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This page gives an overview of some of the most important publications on and about our software. If you are interested in a reprint or any further information please send an email to contact@biosolveit.de.
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| novel developments |
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I. Schellhammer and M. Rarey
FlexX-Scan: Fast Structure-Based Virtual Screening
PROTEINS: Structure, Function, and Genetics 57, 504-517, 2004
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| FlexX |
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M. Rarey, B. Kramer, and T. Lengauer
The particle concept: Placing discrete water molecules during protein-ligand docking predictions
PROTEINS: Structure, Functions, and Genetics, Vol. 34, pp. 17-28, 1999
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M. Rarey, B. Kramer, and T. Lengauer
Docking of hydrophobic ligands with interaction-based matching algorithms
Bioinformatics, Vol. 15, pp. 243-250, 1999
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D. Hoffmann, B. Kramer, T. Washio, T.Steinmetzer, M. Rarey, and T. Lengauer
Two-Stage Method for Protein-Ligand Docking
Journal of Medicinal Chemistry, Vol. 42, pp. 4422-4433, 1999
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B. Kramer, M.Rarey, and T. Lengauer
Evaluation of the FlexX incremental construction algorithm for protein-ligand docking
PROTEINS: Structure, Functions, and Genetics, Vol. 37, pp. 228-241, 1999
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M. Rarey, B. Kramer, and T. Lengauer
Multiple automatic base selection: Protein-ligand docking based on incremental construction without manual intervention
Journal of Computer-Aided Molecular Design, Vol. 11, pp. 369-384, 1997
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B. Kramer, M. Rarey and T. Lengauer
CASP-2 experiences with docking flexible ligands using FlexX
PROTEINS: Structure, Functions, and Genetics, Suppl. 1:1, pp. 221-225, 1997
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M. Rarey, B. Kramer, T. Lengauer, and G. Klebe
Predicting Receptor-Ligand Interactions by an Incremental Construction Algorithm
Journal of Molecular Biology, Vol. 261/ 3, pp. 470-489, 1996
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M. Rarey, S Wefing, and T. Lengauer
Placement of medium-sised molecular fragments into active sites of proteins
Journal of Computer-Aided Molecular Design, Vol. 10, pp. 41-54, 1996
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M. Rarey, S. Wefing, and T. Lengauer
Time-Efficient Docking of Flexible Ligands into Active Sites of Proteins
In: RAWLINGS, C. ET AL.(Editors): Proceedings of the Third International Conference on Intellegent Systems in Molecular Biology, pp. 300-308. AAAI Press, Menlo Park, California, 1995
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| FlexXC |
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M. Rarey and T. Lengauer
A recursive algorithm for efficient combinatorial library docking
to appear in: Perspectives in Drug Discovery and Design
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| FlexX-Pharm |
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H. Claußen, M. Gastreich, V. Apelt, J. Greene, S.A. Hindle, and C. Lemmen
The FlexX Database Docking Environment – Rational Extraction of Receptor-Based Pharmacophores
Current Drug Discovery Technologies, Vol. 1, pp. 49-60, 2004
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S.A. Hindle, M. Rarey, C. Buning, and T. Lengauer
Flexible docking under pharmacophore constraints
Journal of Computer-Aided Molecular Design, Vol. 16, pp. 129-149, 2002
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S.A. Hindle, M. Stahl, and M. Rarey
Flexible Docking under Pharmacophore Type Constraints: Application to Virtual Screening
14th European Symposium on Quantitative Structure-Activity Relationships, Bournemouth, UK, 2002
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| FlexX-Ensemble |
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H. Claußen, C. Buning, M. Rarey, and T. Lengauer
FlexE: Efficient Molecular Docking into Flexible Protein Structures
Journal of Molecular Biology, Vol. 308, pp. 377-395, 2001
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| DDB |
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| FlexS |
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C. Lemmen and T. Lengauer
Fragment-based screening of ligand databases
In: K. Gundertofte and F.S. Jorgensen (Editors): Molecular Modelling and Prediction of Bioactivity, Proceedings of the 12th European Symposium on Quantitative Structure-Activity Relationships (QSAR'98), Plenum
Plenum Press, New York, 1999
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C. Lemmen, T. Lengauer, and G. Klebe
FlexS: A method for fast flexible ligand superposition
Journal of Medicinal Chemistry, Vol. 41, pp. 4502-4520, 1998
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C. Lemmen, C. Hiller, and T. Lengauer
RigFit: A new approach to superimpose ligand molecules
Journal of Computer-Aided Molecular Design, Vol. 12, pp. 491-502, 1998
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C. Lemmen and T. Lengauer
Time-efficient flexible superposition of medium-sised molecules
Journal of Computer-Aided Molecular Design, Vol. 11, pp. 357-368, 1997
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| FTrees |
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A.C. Good, M.A. Hermsmeier, S.A. Hindle
Measuring CAMD technique performance: A virtual screening case study in the design of validation experiments
Journal of Computer-Aided Molecular Design, Vol. 18, pp. 529-536, 2004
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G. Hessler, M. Gastreich, S.A. Hindle, H. Matter, T. Naumann, S. Pfeiffer-Marek, J. Liao, M. Warmuth, K.-H. Baringhaus, and C. Lemmen
Boosting Descriptors for Similarity Searches: Feature Trees Trained by Machine Learning
Abstract EuroQSAR 2004, Instanbul, Turkey, 2004
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M. Rarey and J.S. Dixon
Feature Trees: A new molecular similarity measure based on tree matching
Journal of Computer-Aided Molecular Design, Vol. 12, pp. 471-490, 1998
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| FTrees-FS |
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M. Rarey and M. Stahl
Similarity searching in large combinatorial chemistry spaces
Journal of Computer-Aided Molecular Design, Vol. 15, pp. 197-520, 2001
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| HTSview |
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G. Hessler, M. Zimmermann, H. Matter, A. Evers, T. Naumann, T. Lengauer, and M. Rarey
Multiple-ligand-based virtual screening: Methods and Applications of the MTree approach
Journal of Medicinal Chemistry, submitted (2005)
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M. Zimmermann
Rechnerunterstützte Analyse von HTS-Daten
University of Bonn, Germany, 2003
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| 2Ddraw |
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P. Fricker, M. Gastreich, and M. Rarey
Automated Generation of Structural Molecular Formulas under Constraints
Journal of Chemical Information and Computer Sciences, Vol. 44, pp. 1065-1078, 2004
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| general |
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M. Gastreich, H. Briem, C. Lemmen, and M. Rarey
Addressing the Virtual Screening Challenge – The Flex* Approach
In Virtual Screening in Drug Discovery (Alvarez, J., ed.), pp. 25-46, Decker/CRC Press, 2005
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M. Rarey, C. Lemmen, and H. Matter
Algorithmic Engines in Virtual Screening
in Chemoinformatics in Drug Discovery, Tudor Oprea
Editor, pp 59-115, 2005
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T. Lengauer, C. Lemmen, M. Rarey, and M. Zimmermann
Novel technologies for virtual screening
Drug Discovery Today 9, 27-34, 2004
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M. K. Warmuth, J. Liao, G. Rätsch, M. Mathieson, S. Putta, and C. Lemmen
Active Learning with Support Vector Machines in the Drug Discovery Process
Journal of Chemical Information and Computer Sciences, Vol. 43, pp. 667-673, 2003
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M. Stahl and M. Rarey
Detailed Analysis of Scoring Functions for Virtual Screening
Journal of Medicinal Chemistry, Vol. 44, pp. 1035-1042, 2001
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H. Matter and M. Rarey
Design and Diversity Analysis of Compound Libraries for Lead Discovery
In: Jung, G. (Editor):Combinatorial Organic Chemistry, Wiley-VCH, Weinheim, 1999
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T. Lengauer and M. Rarey
Computational Methods for Biomolecular Docking
Current Opinion in Structural Biology, Vol. 6, pp. 402-406, 1996
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