Analysis of Ligand-Macromolecule Contacts: Computational Methods

Due to the many technological advancements in biology and development of new fields such as biotechnology and bioinformatics, our knowledge of cellular functions has been growing rapidly and Biology has entered the Information Age. Along with the technological advancements has come a rapid increase in identification of biomolecular targets involved in diseases. Recently, structure-based drug design studies have emphasized integration of the clinical, cellular, biochemical, structural, and biophysical knowledge of the target. Due to advances in sequencing the human genome, in chemical synthesis and structure determination of biological targets using X-ray and NMR techniques, and in high-performance computing, many scientists from both experimental and theoretical fields focus on structure-based drug design. As scientists in such wide-ranging disciplines, we must understand the data from and educate one another about the strengths and weaknesses of our various disciplines. Since 1990, we have been using computers to visually evaluate ligand binding. In this review, the author will focus on computational methods that not only visualize but also quantify the nature and strength of ligand-macromolecule contacts. Such quantification can be very useful both for medicinal chemists to design ligands and for molecular biologists to design rational protein design experiments to study the effect of amino acid changes on ligand binding.