B. Gipson, D. Hsu, L.E. Kavraki, and J.C. Latombe. Computational models of protein kinematics and dynamics: Beyond simulationAnnu. Rev. Anal. Chem, 5:273–291, 2012. DOI: 10.1146/annurev-anchem-062011-143024.
BibTeX PDF

T.-H. Chiang, D. Hsu, and J.C. Latombe. Markov dynamic models for long-timescale protein motionBioinformatics, 26(12):i269–i277, 2010. Special issue on Int. Conf. on Intelligent Systems for Molecular Biology (ISMB) 2010.
BibTeX  PDF

A. Nigham, L. Tucker-Kellogg, I. Mihalek, C. Verma, and D. Hsu. pFlexAna: Detecting conformational changes in remotely related proteinsNucleic Acids Res., 36:W246–W251, 2008. DOI: 10.1093/nar/gkn259.
BibTeX  PDF

A. Nigham and D. Hsu. Protein conformational flexibility analysis with noisy data. J. Computational Biology, 15(7):813–828, 2008.
BibTeX

A. Nigham and D. Hsu. Protein conformational flexibility analysis with noisy data. In Proc. ACM Int. Conf. on Computational Biology (RECOMB), pp. 396–411, 2007.
BibTeX  PDF

T.-H. Chiang, M.S. Apaydin, D.L. Brutlag, D. Hsu, and J.C. Latombe. Using stochastic roadmap simulation to predict experimental quantities in protein folding kinetics: Folding rates and phi-valuesJ. Computational Biology, 14(5):578–593, 2007.
BibTeX PDF

T.-H. Chiang, M.S. Apaydin, D.L. Brutlag, D. Hsu, and J.C. Latombe. Predicting experimental quantities in protein folding kinetics using stochastic roadmap simulation. In Proc. ACM Int. Conf. on Computational Biology (RECOMB), pp. 410–424, Springer, 2006.
BibTeX  PDF

M.S. Apaydin, D.L. Brutlag, C. Guestrin, D. Hsu, J.C. Latombe, and C. Varma. Stochastic roadmap simulation: an efficient representation and algorithm for analyzing molecular motionJ. Computational Biology, 10(3-4):247–281, 2003.
BibTeX PDF

D. Brutlag, M.S. Apaydin, C. Guestrin, D. Hsu, C. Varma, A. Singh, and J.-C. Latombe. Using robotics to fold proteins and dock ligandsBioinformatics, 18:S74–S83, 2002.
BibTeX  PDF  HTML

R.-P. Berretty, D. Hsu, L. Kettner, A. Mascarenhas, M.R. Redinbo, and J. Snoeyink. Ligand binding to the pregnane X receptor by geometric matching of hydrogen bonding. In L. Florea and others, editors, Currents in Computational Molecular Biology, pp. 22–23, 2002. The booklet contains extended poster abstracts from RECOMB 2002.
BibTeX PDF

M.S. Apaydin, D.L. Brutlag, C. Guestrin, D. Hsu, and J.C. Latombe. Stochastic conformational roadmaps for computing ensemble properties of molecular motion. In J.-D. Boissonnat and others, editors, Algorithmic Foundations of Robotics V—Proc. Workshop on the Algorithmic Foundations of Robotics (WAFR), pp. 131–148, Springer, 2002.
BibTeX

M.S. Apaydin, D.L. Brutlag, C. Guestrin, D. Hsu, and J.C. Latombe. Stochastic roadmap simulation: An efficient representation and algorithm for analyzing molecular motion. In Proc. ACM Int. Conf. on Computational Biology (RECOMB), pp. 12–21, 2002.
BibTeX PDF