I have recently read "Molecular Modeling: Basic Principles and Applications". It gives a very good introduction for Structural Bioinformatics and also some bits of information for Molecular Simulation. It is a small, light and clearly written book.
The new chapter "Chemogenomic Approaches to Rational Drug Design" has been added to the third edition (I have actually read the second one).
Table of contents:
- Small Molecules.
- A Case Study for Small Molecule Modeling: Dopamine D3 Receptor Antagonists.
- Introduction to Comparative Protein Modeling.
- Virtual Screening and Docking.
- Scope and Limits of Molecular Docking.
- Chemogenomic Approaches to Rational Drug Design.
- A Case Study for Protein Modeling: the Nuclear Hormone Receptor CAR as an example for Comparative Modeling and the Analysis of Protein-Ligand Complexes.