Chapter 1. Small Molecule Docking and Scoring
- Kenny B. Lipkowitz,
- Donald B. Boyd
Published Online: 26 DEC 2001
DOI: 10.1002/0471224413.ch1
Copyright © 2001 John Wiley & Sons, Inc.
Book Title
Reviews in Computational Chemistry, Volume 17
Additional Information
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
Department of Chemistry, Indiana University—Purdue University at Indianapolis, 402 North Blackford Street, Indianapolis, Indiana 46202–3274, USA
Publication History
- Published Online: 26 DEC 2001
- Published Print: 13 JUL 2001
Book Series:
ISBN Information
Print ISBN: 9780471398455
Online ISBN: 9780471224419
- Summary
- Chapter
Keywords:
- docking of small molecules;
- scoring functions;
- computer-aided drug design
Summary
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