publications

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.

LeadIT

  • Maass P, Schulz-Gasch T, Stahl M, Rarey M.
    ReCore: A fast and versatile method for scaffold hopping based on small molecule crystal structure conformations.
    J Chem Inf Model. 2007 Mar-Apr;47(2):390-9. Epub 2007 Feb 17.
  • Reulecke I, Lange G, Albrecht J, Klein R, Rarey M.
    Towards an integrated description of hydrogen bonding and dehydration: decreasing false positives in virtual screening with the HYDE scoring function.
    ChemMedChem. 2008 Jun;3(6):885-97.
  • Stierand K, Rarey M.
    From modeling to medicinal chemistry: automatic generation of two-dimensional complex diagrams.
    ChemMedChem. 2007 Jun;2(6):853-60.
  • Stierand K, Maass PC, Rarey M.
    Molecular complexes at a glance: automated generation of two-dimensional complex diagrams.
    Bioinformatics. 2006 Jul 15;22(14):1710-6. Epub 2006 Apr 21.
  • Lippert T, Rarey M.
    Fast automated placement of polar hydrogen atoms in protein-ligand complexes.
    J Cheminform. 2009 Aug 12;1(1):13.

FlexX

  • 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
  • M. Rarey, B. Kramer, and T. Lengauer
    Docking of hydrophobic ligands with interaction-based matching algorithms
    Bioinformatics, Vol. 15, pp. 243-250, 1999
  • 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
  • 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
  • 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
  • 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
  • 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
  • M. Rarey, S Wefing, and T. Lengauer
    Placement of medium-sized molecular fragments into active sites of proteins
    Journal of Computer-Aided Molecular Design, Vol. 10, pp. 41-54, 1996
  • 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
  • I. Schellhammer and M. Rarey
    FlexX-Scan: Fast Structure-Based Virtual Screening
    PROTEINS: Structure, Function, and Genetics 57, 504-517, 2004
  • Seebeck B, Reulecke I, Kämper A, Rarey M.
    Modeling of metal interaction geometries for protein-ligand docking.
    Proteins. 2008 May 15;71(3):1237-54.

FlexXC

  • M. Rarey and T. Lengauer
    A recursive algorithm for efficient combinatorial library docking
    Perspective in Drug Discovery and Design 20: 63-81, 2000

FlexX-Pharm

  • 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
  • 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
  • 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

FlexX-Ensemble

  • H. Claußen, C. Buning, M. Rarey, and T. Lengauer
    FlexX-Ensemble: Efficient Molecular Docking into Flexible Protein Structures
    Journal of Molecular Biology, Vol. 308, pp. 377-395, 2001

FlexS

  • 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
  • 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
  • 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
  • C. Lemmen and T. Lengauer
    Time-efficient flexible superposition of medium-sized molecules
    Journal of Computer-Aided Molecular Design, Vol. 11, pp. 357-368, 1997

FTrees

  • 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
  • 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
  • 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

FTrees-FS

  • M. Rarey and M. Stahl
    Similarity searching in large combinatorial chemistry spaces
    Journal of Computer-Aided Molecular Design, Vol. 15, pp. 197-520, 2001
  • Lessel U, Wellenzohn B, Lilienthal M, Claussen H.
    Searching Fragment Spaces with feature trees.
    J Chem Inf Model. 2009 Feb;49(2):270-9.
  • Boehm M, Wu TY, Claussen H, Lemmen C.
    Similarity searching and scaffold hopping in synthetically accessible combinatorial chemistry spaces.
    J Med Chem. 2008 Apr 24;51(8):2468-80. Epub 2008 Apr 2.

general

  • 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
  • M. Rarey, C. Lemmen, and H. Matter
    Algorithmic Engines in Virtual Screening
    in Chemoinformatics in Drug Discovery, Tudor Oprea
    Editor, pp 59-115, 2005
  • T. Lengauer, C. Lemmen, M. Rarey, and M. Zimmermann
    Novel technologies for virtual screening
    Drug Discovery Today 9, 27-34, 2004
  • 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
  • M. Stahl and M. Rarey
    Detailed Analysis of Scoring Functions for Virtual Screening
    Journal of Medicinal Chemistry, Vol. 44, pp. 1035-1042, 2001
  • 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
  • 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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