Unit

UNIT 8.12 Flexible Ligand Docking with Glide

  1. Matthew P. Repasky1,
  2. Mee Shelley2,
  3. Richard A. Friesner3

Published Online: 1 JUN 2007

DOI: 10.1002/0471250953.bi0812s18

Lab Protocol Title

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

Additional Information

How to Cite

Repasky, M. P., Shelley, M. and Friesner, R. A. 2007. Flexible Ligand Docking with Glide. Current Protocols in Bioinformatics. 18:8.12:8.12.1–8.12.36.

Author Information

  1. 1

    Schrodinger, L.L.C., New York, New York

  2. 2

    Schrodinger, L.L.C., Portland, Oregon

  3. 3

    Columbia University, New York, New York

Publication History

  1. Published Online: 1 JUN 2007
  2. Published Print: JUN 2007
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Abstract

Glide is a ligand docking program for predicting protein-ligand binding modes and ranking ligands via high-throughput virtual screening. Glide utilizes two different scoring functions, SP and XP GlideScore, to rank-order compounds. Three modes of sampling ligand conformational and positional degrees of freedom are available to determine the optimal ligand orientation relative to a rigid protein receptor geometry. This unit presents protocols for flexible ligand docking with Glide, optionally including ligand constraints or ligand molecular similarities.

Keywords:

  • ligand docking;
  • protein-ligand interactions;
  • protein-ligand binding
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