177. E.A. Coutsias, C. Seok, M.P. Jacobson, and K.A. Dill.  A Kinematic View of Loop Closure  Journal of Computational Chemistry 25: 510-528 (2004). (PDF) (Code)

182. Evangelos A. Coutsias, Chaok Seok, Ken A. Dill.   Using quaternions to calculate RMSD.  Journal of Computational Chemistry, 25 : 1849-1857 (2004). (PDF) (Code)

199. J.D. Chodera, W.C. Swope, J.W. Pitera, C. Seok, and K.A. Dill.   Use of the weighted histogram analysis method for the analysis of simualted and parallel tempering simulations.   Journal of Chemical Theory and Computation, 3: 26--41 (2007). (PDF) (Supplementary Material PDF) (Code)