Molecular modeling has undergone a remarkable transformation in the last 20 years, as biomolecular simulation moves from the realm of specialists to the wider academic community. This book provides thorough introductions and a compilation of step-by-step methods applicable to problems faced by non-specialists – especially those new to the software packages used in molecular modeling. Tips on troubleshooting and avoiding common pitfalls are included, along with chapters covering a wide range of subjects ranging from free energy calculation to applications for drug design. Written by an internationally distinguished panel of investigators and outlining the most striking developments in the field, the book is an invaluable resource for those in the industry, as well as a cutting-edge reference for students and professionals in the fields of chemistry, biochemistry, biology, biophysics and bioinformatics. Links to downloadable software made available by the authors are also provided.