Publications
Mitschke, Jan; Fuss, Janina; Blum, Torsten; Höglund, Annette; Reski, Ralf; Kohlbacher, Oliver; Rensing, Stefan Prediction of dual protein targeting to plant organelles Proceedings of the German Conference on Bioinformatics (GCB 2007), 2007. (BibTeX) @inproceedings{copy_of_ATP, title = {Prediction of dual protein targeting to plant organelles}, author = {Jan Mitschke and Janina Fuss and Torsten Blum and Annette Höglund and Ralf Reski and Oliver Kohlbacher and Stefan Rensing}, year = {2007}, date = {2007-01-01}, publisher = {Proceedings of the German Conference on Bioinformatics (GCB 2007)}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Steffen, Andreas; Thiele, Carolin; Tietze, Simon; Strassnig, Christian; Kämper, Andreas; Lengauer, Thomas; Wenz, Gerhard; Apostolakis, Joannis Improved cyclodextrin-based receptors for camptothecin by inverse virtual screening Chem. Eur. J., 13 (24), pp. 6801-6809, 2007. @article{camptothecin, title = {Improved cyclodextrin-based receptors for camptothecin by inverse virtual screening}, author = {Andreas Steffen and Carolin Thiele and Simon Tietze and Christian Strassnig and Andreas Kämper and Thomas Lengauer and Gerhard Wenz and Joannis Apostolakis}, url = {http://dx.doi.org/10.1002/chem.200700661}, year = {2007}, date = {2007-01-01}, journal = {Chem. Eur. J.}, volume = {13}, number = {24}, pages = {6801-6809}, abstract = {We report the computer-aided optimization of a synthetic receptor for a given guest molecule, based on inverse virtual screening of receptor libraries. As an example, a virtual set of beta-cyclodextrin (beta-CD) derivatives was generated as receptor candidates for the anticancer drug camptothecin. We applied the two docking tools AutoDock and GlamDock to generate camptothecin complexes of every candidate receptor. Scoring functions were used to rank all generated complexes. From the 10 % top-ranking candidates nine were selected for experimental validation. They were synthesized by reaction of heptakis-[6-deoxy-6-iodo]-beta-CD with a thiol compound to form the hepta-substituted beta-CDs. The stabilities of the camptothecin complexes obtained from solubility measurements of five of the nine CD derivatives were significantly higher than for any other CD derivative known from literature. The remaining four CD derivatives were insoluble in water. In addition, corresponding mono-substituted CD derivatives were synthesized that also showed improved binding constants. Among them the 9-H-purine derivative was the best, being comparable to the investigated hepta-substituted beta-CDs. Since the measured binding free energies correlated satisfactorily with the calculated scores, the applied scoring functions appeared to be appropriate for the selection of promising candidates for receptor synthesis.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We report the computer-aided optimization of a synthetic receptor for a given guest molecule, based on inverse virtual screening of receptor libraries. As an example, a virtual set of beta-cyclodextrin (beta-CD) derivatives was generated as receptor candidates for the anticancer drug camptothecin. We applied the two docking tools AutoDock and GlamDock to generate camptothecin complexes of every candidate receptor. Scoring functions were used to rank all generated complexes. From the 10 % top-ranking candidates nine were selected for experimental validation. They were synthesized by reaction of heptakis-[6-deoxy-6-iodo]-beta-CD with a thiol compound to form the hepta-substituted beta-CDs. The stabilities of the camptothecin complexes obtained from solubility measurements of five of the nine CD derivatives were significantly higher than for any other CD derivative known from literature. The remaining four CD derivatives were insoluble in water. In addition, corresponding mono-substituted CD derivatives were synthesized that also showed improved binding constants. Among them the 9-H-purine derivative was the best, being comparable to the investigated hepta-substituted beta-CDs. Since the measured binding free energies correlated satisfactorily with the calculated scores, the applied scoring functions appeared to be appropriate for the selection of promising candidates for receptor synthesis. |
Steffen, Andreas; Karasz, Maximilian; Thiele, Carolin; Lengauer, Thomas; Kämper, Andreas; Wenz, Gerhard; Apostolakis, Joannis Combined similarity and QSPR virtual screening for guest molecules of beta-cyclodextrin New J. Chem., 31 (11), pp. 1941-1949, 2007. @article{cdguests, title = {Combined similarity and QSPR virtual screening for guest molecules of beta-cyclodextrin}, author = {Andreas Steffen and Maximilian Karasz and Carolin Thiele and Thomas Lengauer and Andreas Kämper and Gerhard Wenz and Joannis Apostolakis}, url = {http://dx.doi.org/10.1039/b707856k}, year = {2007}, date = {2007-01-01}, journal = {New J. Chem.}, volume = {31}, number = {11}, pages = {1941-1949}, abstract = {We describe a similarity-based screening approach combined with a quantitative prediction of affinity based on physicochemical descriptors, for the efficient identification of new, high affinity guest molecules of beta-cyclodextrin (beta-CD). Four known beta-CD guest molecules were chosen as query molecules. A subset of the ZINC database with 117 695 molecular entries served as the screening library. For each query the 150 most similar molecules were identified by virtual screening against this library with a graph-based similarity algorithm. Subsequently these molecules were scored by means of a QSPR model. The best-scoring, commercially available molecules were selected for experimental verification (14 in total). Binding free energies were determined by isothermal microcalorimetry (ITC). For three of the four queries, at least one ligand with a higher binding affinity than the corresponding query was found. The approach is a promising high throughput alternative to structure-based virtual screening. While beta-CD was chosen as a test case because of its technical relevance and the availability of many binding data, the applied methodology is transferable to other host–guest systems.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We describe a similarity-based screening approach combined with a quantitative prediction of affinity based on physicochemical descriptors, for the efficient identification of new, high affinity guest molecules of beta-cyclodextrin (beta-CD). Four known beta-CD guest molecules were chosen as query molecules. A subset of the ZINC database with 117 695 molecular entries served as the screening library. For each query the 150 most similar molecules were identified by virtual screening against this library with a graph-based similarity algorithm. Subsequently these molecules were scored by means of a QSPR model. The best-scoring, commercially available molecules were selected for experimental verification (14 in total). Binding free energies were determined by isothermal microcalorimetry (ITC). For three of the four queries, at least one ligand with a higher binding affinity than the corresponding query was found. The approach is a promising high throughput alternative to structure-based virtual screening. While beta-CD was chosen as a test case because of its technical relevance and the availability of many binding data, the applied methodology is transferable to other host–guest systems. |
Neumann, Dirk; Kohlbacher, Oliver; Merkwirth, Christian; Lengauer, Thomas A fully computational model for predicting percutaneous drug absorption J. Chem. Inf. Model., 46 (1), pp. 424–429, 2006. @article{PercutaneousAbs, title = {A fully computational model for predicting percutaneous drug absorption}, author = {Dirk Neumann and Oliver Kohlbacher and Christian Merkwirth and Thomas Lengauer}, url = {http://pubs.acs.org/cgi-bin/sample.cgi/jcisd8/2006/46/i01/abs/ci050332t.html}, year = {2006}, date = {2006-01-01}, journal = {J. Chem. Inf. Model.}, volume = {46}, number = {1}, pages = {424--429}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Moll, Andreas; Hildebrandt, Andreas; Lenhof, Hans-Peter; Kohlbacher, Oliver BALLView: A tool for research and education in molecular modeling Bioinformatics, 22 (3), pp. 365–366, 2006. @article{BALLView, title = {BALLView: A tool for research and education in molecular modeling}, author = {Andreas Moll and Andreas Hildebrandt and Hans-Peter Lenhof and Oliver Kohlbacher}, url = {http://bioinformatics.oxfordjournals.org/cgi/reprint/bti818v1}, year = {2006}, date = {2006-01-01}, journal = {Bioinformatics}, volume = {22}, number = {3}, pages = {365--366}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Baldes, Christiane; König, Petra; Neumann, Dirk; Lenhof, Hans-Peter; Kohlbacher, Oliver; Lehr, Claus-Michael Development of a fluorescence-based assay for screening of modulators of human Organic Anion Transporter 1B3 (OATP1B3) Eur J Pharm Biopharm., 62 (1), pp. 39–43, 2006. @article{OATP13, title = {Development of a fluorescence-based assay for screening of modulators of human Organic Anion Transporter 1B3 (OATP1B3)}, author = {Christiane Baldes and Petra König and Dirk Neumann and Hans-Peter Lenhof and Oliver Kohlbacher and Claus-Michael Lehr}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16129589&query_hl=1}, year = {2006}, date = {2006-01-01}, journal = {Eur J Pharm Biopharm.}, volume = {62}, number = {1}, pages = {39--43}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Lange, Eva; Gröpl, Clemens; Reinert, Knut; Kohlbacher, Oliver; Hildebrandt, Andreas High-Accuracy Peak Picking of Proteomics Data using Wavelet Techniques Proceedings of the Pacific Symposium on Biocomputing (PSB 2006), 2006. @inproceedings{PSB2006_Peaks, title = {High-Accuracy Peak Picking of Proteomics Data using Wavelet Techniques}, author = {Eva Lange and Clemens Gröpl and Knut Reinert and Oliver Kohlbacher and Andreas Hildebrandt}, url = {http://helix-web.stanford.edu/psb06/lange.pdf}, year = {2006}, date = {2006-01-01}, booktitle = {Proceedings of the Pacific Symposium on Biocomputing (PSB 2006)}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Mayr, Bettina; Kohlbacher, Oliver; Reinert, Knut; Sturm, Marc; Gröpl, Clemens; Lange, Eva; Klein, Christoph; Huber, Christian G Absolute Myoglobin Quantitation in Serum by Combining Two-Dimensional Liquid Chromatography-Electrospray Ionization Mass Spectrometry and Novel Data Analysis Algorithms J. Proteome Res., 5 , pp. 414–421, 2006. @article{MyoExptl, title = {Absolute Myoglobin Quantitation in Serum by Combining Two-Dimensional Liquid Chromatography-Electrospray Ionization Mass Spectrometry and Novel Data Analysis Algorithms}, author = {Bettina Mayr and Oliver Kohlbacher and Knut Reinert and Marc Sturm and Clemens Gröpl and Eva Lange and Christoph Klein and Christian G Huber}, url = {http://dx.doi.org/10.1021/pr050344u}, year = {2006}, date = {2006-01-01}, journal = {J. Proteome Res.}, volume = {5}, pages = {414--421}, abstract = {To measure myoglobin, a marker for myocardial infarction, directly in human serum, two-dimensional liquid chromatography in combination with electrospray ionization mass spectrometry was applied as an analytical method. High-abundant serum proteins were depleted by strong anion-exchange chromatography. The myoglobin fraction was digested and injected onto a 60 mm × 0.2 mm i.d. monolithic capillary column for quantitation of selected peptides upon mass spectrometric detection. The addition of known amounts of myoglobin to the serum sample was utilized for calibration, and horse myoglobin was added as an internal standard to improve reproducibility. Calibration graphs were linear and facilitated the reproducible and accurate determination of the myoglobin amount present in serum. Manual data evaluation using integrated peak areas and an automated multistage algorithm fitting two-dimensional models of peptide elution profiles and isotope patterns to the mass spectrometric raw data were compared. When the automated method was applied, a myoglobin concentration of 460 pg/μL serum was determined with a maximum relative deviation from the theoretical value of 10.1% and a maximum relative standard deviation of 13.4%.}, keywords = {}, pubstate = {published}, tppubtype = {article} } To measure myoglobin, a marker for myocardial infarction, directly in human serum, two-dimensional liquid chromatography in combination with electrospray ionization mass spectrometry was applied as an analytical method. High-abundant serum proteins were depleted by strong anion-exchange chromatography. The myoglobin fraction was digested and injected onto a 60 mm × 0.2 mm i.d. monolithic capillary column for quantitation of selected peptides upon mass spectrometric detection. The addition of known amounts of myoglobin to the serum sample was utilized for calibration, and horse myoglobin was added as an internal standard to improve reproducibility. Calibration graphs were linear and facilitated the reproducible and accurate determination of the myoglobin amount present in serum. Manual data evaluation using integrated peak areas and an automated multistage algorithm fitting two-dimensional models of peptide elution profiles and isotope patterns to the mass spectrometric raw data were compared. When the automated method was applied, a myoglobin concentration of 460 pg/μL serum was determined with a maximum relative deviation from the theoretical value of 10.1% and a maximum relative standard deviation of 13.4%. |
Moll, Andreas; Hildebrandt, Andreas; Lenhof, Hans-Peter; Kohlbacher, Oliver BALLView: An object-oriented molecular visualization and modeling framework J. Comput.-Aided Mol. Des., 19 (11), pp. 791, 2006. @article{BV.JCAMD, title = {BALLView: An object-oriented molecular visualization and modeling framework}, author = {Andreas Moll and Andreas Hildebrandt and Hans-Peter Lenhof and Oliver Kohlbacher}, url = {http://dx.doi.org/10.1007/s10822-005-9027-x}, year = {2006}, date = {2006-01-01}, journal = {J. Comput.-Aided Mol. Des.}, volume = {19}, number = {11}, pages = {791}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Sturm, Marc; Quinten, Sascha; Huber, Christian G; Kohlbacher, Oliver A machine learning approach for prediction of DNA and peptide retention times Huber, Christian; Kohlbacher, Oliver; Reinert, Knut (Ed.): Proceedings of the Dagstuhl Seminar on Computational Proteomics 2005, Internationales Begegnungs- und Forschungszentrum (IBFI), Schloss Dagstuhl, Germany, 2006. @inproceedings{DNA-RT-Dagstuhl-2006, title = {A machine learning approach for prediction of DNA and peptide retention times}, author = {Marc Sturm and Sascha Quinten and Christian G Huber and Oliver Kohlbacher}, editor = {Christian Huber and Oliver Kohlbacher and Knut Reinert}, url = {http://drops.dagstuhl.de/opus/volltexte/2006/548}, year = {2006}, date = {2006-01-01}, booktitle = {Proceedings of the Dagstuhl Seminar on Computational Proteomics 2005}, publisher = {Internationales Begegnungs- und Forschungszentrum (IBFI), Schloss Dagstuhl, Germany}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Kerzmann, Andreas; Neumann, Dirk; Kohlbacher, Oliver SLICK - Scoring and Energy Functions for Protein-Carbohydrate Interactions J. Chem. Inf. Model., 46 , pp. 1635-1642, 2006. @article{SLICK, title = {SLICK - Scoring and Energy Functions for Protein-Carbohydrate Interactions}, author = {Andreas Kerzmann and Dirk Neumann and Oliver Kohlbacher}, url = {http://dx.doi.org/10.1021/ci050422y}, year = {2006}, date = {2006-01-01}, journal = {J. Chem. Inf. Model.}, volume = {46}, pages = {1635-1642}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Küntzer, Jan; Blum, Torsten; Gerasch, Andreas; Backes, Christina; Hildebrandt, Andreas; Kaufmann, Michael; Kohlbacher, Oliver; Lenhof, Hans-Peter BN++ - A Biological Information System Proceedings of the 3rd International Workshop Integrative Bioinformatics, Rothamsted Research, 2006. @inproceedings{InproceedingsReference.2006-07-28.1716726743, title = {BN++ - A Biological Information System}, author = {Jan Küntzer and Torsten Blum and Andreas Gerasch and Christina Backes and Andreas Hildebrandt and Michael Kaufmann and Oliver Kohlbacher and Hans-Peter Lenhof}, url = {http://www.rothamsted.bbsrc.ac.uk/bab/conf/ibiof/abslister.php}, year = {2006}, date = {2006-01-01}, booktitle = {Proceedings of the 3rd International Workshop Integrative Bioinformatics}, publisher = {Rothamsted Research}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Huson, Daniel H; Kohlbacher, Oliver; Lupas, Andrei; Nieselt, Kay; Zell, Andreas German Conference on Bioinformatics Gesellschaft für Informatik e.V., Bonner Köllen Verlag, 2006. @book{BookReference.2006-09-27.8017853040, title = {German Conference on Bioinformatics}, author = {Daniel H Huson and Oliver Kohlbacher and Andrei Lupas and Kay Nieselt and Andreas Zell}, url = {http://www.gi-ev.de/service/publikationen/lni/gi-edition-lecture-notes-in-informatics-lni-p-83/}, year = {2006}, date = {2006-01-01}, volume = {P-83}, publisher = {Gesellschaft für Informatik e.V.}, address = {Bonner Köllen Verlag}, keywords = {}, pubstate = {published}, tppubtype = {book} } |
Kohlbacher, Oliver; Quinten, Sascha; Sturm, Marc; Mayr, Bettina; Huber, Christian Structure-Activity Relationships in Chromatography: Retention Prediction of Oligonucleotides with Support Vector Regression Angew. Chemie Int. Ed., 45 (42), pp. 7009-7012, 2006. @article{AngewOligos, title = {Structure-Activity Relationships in Chromatography: Retention Prediction of Oligonucleotides with Support Vector Regression}, author = {Oliver Kohlbacher and Sascha Quinten and Marc Sturm and Bettina Mayr and Christian Huber}, url = {http://dx.doi.org/10.1002/anie.200602561}, year = {2006}, date = {2006-01-01}, journal = {Angew. Chemie Int. Ed.}, volume = {45}, number = {42}, pages = {7009-7012}, abstract = {Secondary structures of biopolymers have a significant influence on their molecular interactions with surfaces. With the aid of machine learning through support vector regression, the retention of oligonucleotides was modeled in ion-pair reversed-phase chromatography with high prediction accuracy (see diagram).}, keywords = {}, pubstate = {published}, tppubtype = {article} } Secondary structures of biopolymers have a significant influence on their molecular interactions with surfaces. With the aid of machine learning through support vector regression, the retention of oligonucleotides was modeled in ion-pair reversed-phase chromatography with high prediction accuracy (see diagram). |
Peifer, Christian; Krasowski, Agata; Hämmerle, Nina; Kohlbacher, Oliver; Dannhardt, Gerd; Totzke, Frank; Schächtele, Christoph; Laufer, Stefan Profile and Molecular Modeling of 3-(Indole-3-yl)-4-(3,4,5-trimethoxyphenyl)-1 H-pyrrole-2,5-dione (1) as a Highly Selective VEGF-R2/3 Inhibitor J. Med. Chem., 49 (25), pp. 7549-7553, 2006. @article{VEGFR-2, title = {Profile and Molecular Modeling of 3-(Indole-3-yl)-4-(3,4,5-trimethoxyphenyl)-1 H-pyrrole-2,5-dione (1) as a Highly Selective VEGF-R2/3 Inhibitor}, author = {Christian Peifer and Agata Krasowski and Nina Hämmerle and Oliver Kohlbacher and Gerd Dannhardt and Frank Totzke and Christoph Schächtele and Stefan Laufer}, url = {http://dx.doi.org/10.1021/jm0609871}, year = {2006}, date = {2006-01-01}, journal = {J. Med. Chem.}, volume = {49}, number = {25}, pages = {7549-7553}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Höglund, Annette; Blum, Torsten; Brady, Scott; Dönnes, Pierre; Miguel, John San; Rocheford, Matthew; Kohlbacher, Oliver; Shatkay, Hagit Significantly improved prediction of subcellular localization by integrating text and protein sequence data Proceedings of the Pacific Symposium on Biocomputing (PSB 2006), PSB, 2006. @inproceedings{psb2006_TextLoc, title = {Significantly improved prediction of subcellular localization by integrating text and protein sequence data}, author = {Annette Höglund and Torsten Blum and Scott Brady and Pierre Dönnes and John San Miguel and Matthew Rocheford and Oliver Kohlbacher and Hagit Shatkay}, url = {http://helix-web.stanford.edu/psb06/hoglund.pdf}, year = {2006}, date = {2006-01-01}, booktitle = {Proceedings of the Pacific Symposium on Biocomputing (PSB 2006)}, publisher = {PSB}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Höglund, Annette; Dönnes, Pierre; Blum, Torsten; Adolph, Hans-Werner; Kohlbacher, Oliver MultiLoc: prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs, and amino acid composition Bioinformatics, 22 (10), pp. 1158-65, 2006. @article{MultiLocGCB, title = {MultiLoc: prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs, and amino acid composition}, author = {Annette Höglund and Pierre Dönnes and Torsten Blum and Hans-Werner Adolph and Oliver Kohlbacher}, url = {http://bioinformatics.oxfordjournals.org/cgi/reprint/btl002v1}, year = {2006}, date = {2006-01-01}, journal = {Bioinformatics}, volume = {22}, number = {10}, pages = {1158-65}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Dönnes, Pierre; Kohlbacher, Oliver SVMHC: a server for prediction of MHC-binding peptides Nucleic Acids Res., 34 , pp. W194-W197, 2006. @article{SVMHC_NAR, title = {SVMHC: a server for prediction of MHC-binding peptides}, author = {Pierre Dönnes and Oliver Kohlbacher}, url = {http://nar.oxfordjournals.org/cgi/content/full/34/suppl_2/W194}, year = {2006}, date = {2006-01-01}, journal = {Nucleic Acids Res.}, volume = {34}, pages = {W194-W197}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Reinert, Knut; Kohlbacher, Oliver; Gröpl, Clemens; Lange, Eva; Schulz-Trieglaff, Ole; Sturm, Marc; Pfeifer, Nico OpenMS - A Framework for Quantitative HPLC/MS-Based Proteomics Huber, Christian G; Kohlbacher, Oliver; Reinert, Knut (Ed.): Computational Proteomics, Internationales Begegnungs- und Forschungszentrum fuer Informatik (IBFI), Schloss Dagstuhl, Germany, 2006. @inproceedings{OpenMSDagstuhl, title = {OpenMS - A Framework for Quantitative HPLC/MS-Based Proteomics}, author = {Knut Reinert and Oliver Kohlbacher and Clemens Gröpl and Eva Lange and Ole Schulz-Trieglaff and Marc Sturm and Nico Pfeifer}, editor = {Christian G Huber and Oliver Kohlbacher and Knut Reinert}, url = {http://drops.dagstuhl.de/opus/volltexte/2006/546}, year = {2006}, date = {2006-01-01}, booktitle = {Computational Proteomics}, publisher = {Internationales Begegnungs- und Forschungszentrum fuer Informatik (IBFI), Schloss Dagstuhl, Germany}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Gröpl, Clemens; Lange, Eva; Reinert, Knut; Kohlbacher, Oliver; Sturm, Marc; Huber, Christian; Mayr, Bettina; Klein, Christoph Algorithms for the automated absolute quantification of diagnostic markers in complex proteomics samples Glen, Diederichs Kohlbacher Fischer Berthold K O I M R (Ed.): Proceedings of the 1st Symposium on Computational Life Sciences (CLS 2005), pp. 151–161, Springer LNBI 3695, 2005. @inproceedings{MyoCLS2005, title = {Algorithms for the automated absolute quantification of diagnostic markers in complex proteomics samples}, author = {Clemens Gröpl and Eva Lange and Knut Reinert and Oliver Kohlbacher and Marc Sturm and Christian Huber and Bettina Mayr and Christoph Klein}, editor = {Diederichs Kohlbacher Fischer K O I M. Berthold R. Glen}, url = {www.complife.org}, year = {2005}, date = {2005-01-01}, booktitle = {Proceedings of the 1st Symposium on Computational Life Sciences (CLS 2005)}, pages = {151--161}, publisher = {Springer LNBI 3695}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Höglund, Annette; Dönnes, Pierre; Blum, Torsten; Adolph, Hans-Werner; Kohlbacher, Oliver Using N-terminal targeting sequences, amino acid composition, and sequence motifs for predicting protein subcellular localization Kurtz, Matthias Rarey Andrew Torda Stefan (Ed.): Proceedings of the German Conference on Bioinformatics (GCB 2005), pp. 45–59, GI, 2005. @inproceedings{MultiLoc_GCB05, title = {Using N-terminal targeting sequences, amino acid composition, and sequence motifs for predicting protein subcellular localization}, author = {Annette Höglund and Pierre Dönnes and Torsten Blum and Hans-Werner Adolph and Oliver Kohlbacher}, editor = {Matthias Rarey Andrew Torda Stefan Kurtz}, url = {MultiLoc_2005.pdf}, year = {2005}, date = {2005-01-01}, booktitle = {Proceedings of the German Conference on Bioinformatics (GCB 2005)}, pages = {45--59}, publisher = {GI}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Klein, Christoph L; Kohlbacher, Oliver; Huber, Christian; Reinert, Knut Reference methods and materials in standardisation and quality assurance FEBS J., 272 (S1), 2005, (in press). (BibTeX) @article{RefMat, title = {Reference methods and materials in standardisation and quality assurance}, author = {Christoph L Klein and Oliver Kohlbacher and Christian Huber and Knut Reinert}, year = {2005}, date = {2005-01-01}, journal = {FEBS J.}, volume = {272}, number = {S1}, note = {in press}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Rausch, Christian; Weber, Tilmann; Kohlbacher, Oliver; Wohlleben, Wolfgang; Huson, Daniel Specificity prediction of adenylation domains in nonribosomal peptide synthetases (NRPS) using Transductive Support Vector Machines (TSVM) Nucl. Acids Res., 33 (18), pp. 5799-5808, 2005. @article{NRPSPred, title = {Specificity prediction of adenylation domains in nonribosomal peptide synthetases (NRPS) using Transductive Support Vector Machines (TSVM)}, author = {Christian Rausch and Tilmann Weber and Oliver Kohlbacher and Wolfgang Wohlleben and Daniel Huson}, url = {http://www.pubmedcentral.gov/articlerender.fcgi?tool=pubmed&pubmedid=16221976}, year = {2005}, date = {2005-01-01}, journal = {Nucl. Acids Res.}, volume = {33}, number = {18}, pages = {5799-5808}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Berthold, Michael; Glen, Robert; Diederichs, Kay; Kohlbacher, Oliver; Fischer, Ingrid Computational Life Sciences Springer Lecture notes in Bioinformatics, 2005. @book{CLS2005b, title = {Computational Life Sciences}, author = {Michael Berthold and Robert Glen and Kay Diederichs and Oliver Kohlbacher and Ingrid Fischer}, url = {http://www.springeronline.com/3-540-29104-0}, year = {2005}, date = {2005-01-01}, volume = {3695}, publisher = {Springer Lecture notes in Bioinformatics}, keywords = {}, pubstate = {published}, tppubtype = {book} } |
Moll, Andreas; Hildebrandt, Andreas; Kerzmann, Andreas; Lenhof, Hans-Peter; Kohlbacher, Oliver BALLView - An Open Source Tool for Molecular Modeling and Visualization Haasis, Klumpp Spath D D K (Ed.): Tagungsband zum doIT Software-Forschungstag 2005, pp. 203–214, MFG Stiftung, Stuttgart, 2005. (BibTeX) @inproceedings{InproceedingsReference.2006-01-19.8468200784, title = {BALLView - An Open Source Tool for Molecular Modeling and Visualization}, author = {Andreas Moll and Andreas Hildebrandt and Andreas Kerzmann and Hans-Peter Lenhof and Oliver Kohlbacher}, editor = {Klumpp D D. Spath K. Haasis}, year = {2005}, date = {2005-01-01}, booktitle = {Tagungsband zum doIT Software-Forschungstag 2005}, pages = {203--214}, publisher = {MFG Stiftung}, address = {Stuttgart}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Höglund, A; Dönnes, P; Adolph, HW; Kohlbacher, O From prediction of subcellular localization to functional classification: Discrimination of DNA-packing and other nuclear proteins Online Journal of Bioinformatics, 6 (1), pp. 51-64, 2005. @article{lokeroref, title = {From prediction of subcellular localization to functional classification: Discrimination of DNA-packing and other nuclear proteins}, author = {A Höglund and P Dönnes and HW Adolph and O Kohlbacher}, url = {http://www.comcen.com.au/~journals/dnapackingabs2005.htm}, year = {2005}, date = {2005-01-01}, journal = {Online Journal of Bioinformatics}, volume = {6}, number = {1}, pages = {51-64}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Supper, Jochen; Dönnes, Pierre; Kohlbacher, Oliver Analysis of MHC-Peptide Binding Using Amino Acid Property-Based Decision Rules Springer Lecture Notes in Computer Science (LNCS), 3686 , pp. 446-453, 2005. @article{MHCDR, title = {Analysis of MHC-Peptide Binding Using Amino Acid Property-Based Decision Rules}, author = {Jochen Supper and Pierre Dönnes and Oliver Kohlbacher}, url = {https://link.springer.com/content/pdf/10.1007/11551188_48.pdf}, year = {2005}, date = {2005-01-01}, journal = {Springer Lecture Notes in Computer Science (LNCS)}, volume = {3686}, pages = {446-453}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Dönnes, Pierre; Kohlbacher, Oliver Integrated modelling of the major events in the MHC class I antigen processing pathway Protein Sci., 14 (8), pp. 2132-2140, 2005. @article{WAPP, title = {Integrated modelling of the major events in the MHC class I antigen processing pathway}, author = {Pierre Dönnes and Oliver Kohlbacher}, url = {http://dx.doi.org/10.1110/ps.051352405}, year = {2005}, date = {2005-01-01}, journal = {Protein Sci.}, volume = {14}, number = {8}, pages = {2132-2140}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Schuler, Mathias M; Dönnes, Pierre; Nastke, Maria-Dorothea; Kohlbacher, Oliver; Rammensee, Hans-Georg; Stevanovic, Stefan SNEP: SNP-derived Epitope Prediction program for minor H antigens. Immunogenetics, 57 (11), pp. 816-820, 2005. @article{SNEP, title = {SNEP: SNP-derived Epitope Prediction program for minor H antigens.}, author = {Mathias M Schuler and Pierre Dönnes and Maria-Dorothea Nastke and Oliver Kohlbacher and Hans-Georg Rammensee and Stefan Stevanovic}, url = {http://www.springerlink.com/openurl.asp?genre=article&id=doi:10.1007/s00251-005-0054-5}, year = {2005}, date = {2005-01-01}, journal = {Immunogenetics}, volume = {57}, number = {11}, pages = {816-820}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Schuler, Mathias; Dönnes, Pierre; Nastke, Maria; Kohlbacher, Oliver; Rammensee, H-G; Stevanovic, Stefan SNEP: SNP-derived Epitope Prediction program for minor H antigens Kabelitz, Dietrich (Ed.): Joint Annual Meeting of the German and Scandinavian Societies of Immunology, 21-24 September 2005, Kiel, Germany, pp. 361-622, Immunobiology 210(6-8), 2005. (BibTeX) @inproceedings{InproceedingsReference.2006-01-03.7145695050, title = {SNEP: SNP-derived Epitope Prediction program for minor H antigens}, author = {Mathias Schuler and Pierre Dönnes and Maria Nastke and Oliver Kohlbacher and H-G Rammensee and Stefan Stevanovic}, editor = {Dietrich Kabelitz}, year = {2005}, date = {2005-01-01}, booktitle = {Joint Annual Meeting of the German and Scandinavian Societies of Immunology, 21-24 September 2005, Kiel, Germany}, pages = {361-622}, publisher = {Immunobiology 210(6-8)}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Neumann, Dirk; Lehr, Claus-Michael; Lenhof, Hans-Peter; Kohlbacher, Oliver Computational modeling of the sugarlectin interaction Advanced Drug Delivery Reviews, 56 (4), pp. 437-457, 2004. @article{ADDR, title = {Computational modeling of the sugarlectin interaction}, author = {Dirk Neumann and Claus-Michael Lehr and Hans-Peter Lenhof and Oliver Kohlbacher}, url = {http://dx.doi.org/10.1016/j.addr.2003.10.019}, year = {2004}, date = {2004-01-01}, journal = {Advanced Drug Delivery Reviews}, volume = {56}, number = {4}, pages = {437-457}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Kohlbacher, Oliver; Reinert, Knut Differenzielle Proteomanalyse - Experimentelle Methoden, Algorithmische Herausforderungen IT - Information Technology, 46 (1), pp. 31-38, 2004, (article in German). @article{IT_Proteomik, title = {Differenzielle Proteomanalyse - Experimentelle Methoden, Algorithmische Herausforderungen}, author = {Oliver Kohlbacher and Knut Reinert}, url = {http://www-bs.informatik.uni-tuebingen.de/Members/oliver/PDF/it0401_031.pdf}, year = {2004}, date = {2004-01-01}, journal = {IT - Information Technology}, volume = {46}, number = {1}, pages = {31-38}, note = {article in German}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Höglund, Annette; Kohlbacher, Oliver From sequence to structure and back again: approaches for predicting protein-DNA binding Proteome Science, 2 , pp. 3, 2004. @article{SequenceToStructureAndBackAgain, title = {From sequence to structure and back again: approaches for predicting protein-DNA binding}, author = {Annette Höglund and Oliver Kohlbacher}, url = {http://www.proteomesci.com/content/2/1/3}, year = {2004}, date = {2004-01-01}, journal = {Proteome Science}, volume = {2}, pages = {3}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Hildebrandt, Andreas; Blossey, Ralf; Rjasanow, Sergej; Kohlbacher, Oliver; Lenhof, Hans-Peter Novel formulation of nonlocal electrostatics Phys. Rev. Lett., 93 , pp. 108104, 2004. @article{NLES, title = {Novel formulation of nonlocal electrostatics}, author = {Andreas Hildebrandt and Ralf Blossey and Sergej Rjasanow and Oliver Kohlbacher and Hans-Peter Lenhof}, url = {http://scitation.aip.org/getpdf/servlet/GetPDFServlet?filetype=pdf&id=PRLTAO000093000010108104000001&idtype=cvips}, year = {2004}, date = {2004-01-01}, journal = {Phys. Rev. Lett.}, volume = {93}, pages = {108104}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Istrail, Sorin; Florea, Liliana; Halldorsson, Bjarni V; Kohlbacher, Oliver; Schwartz, Russell S; Yap, Von Bing; Yewdell, Jonathan W; Hoffman, Stephen L Comparative Immuno-Peptidomics of Humans and their Pathogens Proc. Natl. Acad. Sci. USA, 101 (36), pp. 13268, 2004. @article{PNASPeptidomics, title = {Comparative Immuno-Peptidomics of Humans and their Pathogens}, author = {Sorin Istrail and Liliana Florea and Bjarni V Halldorsson and Oliver Kohlbacher and Russell S Schwartz and Von Bing Yap and Jonathan W Yewdell and Stephen L Hoffman}, url = {http://www.pnas.org/cgi/reprint/0404740101}, year = {2004}, date = {2004-01-01}, journal = {Proc. Natl. Acad. Sci. USA}, volume = {101}, number = {36}, pages = {13268}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Dönnes, Pierre; Höglund, Annette; Sturm, Marc; Comtesse, Nicole; Backes, Christina; Meese, Eckart; Kohlbacher, Oliver; Lenhof, Hans-Peter Integrative analysis of cancer-related data using CAP FASEB Journal, 18 (12), pp. 1465-1467, 2004. @article{CAP.FASEBJ.2004, title = {Integrative analysis of cancer-related data using CAP}, author = {Pierre Dönnes and Annette Höglund and Marc Sturm and Nicole Comtesse and Christina Backes and Eckart Meese and Oliver Kohlbacher and Hans-Peter Lenhof}, url = {http://www.fasebj.org/cgi/content/abstract/04-1797fjev1}, year = {2004}, date = {2004-01-01}, journal = {FASEB Journal}, volume = {18}, number = {12}, pages = {1465-1467}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Dönnes, Pierre; Höglund, Annette Predicting Protein Subcellular Localization: Past, Present, and Future Genomics Proteomics Bioinformatics, 2 (4), pp. 209–215, 2004. @article{LocationReview, title = {Predicting Protein Subcellular Localization: Past, Present, and Future}, author = {Pierre Dönnes and Annette Höglund}, url = {https://www.ncbi.nlm.nih.gov/pubmed/15901249}, year = {2004}, date = {2004-01-01}, journal = {Genomics Proteomics Bioinformatics}, volume = {2}, number = {4}, pages = {209--215}, abstract = {Functional characterization of every single protein is a major challenge of the post-genomic era. The large-scale analysis of a cell's proteins, proteomics, seeks to provide these proteins with reliable annotations regarding their interaction partners and functions in the cellular machinery. An important step on this way is to determine the subcellular localization of each protein. Eukaryotic cells are divided into subcellular compartments, or organelles. Transport across the membrane into the organelles is a highly regulated and complex cellular process. Predicting the subcellular localization by computational means has been an area of vivid activity during recent years. The publicly available prediction methods differ mainly in four aspects: the underlying biological motivation, the computational method used, localization coverage, and reliability, which are of importance to the user. This review provides a short description of the main events in the protein sorting process and an overview of the most commonly used methods in this field.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Functional characterization of every single protein is a major challenge of the post-genomic era. The large-scale analysis of a cell's proteins, proteomics, seeks to provide these proteins with reliable annotations regarding their interaction partners and functions in the cellular machinery. An important step on this way is to determine the subcellular localization of each protein. Eukaryotic cells are divided into subcellular compartments, or organelles. Transport across the membrane into the organelles is a highly regulated and complex cellular process. Predicting the subcellular localization by computational means has been an area of vivid activity during recent years. The publicly available prediction methods differ mainly in four aspects: the underlying biological motivation, the computational method used, localization coverage, and reliability, which are of importance to the user. This review provides a short description of the main events in the protein sorting process and an overview of the most commonly used methods in this field. |
Kerzmann, Andreas; Neumann, Dirk; Kohlbacher, Oliver High-Accuracy Prediction of Protein-Carbohydrate Interactions Trends in Glycoscience and Glycotechnology, 16 , pp. S26, 2004. (BibTeX) @article{Carbohydrate, title = {High-Accuracy Prediction of Protein-Carbohydrate Interactions}, author = {Andreas Kerzmann and Dirk Neumann and Oliver Kohlbacher}, year = {2004}, date = {2004-01-01}, journal = {Trends in Glycoscience and Glycotechnology}, volume = {16}, pages = {S26}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Florea, Liliana; Halldórsson, Bjarni; Kohlbacher, Oliver; Schwartz, Russell; Hoffman, Stephen; Istrail, Sorin Epitope Prediction Algorithms for Peptide based Vaccine Design Proceedings of the 2nd IEEE Computer Society Conference on Bioinformatics, pp. 17-26, IEEE Computer Society, 2003, (PMID: 16826643). @inproceedings{FHKSHI2003, title = {Epitope Prediction Algorithms for Peptide based Vaccine Design}, author = {Liliana Florea and Bjarni Halldórsson and Oliver Kohlbacher and Russell Schwartz and Stephen Hoffman and Sorin Istrail}, url = {http://csdl.computer.org/comp/proceedings/csb/2003/2000/00/20000017abs.htm}, year = {2003}, date = {2003-01-01}, booktitle = {Proceedings of the 2nd IEEE Computer Society Conference on Bioinformatics}, pages = {17-26}, publisher = {IEEE Computer Society}, note = {PMID: 16826643}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Hildebrandt, Andreas; Kohlbacher, Oliver; Blossey, Ralf; Lenhof, Hans-Peter Using nonlocal electrostatics for solvation free energy computations: ions and small molecules 2003. @preprint{NonlocalESPreprint, title = {Using nonlocal electrostatics for solvation free energy computations: ions and small molecules}, author = {Andreas Hildebrandt and Oliver Kohlbacher and Ralf Blossey and Hans-Peter Lenhof}, url = {http://arXiv.org/abs/physics/0212074}, year = {2003}, date = {2003-01-01}, keywords = {}, pubstate = {published}, tppubtype = {preprint} } |
Sandelin, Albin; Höglund, Annette; Lenhard, Boris; Wasserman, Wyeth Integrated analysis of yeast regulatory sequences for biologically linked clusters of genes Funct Integr Genomics, 3 (3), pp. 125-134, 2003. (BibTeX) @article{ArticleReference.2003-11-24.6775351915, title = {Integrated analysis of yeast regulatory sequences for biologically linked clusters of genes}, author = {Albin Sandelin and Annette Höglund and Boris Lenhard and Wyeth Wasserman}, year = {2003}, date = {2003-01-01}, journal = {Funct Integr Genomics}, volume = {3}, number = {3}, pages = {125-134}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Althaus, Ernst; Kohlbacher, Oliver; Lenhof, Hans Peter; Müller, Peter A Combinatorial Approach to Protein Docking with Flexible Side-Chains J. Comput. Biol., 9 (4), pp. 597-612, 2002. @article{AKLM2002, title = {A Combinatorial Approach to Protein Docking with Flexible Side-Chains}, author = {Ernst Althaus and Oliver Kohlbacher and Hans Peter Lenhof and Peter Müller}, doi = {https://doi.org/10.1089/106652702760277336}, year = {2002}, date = {2002-01-01}, journal = {J. Comput. Biol.}, volume = {9}, number = {4}, pages = {597-612}, abstract = {Rigid-body docking approaches are not sufficient to predict the structure of a protein complex from the unbound (native) structures of the two proteins. Accounting for side chain flexibility is an important step towards fully flexible protein docking. This work describes an approach that allows conformational flexibility for the side chains while keeping the protein backbone rigid. Starting from candidates created by a rigid-docking algorithm, we demangle the side chains of the docking site, thus creating reasonable approximations of the true complex structure. These structures are ranked with respect to the binding free energy. We present two new techniques for side chain demangling. Both approaches are based on a discrete representation of the side chain conformational space by the use of a rotamer library. This leads to a combinatorial optimization problem. For the solution of this problem, we propose a fast heuristic approach and an exact, albeit slower, method that uses branch-and-cut techniques. As a test set, we use the unbound structures of three proteases and the corresponding protein inhibitors. For each of the examples, the highest-ranking conformation produced was a good approximation of the true complex structure.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Rigid-body docking approaches are not sufficient to predict the structure of a protein complex from the unbound (native) structures of the two proteins. Accounting for side chain flexibility is an important step towards fully flexible protein docking. This work describes an approach that allows conformational flexibility for the side chains while keeping the protein backbone rigid. Starting from candidates created by a rigid-docking algorithm, we demangle the side chains of the docking site, thus creating reasonable approximations of the true complex structure. These structures are ranked with respect to the binding free energy. We present two new techniques for side chain demangling. Both approaches are based on a discrete representation of the side chain conformational space by the use of a rotamer library. This leads to a combinatorial optimization problem. For the solution of this problem, we propose a fast heuristic approach and an exact, albeit slower, method that uses branch-and-cut techniques. As a test set, we use the unbound structures of three proteases and the corresponding protein inhibitors. For each of the examples, the highest-ranking conformation produced was a good approximation of the true complex structure. |
Neumann, Dirk; Kohlbacher, Oliver; Lenhof, Hans-Peter; Lehr, Claus-Michael Protein-sugar interactions: Calculated versus experimental binding energies Eur. J. Biochem., 269 (5), pp. 1518-1524, 2002. @article{NKLL2000, title = {Protein-sugar interactions: Calculated versus experimental binding energies}, author = {Dirk Neumann and Oliver Kohlbacher and Hans-Peter Lenhof and Claus-Michael Lehr}, url = {http://www.blackwell-synergy.com/openurl?genre=article&sid=nlm:pubmed&issn=0014-2956&date=2002&volume=269&issue=5&spage=1518}, year = {2002}, date = {2002-01-01}, journal = {Eur. J. Biochem.}, volume = {269}, number = {5}, pages = {1518-1524}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Neumann, Dirk; Kerzmann, Andreas; Kohlbacher, Oliver Modelling the sugar-lectin interaction by computer simulated docking Abstracts of the 20th Interlec Meeting, pp. 116, University of Copenhagen, Copenhagen, Denmark, 2002. (BibTeX) @inproceedings{NKK2002, title = {Modelling the sugar-lectin interaction by computer simulated docking}, author = {Dirk Neumann and Andreas Kerzmann and Oliver Kohlbacher}, year = {2002}, date = {2002-01-01}, booktitle = {Abstracts of the 20th Interlec Meeting}, pages = {116}, publisher = {University of Copenhagen, Copenhagen, Denmark}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Sirava, Marite; Schäfer, Thomas; Eiglsperger, Markus; Kaufmann, Michael; Kohlbacher, Oliver; Bornberg-Bauer, Erich; Lenhof, Hans-Peter BioMiner - modeling, analysing, and visualizing biochemical pathways and networks Bioinformatics, 19 (10), pp. S219-230, 2002. @article{SSEKKBL2002, title = {BioMiner - modeling, analysing, and visualizing biochemical pathways and networks}, author = {Marite Sirava and Thomas Schäfer and Markus Eiglsperger and Michael Kaufmann and Oliver Kohlbacher and Erich Bornberg-Bauer and Hans-Peter Lenhof}, url = {http://bioinformatics.oupjournals.org/cgi/reprint/18/suppl_2/S219}, year = {2002}, date = {2002-01-01}, journal = {Bioinformatics}, volume = {19}, number = {10}, pages = {S219-230}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Dönnes, Pierre; Elofsson, Arne Prediction of MHC class I binding peptides, using SVMHC BMC Bioinformatics, 3 (25), 2002. @article{SVMHC, title = {Prediction of MHC class I binding peptides, using SVMHC}, author = {Pierre Dönnes and Arne Elofsson}, url = {http://www.biomedcentral.com/1471-2105/3/25}, year = {2002}, date = {2002-01-01}, journal = {BMC Bioinformatics}, volume = {3}, number = {25}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Kohlbacher, Oliver; Burchardt, Andreas; Moll, Andreas; Hildebrandt, Andreas; Bayer, Peter; Lenhof, Hans-Peter Structure prediction of protein complexes by a NMR-based protein docking algorithm J. Biomol. NMR, 20 , pp. 15-21, 2001. @article{articleKBM2001, title = {Structure prediction of protein complexes by a NMR-based protein docking algorithm}, author = {Oliver Kohlbacher and Andreas Burchardt and Andreas Moll and Andreas Hildebrandt and Peter Bayer and Hans-Peter Lenhof}, url = {https://link.springer.com/article/10.1023/A:1011216130486}, year = {2001}, date = {2001-01-01}, journal = {J. Biomol. NMR}, volume = {20}, pages = {15-21}, abstract = {Protein docking algorithms can be used to study the driving forces and reaction mechanisms of docking processes. They are also able to speed up the lengthy process of experimental structure elucidation of protein complexes by proposing potential structures. In this paper, we are discussing a variant of the protein-protein docking problem, where the input consists of the tertiary structures of proteins A and B plus an unassigned one-dimensional 1H-NMR spectrum of the complex AB. We present a new scoring function for evaluating and ranking potential complex structures produced by a docking algorithm. The scoring function computes a `theoretical' 1H-NMR spectrum for each tentative complex structure and subtracts the calculated spectrum from the experimental one. The absolute areas of the difference spectra are then used to rank the potential complex structures. In contrast to formerly published approaches (e.g. [Morelli et al. (2000) Biochemistry, 39, 2530–2537]) we do not use distance constraints (intermolecular NOE constraints). We have tested the approach with four protein complexes whose three-dimensional structures are stored in the PDB data bank [Bernstein et al. (1977)] and whose 1H-NMR shift assignments are available from the BMRB database. The best result was obtained for an example, where all standard scoring functions failed completely. Here, our new scoring function achieved an almost perfect separation between good approximations of the true complex structure and false positives.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Protein docking algorithms can be used to study the driving forces and reaction mechanisms of docking processes. They are also able to speed up the lengthy process of experimental structure elucidation of protein complexes by proposing potential structures. In this paper, we are discussing a variant of the protein-protein docking problem, where the input consists of the tertiary structures of proteins A and B plus an unassigned one-dimensional 1H-NMR spectrum of the complex AB. We present a new scoring function for evaluating and ranking potential complex structures produced by a docking algorithm. The scoring function computes a `theoretical' 1H-NMR spectrum for each tentative complex structure and subtracts the calculated spectrum from the experimental one. The absolute areas of the difference spectra are then used to rank the potential complex structures. In contrast to formerly published approaches (e.g. [Morelli et al. (2000) Biochemistry, 39, 2530–2537]) we do not use distance constraints (intermolecular NOE constraints). We have tested the approach with four protein complexes whose three-dimensional structures are stored in the PDB data bank [Bernstein et al. (1977)] and whose 1H-NMR shift assignments are available from the BMRB database. The best result was obtained for an example, where all standard scoring functions failed completely. Here, our new scoring function achieved an almost perfect separation between good approximations of the true complex structure and false positives. |
Turner, Russell J; Chaturvedi, Kabir; Edwards, Nathan J; Fasulo, Daniel; Halpern, Aaron L; Huson, Daniel H; Remington, Karin A; Schwartz, Russell; Walenz, Brian; Yooseph, Shibu; Istrail, Sorin Visualization Challenges for a New Cyberpharmaceutical Computing Paradigm Proceedings of the IEEE Symposium on Parallel and Large-Data Visualization and Graphics (PVG2001), pp. 7–18, San Diego, USA,, 2001. (BibTeX) @inproceedings{procTur2001, title = {Visualization Challenges for a New Cyberpharmaceutical Computing Paradigm}, author = {Russell J Turner and Kabir Chaturvedi and Nathan J Edwards and Daniel Fasulo and Aaron L Halpern and Daniel H Huson and Karin A Remington and Russell Schwartz and Brian Walenz and Shibu Yooseph and Sorin Istrail}, year = {2001}, date = {2001-01-01}, booktitle = {Proceedings of the IEEE Symposium on Parallel and Large-Data Visualization and Graphics (PVG2001)}, pages = {7--18}, address = {San Diego, USA,}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Kohlbacher, Oliver; Burchardt, Andreas; Hildebrandt, Andreas; Moll, Andreas; Bayer, Peter; Lenhof, Hans-Peter A NMR-spectra-based scoring function for protein docking Sankoff, David; Lengauer, Thomas (Ed.): RECOMB 2001, Proceedings of the Fifth Annual International Conference on Computational Molecular Biology, pp. 169-177, ACM press, 2001. @inproceedings{KBHMBL2000, title = {A NMR-spectra-based scoring function for protein docking}, author = {Oliver Kohlbacher and Andreas Burchardt and Andreas Hildebrandt and Andreas Moll and Peter Bayer and Hans-Peter Lenhof}, editor = {David Sankoff and Thomas Lengauer}, url = {http://portal.acm.org/citation.cfm?doid=369133.369194}, year = {2001}, date = {2001-01-01}, booktitle = {RECOMB 2001, Proceedings of the Fifth Annual International Conference on Computational Molecular Biology}, pages = {169-177}, publisher = {ACM press}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Kohlbacher, Oliver BALL - A Framework for Rapid Application Development in Molecular Modeling Beiträge zum Heinz-Billing-Preis 2000, pp. 13-28, Gesellschaft für wissenschaftliche Datenverarbeitung mbH, Göttingen, 2001. @incollection{Koh2000, title = {BALL - A Framework for Rapid Application Development in Molecular Modeling}, author = {Oliver Kohlbacher}, url = {http://www.billingpreis.mpg.de/hbp00/kohlbacher.pdf}, year = {2001}, date = {2001-01-01}, booktitle = {Beiträge zum Heinz-Billing-Preis 2000}, pages = {13-28}, publisher = {Gesellschaft für wissenschaftliche Datenverarbeitung mbH}, address = {Göttingen}, keywords = {}, pubstate = {published}, tppubtype = {incollection} } |