Research Topics
| Matthias RareySummaryAffiliation: University of Hamburg Country: Germany Publications
| Collaborators
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Detail Information
Publications
Exploring fragment spaces under multiple physicochemical constraintsJuri Pärn
Center for Bioinformatics, Hamburg, Germany
J Comput Aided Mol Des 21:327-40. 2007..We characterized the target-specific fragment spaces and were able to enumerate the complete chemical subspaces for most of the targets...- Consistent two-dimensional visualization of protein-ligand complex seriesKatrin Stierand
Center for Bioinformatics ZBH, University of Hamburg, Bundesstraße 43, 20146 Hamburg, Germany
J Cheminform 3:21. 2011..abstract:.. - Fast automated placement of polar hydrogen atoms in protein-ligand complexesTobias Lippert
Center for Bioinformatics, 20146 Hamburg, Germany
J Cheminform 1:13. 2009..Also, side-chain flips in glutamine and asparagine and histidine residues, which are common crystallographic ambiguities must be identified before structure-based calculations can be conducted... - Towards an integrated description of hydrogen bonding and dehydration: decreasing false positives in virtual screening with the HYDE scoring functionIngo Reulecke
Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
ChemMedChem 3:885-97. 2008.... - De novo design by pharmacophore-based searches in fragment spacesTobias Lippert
Center for Bioinformatics, University of Hamburg, Bundesstr 43, 20146 Hamburg, Germany
J Comput Aided Mol Des 25:931-45. 2011..The program has been tested on several published pharmacophores and is shown to be able to reproduce scaffold hops from the literature, which resulted in new chemical entities... - From modeling to medicinal chemistry: automatic generation of two-dimensional complex diagramsKatrin Stierand
Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
ChemMedChem 2:853-60. 2007..The success rate for complexes with ligands which have a molecular weight <500 Da is 87%... - Conformational sampling for large-scale virtual screening: accuracy versus ensemble sizeAxel Griewel
Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
J Chem Inf Model 49:2303-11. 2009..A comparison to CATALYST and OMEGA shows that TCG achieves a comparable performance in terms of accuracy. Furthermore, it performs well with respect to the trade-off between accuracy and ensemble size... - TrixX: structure-based molecule indexing for large-scale virtual screening in sublinear timeIngo Schellhammer
Center for Bioinformatics, Research Group for Computational Molecular Design, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
J Comput Aided Mol Des 21:223-38. 2007..With computing times clearly below one second per compound, TrixX counts among the fastest virtual screening tools currently available and is nearly two orders of magnitude faster than standard FlexX... - NAOMI: on the almost trivial task of reading molecules from different file formatsSascha Urbaczek
Center for Bioinformatics ZBH, Bundesstrasse 43, 20146 Hamburg, Germany
J Chem Inf Model 51:3199-207. 2011..NAOMI's functionality is tested by round robin file IO exercises with public data sets, which we believe should become a standard test for every cheminformatics tool... - Modeling of metal interaction geometries for protein-ligand dockingBirte Seebeck
University of Hamburg, Center for Bioinformatics, Bundesstrasse 43, 20146 Hamburg, Germany
Proteins 71:1237-54. 2008..Secondly, the new metal interaction model was tested in terms of predicting protein-ligand complexes. In the majority of test cases, the new interaction model resulted in an improved docking accuracy of the top ranking placements... - From activity cliffs to target-specific scoring models and pharmacophore hypothesesBirte Seebeck
Center for Bioinformatics Hamburg ZBH, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
ChemMedChem 6:1630-9, 1533. 2011..The activity-cliff-based approach shows an improved enrichment over the generic empirical scoring function for various protein targets in the validation set... - Beyond the virtual screening paradigm: structure-based searching for new lead compoundsJochen Schlosser
Center for Bioinformatics, Research Group for Computational Molecular Design, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
J Chem Inf Model 49:800-9. 2009..In addition to that several comparative enrichment experiments show that TrixX BMI is on a competitive basis to established virtual screening technology, while the observed runtimes are clearly below one second per compound... - Analyzing the topology of active sites: on the prediction of pockets and subpocketsAndrea Volkamer
Research Group for Computational Molecular Design, Bundesstr 43, 20146 Hamburg, Germany
J Chem Inf Model 50:2041-52. 2010..Consideration of subpockets produces an increase in coverage yielding a success rate of 83% for the latter measure... - Combining global and local measures for structure-based druggability predictionsAndrea Volkamer
University of Hamburg, Center for Bioinformatics, Bundesstr 43, 20146 Hamburg, Germany
J Chem Inf Model 52:360-72. 2012..Incorporating local pocket properties is another step toward a reliable descriptor-based druggability prediction... - SwiFT: an index structure for reduced graph descriptors in virtual screening and clusteringJ Robert Fischer
Center for Bioinformatics Hamburg, University of Hamburg, Bundesstrasse 43, D 20146 Hamburg, Germany
J Chem Inf Model 47:1341-53. 2007..The search tree built for indexing can also be used to identify duplicated feature trees... - Recore: a fast and versatile method for scaffold hopping based on small molecule crystal structure conformationsPatrick Maass
Center for Bioinformatics Hamburg, University of Hamburg, Bundesstrasse 43, D 20146 Hamburg, Germany
J Chem Inf Model 47:390-9. 2007..For the validation of the approach, three different design scenarios have been used. The results obtained show that our approach is able to propose new valid scaffold topologies... - From structure diagrams to visual chemical patternsKaren Schomburg
Research Group for Computational Molecular Design, Center for Bioinformatics, University of Hamburg, Hamburg, Germany
J Chem Inf Model 50:1529-35. 2010..Taking recent chemical publications from various fields, we demonstrate the wide application range of a graphical chemical pattern language... - Molecular complexes at a glance: automated generation of two-dimensional complex diagramsKatrin Stierand
Center for Bioinformatics (ZBH, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
Bioinformatics 22:1710-6. 2006..AVAILABILITY: The method is available as a webservice at http://www.zbh.uni-hamburg.de/poseview... - Improving similarity-driven library design: customized matching and regioselective feature treesJ Robert Fischer
Center for Bioinformatics ZBH, University of Hamburg, Hamburg, Germany
J Chem Inf Model 51:2156-63. 2011..Subsequently we investigate the improvements on library design by reviewing the design scenarios which were already used for the evaluation of LoFT... - FlexX-Scan: fast, structure-based virtual screeningIngo Schellhammer
University of Hamburg, Center for Bioinformatics (ZBH, Research Group for Computational Molecular Design, Hamburg, Germany
Proteins 57:504-17. 2004..With FlexX-Scan, we achieved comparable enrichments to standard FlexX, with an averaged computing time of 5-10 s per compound, depending on parametrization... - Novel technologies for virtual screeningThomas Lengauer
Max Planck Institute for Informatics, Stuhlsatzenhausweg 85, 66123 Saarbrucken, Germany
Drug Discov Today 9:27-34. 2004..The in silico procedure of virtual screening (VS) and its relationship to the experimental procedure, HTS, is discussed, new developments in the field are summarized and perspectives on future research are offered... - Multiple-ligand-based virtual screening: methods and applications of the MTree approachGerhard Hessler
Drug Design, Chemical Sciences, Sanofi-Aventis Deutschland GmbH, Frankfurt, Germany
J Med Chem 48:6575-84. 2005..Furthermore, relevant molecular features, which are known to be important for affinity to the target, are identified by this new methodology... - Flexible docking under pharmacophore type constraintsSally A Hindle
Fraunhofer Institute for Algorithms and Scientific Computing, Schloss Birlinghoven, Sankt Augustin, Germany
J Comput Aided Mol Des 16:129-49. 2002..However, in general FLEXX-PHARM maintained or improved the enrichment shown with FLEXX, while completing the screen in considerably less run time...