Huo Group
                                                        Computational Chemistry & Biophysics

H. Liu, M. Li, J. Fan and S. Huo. “Inherent Structure Versus Geometric Metric for State Space Discretization”. Journal of computational chemistry. 2016 early view.

M. Duan, H. Liu, M. Li, L. Han and S. Huo. “Network representation of conformational transitions between hidden intermediates of Rd-apocytochrome b562”. J. Chem. Phys. 143(13), 135101 (2015).

M. Duan, M. Li, L. Han, and S. Huo, "Euclidean sections of protein conformation space and their implications in dimensionality reduction". Proteins: Structure, Function, and Bioinformatics. 82(10), 2585-2596 (2014).


M. Li, M. Duan, J. Fan, L. Han and S. Huo. “Graph representation of protein free energy landscape”. J. Chem. Phys. 139: 185101 (2013).

M. Duan, J. Fan, M. Li, L. Han and S. Huo. "Evaluation of Dimensionality-Reduction Methods from Peptide Folding–Unfolding Simulations". J. Chem. Theory Comput. 9(5): 2490-2497 (2013).

M. Duan, J. Fan, and S. Huo. "Conformations of Islet Amyloid Polypeptide Monomers in a Membrane Environment: Implications for Fibril Formation". PLoS ONE 7(11): e47150 (2012).

H. Liu, S. Huo. "Effects of two solvent conditions on the free energy landscape of the BBL peripheral subunit binding domain". J. Phys. Chem. B. 116: 646-652 (2012).

J. Fan, M. Duan, D. Li, H. Wu, H. Yang, L. Han, S. Huo. "Observation of two families of folding pathways of BBL". Biophys. J. 100: 2457-2465 (2011).

H. Wu, A. Canfield, J. Adhikari, S. Huo. "Quantum mechanical studies on model alpha-pleated sheets". J Comput. Chem. 31: 1216-1223 (2010).

D. Li, S. Mohanty, A. Irbäck, S. Huo.  "Formation and Growth of Oligomers: A Monte Carlo study of an amyloid Tau fragment". PLoS Comput. Biol. 4(12):  e1000238 (2008).

C. Lim, H. Yang, M. Yang, C. Wang, J. Shi, E. A. Berg, D. R. Pimentel,  J. K. Gwathmey, R. J. Hajjar, M. Helmes, C. Costello, S. Huo, R. Liao. "A novel mutant cardiac troponin C. disrupts molecular motions critical for calcium binding affinity and cardiomyocyte contractility". Biophys. J. 94: 3577-3589 (2008). (On the Cover of May 1st issue) 

D. Li, H. Yang, L. Han, S. Huo. "Predicting the folding pathway of engrailed homeodomain with a probabilistic roadmap enhanced reaction-path algorithm". Biophys. J. 94: 1622-1629 (2008).

D. Li, M. Khanlarzadeh, J. Wang, S. Huo, R. Brüschweiler. "Evaluation of configurational entropy methods from peptide folding-unfolding simulation". J. Phys. Chem. B. 111:13807-13813 (2007).

D. Li, L. Han, S. Huo. "Structural and pathway complexity of β-strand reorganization within aggregates of human transthyretin(105-115) peptide". J. Phys. Chem. B. 111: 5425-5433 (2007).

H. Yang, H. Wu, D. Li, L. Han, S. Huo. "Temperature-Dependent probabilistic roadmap: algorithm for calculating variationally optimized conformational transition pathways". J. Chem. Theory Comput. 3: 17-25 (2007). 

M. Yang, B. Yordanov Y. Levy, R. Brüschweiler, and S. Huo. "Sequence-Dependent unfolding pathway plays a critical role in the amyloidogenicity of transthyretin". Biochemistry. 45: 11992-12002 (2006).

J. Zhao, D. J. Nelson, S. Huo. "Potential influence of Asp in the Ca2+ coordination position 5 of Parvalbumin on the calcium binding affinity: A computational study". J. Inorg. Biochem. 100: 1879-1887 (2006).

M. Yang, M. Lei, B. Yordanov, S. Huo. "Peptide plane can flip in two opposite directions: implication in amyloid formation of transthyretin". J. Phys. Chem. B. 110: 5829-5833 (2006).
M. Yang, M. Lei, R. Brüschweiler, S. Huo. "Initial conformational changes of human transthyretin under partially denaturing conditions". Biophys. J. 89: 433-443 (2005).

M. Lei, M. Yang, S. Huo. "Intrinsic versus mutation dependent instability/flexibility: A comparative analysis of the structure and dynamics of wild-type transthyretin and its pathogenic variants". J. Struct. Biol. 148: 153-168, (2004).

M. Yang, M. Lei, S. Huo. "Why is Leu55Pro55 transthyretin variant the most amyloidogenic: Insight from molecular dynamics simulations of transthyetin monomers". Prot. Sci. 12: 1222-1231 (2003).

S. Huo,  I. Massova, P.A. Kollman. "Computational alanine scanning of the 1:1 Human growth Hormone-Receptor complex". J. Comput. Chem. 23: 15-27 (2002). 

S. Huo, J. E. Straub. "The MaxFlux algorithm for calculating variationally optimized reaction paths for conformational transitions in many body systems at finite temperature". J. Chem. Phys. 107: 5000-5006 (1997).