Computational chemistry and molecular modeling of electron-transfer proteins

The methods of computational chemistry and molecular modeling are becoming more and more accessible to biochemists with the advent of fast, inexpensive graphics workstations and well-tested computer programs. The state of the art in small molecules allows chemists to use these programs as "black boxes" and be confident of the results at an amazingly high level of precision. This is not the case, however, for biological macro-molecules at this time. Therefore, it is necessary before using the programs listed in Section I that we familiarize ourselves with their theoretical basis and limitations. It is also important that they be used in the context of the accumulated literature on their use. The survey given in this chapter is intended as an introduction to these tools and as a source for initiating the discovery process with the literature cited.