigating the Sugar-Lectin Interaction by Computational Chemistry: Tunneling the Epithelial Barrier
In: Abstracts of the 18th Interlec Meeting, pp. 549.