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Matthias Rarey

Matthias Rarey

D-Index & Metrics

Computer Science

D-Index
56
Citations
19347
World Ranking
3970
National Ranking
176

Overview

Matthias Rarey is affiliated with the Universität Hamburg in Germany, where their research focuses primarily on the intersection of biochemistry, genetics, molecular biology, and computer science. Their work integrates computational methods with molecular biology to advance the understanding of protein structures, enzyme functionality, and drug discovery techniques.

With a substantial publication record across several fields, the scientist has contributed notably to:

  • Computational Drug Discovery Methods
  • Protein Structure and Dynamics
  • Enzyme Structure and Function
  • Chemical Synthesis and Analysis
  • Machine Learning in Materials Science
  • Analytical Chemistry and Chromatography
  • Microbial Natural Products and Biosynthesis

Their extensive work spans several subfields including molecular biology, computational theory and mathematics, materials chemistry, spectroscopy, and pharmacology. This multidisciplinary approach supports advancements in molecular modeling and drug design.

Frequent publication venues for their work include:

  • Journal of Chemical Information and Modeling
  • Journal of Computer-Aided Molecular Design
  • bioRxiv (Cold Spring Harbor Laboratory)
  • Nucleic Acids Research
  • Wiley Interdisciplinary Reviews Computational Molecular Science

Among their recent published papers are:

  • "X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease," 2021, Science
  • "ProteinsPlus: interactive analysis of protein-ligand binding interfaces," 2020, Nucleic Acids Research
  • "ProteinsPlus: a comprehensive collection of web-based molecular modeling tools," 2022, Nucleic Acids Research
  • "Exploration of Ultralarge Compound Collections for Drug Discovery," 2022, Journal of Chemical Information and Modeling
  • "Binding Site Detection Remastered: Enabling Fast, Robust, and Reliable Binding Site Detection and Descriptor Calculation with DoGSite3," 2023, Journal of Chemical Information and Modeling

The scientist regularly collaborates with several co-authors, including:

  • Christiane Ehrt
  • Florian Flachsenberg
  • Joel Graef
  • Patrick Penner
  • Torben Gutermuth

Matthias Rarey's research integrates computational tools and experimental methods to investigate protein-ligand interactions and contribute to the development of computational drug discovery protocols. Their work is positioned at the convergence of computational theory and molecular biology, providing insights that are disseminated through reputed scientific journals dedicated to chemical information, molecular design, and nucleic acid research.

Best Publications

  • A Fast Flexible Docking Method using an Incremental Construction Algorithm

    Matthias Rarey;Bernd Kramer;Thomas Lengauer;Gerhard Klebe

  • Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking.

    Bernd Kramer;Matthias Rarey;Thomas Lengauer

  • Computational methods for biomolecular docking

    Thomas Lengauer;Matthias Rarey

  • Detailed Analysis of Scoring Functions for Virtual Screening

    Martin Stahl;Matthias Rarey

  • FlexE: efficient molecular docking considering protein structure variations.

    H Claussen;C Buning;M Rarey;T Lengauer

  • DoGSiteScorer: a web server for automatic binding site prediction, analysis and druggability assessment.

    Andrea Volkamer;Daniel Kuhn;Friedrich Rippmann;Matthias Rarey

  • On the art of compiling and using 'drug-like' chemical fragment spaces.

    Jörg Degen;Christof Wegscheid-Gerlach;Andrea Zaliani;Matthias Rarey

  • Combining Global and Local Measures for Structure-Based Druggability Predictions

    Andrea Volkamer;Daniel Kuhn;Thomas Grombacher;Friedrich Rippmann

  • Molecular complexes at a glance

    Katrin Stierand;Patrick C. Maaß;Matthias Rarey

  • Feature trees: a new molecular similarity measure based on tree matching.

    Matthias Rarey;J. Scott Dixon

  • Drawing the PDB: Protein−Ligand Complexes in Two Dimensions

    Katrin Stierand;Matthias Rarey

  • In Need of Bias Control: Evaluating Chemical Data for Machine Learning in Structure-Based Virtual Screening

    Jochen Sieg;Florian Flachsenberg;Matthias Rarey

  • Analyzing the topology of active sites: on the prediction of pockets and subpockets.

    Andrea Volkamer;Axel Griewel;Thomas Grombacher;Matthias Rarey

  • A consistent description of HYdrogen bond and DEhydration energies in protein-ligand complexes: methods behind the HYDE scoring function.

    Nadine Schneider;Gudrun Lange;Sally A. Hindle;Robert Klein

  • Placement of medium-sized molecular fragments into active sites of proteins.

    Matthias Rarey;Stephan Wefing;Thomas Lengauer

  • Multiple automatic base selection: protein-ligand docking based on incremental construction without manual intervention.

    Matthias Rarey;Bernd Kramer;Thomas Lengauer

  • Novel technologies for virtual screening

    Thomas Lengauer;Christian Lemmen;Matthias Rarey;Marc Zimmermann

  • ProteinsPlus: a web portal for structure analysis of macromolecules.

    Rainer Fährrolfes;Stefan Bietz;Florian Flachsenberg;Agnes Meyder

  • Small Molecule Docking and Scoring

    Ingo Muegge;Matthias Rarey

  • ProteinsPlus: interactive analysis of protein-ligand binding interfaces.

    Katrin Schöning-Stierand;Konrad Diedrich;Rainer Fährrolfes;Florian Flachsenberg

  • Flexible docking under pharmacophore type constraints.

    Sally A. Hindle;Matthias Rarey;Christian Buning;Thomas Lengauer

Frequent Co-Authors

Henry N. Chapman
Henry N. Chapman Universität Hamburg
Rolf Hilgenfeld
Rolf Hilgenfeld University of Lübeck
Dušan Turk
Dušan Turk Jožef Stefan Institute
Thomas Lengauer
Thomas Lengauer Max Planck Institute for Informatics
Benjamin L. Schulz
Benjamin L. Schulz University of Queensland
Joachim Hauber
Joachim Hauber Heinrich-Pette-Institute
Russell J. Cox
Russell J. Cox University of Hannover
Rebecca C. Wade
Rebecca C. Wade Heidelberg Institute for Theoretical Studies
An-Ping Zeng
An-Ping Zeng Hamburg University of Technology
Antony J. Williams
Antony J. Williams Environmental Protection Agency

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