Chapter 1. Small Molecule Docking and Scoring

  1. Kenny B. Lipkowitz and
  2. Donald B. Boyd
  1. Ingo Muegge1 and
  2. Matthias Rarey2

Published Online: 26 DEC 2001

DOI: 10.1002/0471224413.ch1

Reviews in Computational Chemistry, Volume 17

Reviews in Computational Chemistry, Volume 17

How to Cite

Muegge, I. and Rarey, M. (2001) Small Molecule Docking and Scoring, in Reviews in Computational Chemistry, Volume 17 (eds K. B. Lipkowitz and D. B. Boyd), John Wiley & Sons, Inc., New York, USA. doi: 10.1002/0471224413.ch1

Editor Information

  1. Department of Chemistry, Indiana University—Purdue University at Indianapolis, 402 North Blackford Street, Indianapolis, Indiana 46202–3274, USA

Author Information

  1. 1

    Bayer Research Center, 400 Morgan Lane, West Haven, Connecticut 06516

  2. 2

    German National Research Center for Information Technology (GMD), Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, D-53754 Sankt Augustin, Germany

Publication History

  1. Published Online: 26 DEC 2001
  2. Published Print: 13 JUL 2001

ISBN Information

Print ISBN: 9780471398455

Online ISBN: 9780471224419



  • docking of small molecules;
  • scoring functions;
  • computer-aided drug design


Chapter 1 is a tutorial on small molecules docking to proteins primarily. Determination of the structure of ligand-receptor complexes is important to computer-aided drug design. Topics covered include:

  • Algorithms for Molecular Docking

  • The Docking Problem

  • Placing Fragments and Rigid Molecules

  • Flexible Ligand Docking

  • Handling Protein Flexibility

  • Docking of Combinatorial Libraries

  • Shape and Chemical Complementary Scores

  • Force Field Scoring

  • Empirical Scoring Functions

  • Knowledge-Based Scoring Functions

  • Comparing Scoring Functions in Docking Experiments – Consensus scoring

  • Protein Data Preparation

  • Ligand Database Preparation

  • Docking Calculation

  • Post-Processing

  • Docking as Virtual Screening Tool

  • Docking as a Ligand Design Tool