A Complexity Measurement for de novo Protein Folding Michael Scott Brown1, Olivia Minh Trang Hua2*, James A. Coker1 Michael.brown@umuc.edu, oliviamhua@gmail.com, James.Coker@umuc.edu 1The Graduate School, ITS Department, University of Maryland, University College 2Department of Chemistry, Saint Mary’s College of California, Moraga, CA, USA *Currently at University of California-Merced Actual full text article can be found here: http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=7300282 Abstract Predicting how a protein folds based solely on its amino acid sequence is an ongoing challenge for the fields of Bioinformatics and Computer Science. Previous attempts to solve this problem have relied on algorithms and a specific set of benchmark proteins. However, there is currently no method for determining if the set of benchmark proteins share a similar level of complexity with proteins of similar size. As a result, a larger variety of benchmarks might be needed to evade this problem and a measure of complexity established to determine the validity of all benchmarks. We propose here the Ouroboros Complexity Measurement for the de novo folding of proteins. This measurement is easy to compute (not an NP hard problem) and allows the comparing of protein complexity. Keywords—protein; folding; complexity; de novo; structure; benchmark