Searching for the Native Structures of Proteins

Protein structure prediction is one of the major challenges in bioinformatics today. Throughout the past five decades many different algorithmic approaches have been attempted, and while progress has been made the problem remains unsolvable even for many small proteins. While the general objective is to predict the three-dimensional structure from primary sequence, our current knowledge and computational power is simply insufficient to solve a problem of such high complexity. Some prediction algorithms do, however, appear to perform better than others, although it is not always obvious which ones they are and it is perhaps even less obvious why that is. In this review the reported performance results from 18 different recently published prediction algorithms are compared. Furthermore, the general algorithmic settings most likely responsible for the difference in the reported performance are identified, and the specific settings of each of the 18 prediction algorithms are also compared. The average normalized RMSD score reported range from 11.17 to 3.48. With a performance measure including both RMSD scores and CPU time, the currently best performing prediction algorithm is identified to be the I-TASSER algorithm. Two of the algorithmic settings – protein representation and fragment assembly – were found to have definite positive influence on the running time and the predicted structures respectively. There thus appear to be a clear benefit from incorporating this knowledge in the design of new prediction algorithms.