Introduction. Biomolecular simulation

Introduction. Biomolecular simulation.

'Everything that living things do can be understood in terms of the jigglings and wigglings of atoms' as Richard Feynman provocatively stated nearly 50 years ago. But how can we 'see' this wiggling and jiggling and understand how it drives biology? Increasingly, computer simulations of biological macromolecules are helping to meet this challenge.

Introduction to biomolecular NMR spectroscopy

An Introduction to Biomolecular Graphics

One need only compare the number of three-dimensional molecular illustrations in the first (1990) and third (2004) editions of Voet & Voet’s Biochemistry in order to appreciate this field’s profound communicative value in modern biological sciences – ranging from medicine, physiology, and cell biology, to pharmaceutical chemistry and drug design, to structural and computational biology. The cli...

The Amber biomolecular simulation programs

We describe the development, current features, and some directions for future development of the Amber package of computer programs. This package evolved from a program that was constructed in the late 1970s to do Assisted Model Building with Energy Refinement, and now contains a group of programs embodying a number of powerful tools of modern computational chemistry, focused on molecular dynam...

Equilibrium Sampling in Biomolecular Simulation

Equilibrium sampling of biomolecules remains an unmet challenge after more than 30 years of atomistic simulation. Efforts to enhance sampling capability, which are reviewed here, range from the development of new algorithms to parallelization to novel uses of hardware. Special focus is placed on classifying algorithms — most of which are underpinned by a few key ideas — in order to understand t...