Current Trends in Protein Docking

Art Eunsung Cho

Department of Biotechnology and Bioinformatics,

Korea University

An ultimate goal of the bioinformatics revolution is biofunctionomics, the prediction of the function of every protein in the genome.  The first step in predicting function is to predict where various ligands bind to the protein and how strongly.  There has been a great deal of progress in using theory and computation to dock small ligands to the 3D structures of proteins during last few decades.  Protein docking has been a major tool in this endeavor.  In recent years has it seen a boost, and become an essential tool for drug discovery.

The objective of this tutorial will be to provide an overview of docking technology and its programs.  Attendees will be guided through some of the techniques used in docking industry.  In that process, s/he will be given an opportunity to learn about the latest docking programs.

The tutorial will start with a technological overview with history of docking.  In this part, the usage of docking in pharmaceutical industry will also be reviewed.  Next, a couple of docking programs will be introduced and their functions will be demonstrated.  Subsequently, a comparison with other docking programs will be provided.  Lastly, some novel docking methods will be explained and speculation on the future direction of the industry will be presented.

Tentative Content List

General Overview

             Contents of tutorial

Introduction

             A brief history of docking

             Evolution of docking technology

             Docking in pharmaceutical industry

Docking Programs

             UCSF DOCK4.0

             Glide

             Comparison of docking programs

Novel Methods in Docking

             QM/MM docking

             ICM