Small Molecule Docking and Scoring

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