Optimization algorithms and natural computing in drug discovery

Recent efforts in structural biology have lead to considerable growth in the number of structures available which are potential drug targets. Considerable progress in docking algorithms has enabled in silico screening as an attractive alternative to traditional screening for drug leads and optimization, because in vitro high-throughput screening of compounds is costly and relatively inefficient. In molecular modeling one is often confronted with hard problems, such as highly complicated energy landscapes in many dimensions and a combinatorial explosion of the number of possible solutions. Recently, however, several algorithms based on situations in nature have appeared and in this review we illustrate their strengths and weaknesses.: