The undergraduate student, graduate student, and postdoctoral fellow co-authors directly under my supervision are indicated by *, underline, and ||, respectively. The corresponding author’s name is in bold.
Waters, K. L., Rich, K. J., Schwaegerle, N. D., Yang, T., Huo, S., Spratt, D. E. (2024) “The disordered negatively charged C-terminus of the large HECT E3 ubiquitin ligase HERC2 provides structural and thermal stability to the HECT C-lobe”, Protein Sci. 33, e5229.
Yang, T., Han, L., and Huo, S. (2022) “Dynamics and Allosteric Information Pathways of Unphosphorylated c‑Cbl”, J. Chem. Inf. Model. 62, 6148.
Le, A.*, Xu, M., Yang, T., Barrows, L.*, Fontaine, D.*, Huo, S., and Jakobsche, C. E. (2022) “Contrasting solution-state properties within a family of amyloid bindingmolecular tools”, Tetrahedron 116, 132817.
Tan, Q., Liu, H., Duan, M.||, and Huo, S. (2021) “Interplay between Human Islet Amyloid Polypeptide Aggregates and Micro-heterogeneous Membranes”, BBA – Biomembranes 1863, 183691.
Tan, Q., Duan, M.,|| Li, M.,|| Han, L., and Huo, S. (2019) “Approximating Dynamic Proximity with a Hybrid Geometry Energy-based Kernel for Diffusion Maps”, J. Chem. Phys. 151, 105101.
Liu, H., Tan, Q., Han, L., Huo, S. (2017) “Observations on AMBER Force Field Performance under the Conditions of Low pH and High Salt Concentrations”, J. Phys. Chem. B. 121, 9838-9847.
Reardon, M. B., Xu, M., Tan, Q., Baumgartel, P. G.*, Augur, D. J.*, Huo, S., Jakobsche, C. E. (2016) “Long-Range Reactivity Modulations in Geranyl Chloride Derivatives”, J. Org. Chem. 81, 10964-10974. DOI:10.1021/acs.joc.6b01759.
Liu, H., Li, M.,|| Fan, J., and Huo, S. (2016) “Inherent Structure Versus Geometric Metric for State Space Discretization”, J. Compt. Chem. 37, 1251–1258. DOI:10.1002/jcc.24315
Duan, M.,|| Liu, H., Li, M.,|| and Huo, S. (2015) “Network Representation of Conformational Transitions between Hidden Intermediates of Rd-apocytochrome b562”, J. Chem. Phys. 143, 135101.
Duan, M.,|| Han, L., Rudolph, L., and Huo, S. (2014) “Geometric Issues in Dimensionality Reduction and Protein Conformation Space”, Proceeding of Robotics Methods for Structural and Dynamic Modeling of Molecular Systems.
Duan, M.,|| Li, M.,|| Han, L., and Huo, S. (2014) “Euclidean Sections of Protein Conformation Space and Their Implications in Dimensionality Reduction”, Proteins: Structure, Function, and Bioinformatics. 82:2585–2596.
Li, M.,|| Duan, M.,|| Fan, J., Han, L., and Huo, S. (2013) “Graph Representation of Protein Free Energy Landscape”, J. Chem. Phys. 139: 185101.
Duan, M.,|| Fan, J. Li, M.||, Han, L. and Huo, S. (2013) “Evaluation of Dimensionality-Reduction Methods from Peptide Folding−Unfolding Simulations”, J. Chem. Theory. Compt. 9(5): 2490-2497.
Duan, M.|| Fan, J., and Huo, S. (2012) “Conformations of Islet Amyloid Polypeptide Monomers in a Membrane Environment: Implications for Fibril Formation”, PLoSONE 7(11): e47150.
Liu, H. and Huo, S. (2012) “Effects of Two Solvent Conditions on the Free Energy Landscape of the BBL Peripheral Subunit Binding Domain”, J. Phys. Chem. B. 116: 646-652.
Fan, J., Duan, M.,|| Li, D.,|| Wu, H., Yang, H., Han, L., and Huo, S. (2011) “Observation of Two Families of Folding Pathways of BBL”, Biophys. J. 100: 2457–2465.
Wu, H., Canfield, A.,* Adhikari, J., and Huo, S. (2010) “Quantum Mechanical Studies on Model a-Pleated Sheets”, J. Compt. Chem. 31: 1216–1223.
Li, D.,|| Mohanty, S., Irbäck, A., and Huo, S. (2008) “Formation and Growth of Oligomers: A Monte Carlo Study of an Amyloid Tau Fragment”, PLoS Comput. Biol. 4(12): e1000238.
Lim, C., Yang, H., Yang, M., Wang, C., Shi, J., Berg, E. A., Pimentel, D. R., Gwathmey, J. K., Hajjar, R. J., Helmes, M., Costello, C., Huo, S., and Liao. R. (2008) “A Novel Mutant Cardiac Troponin C Disrupts Molecular Motions Critical for Calcium Binding Affinity and Cardiomyocyte Contractility”, Biophys. J. 94, 3577-3589. (Cover).
Li, D.||, Yang, H., Han, L., and Huo, S. (2008) “Predicting the Folding Pathway of Engrailed Homeodomain with a Probabilistic Roadmap Enhanced Reaction-path Algorithm”, Biophys. J. 94, 1622-1629.
Li, D.||, Khanlarzadeh, M., Wang, J., Huo, S., and Bruschweiler, R. (2007) “Evaluation of Configurational Entropy Methods from Peptide Folding-Unfolding Simulation”, J. Phys. Chem. B. 111, 13807-13813.
Li, D.||, Han, L., Huo, S. (2007) “Structural and Pathway Complexity of β-strand Reorganization within Aggregates of Human Transthyretin(105-115) Peptide”, J. Phys. Chem. B. 111, 5425-5433.
Yang, H., Wu, H., Li, D. ||, Han, L., and Huo, S. (2007) “Temperature-Dependent Probabilistic Roadmap: Algorithm for Calculating Variationally Optimized Conformational Transition Pathways”, J. Chem. Theory Comput. 3, 17-25.
Yang, M., Yordanov, B.*, Levy, Y., Brüschweiler, R., and Huo, S. (2006) “The Sequence-Dependent Unfolding Pathway Plays a Critical Role in the Amyloidogenicity of Transthyretin”, Biochemistry. 45, 11992-12002.
Zhao, J., Nelson, D. J., and Huo, S. (2006) “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.
Yang, M., Lei, M.||, Yordanov B.*, and Huo, S. (2006) “Peptide Plane Can Flip in Two Opposite Directions: Implication in Amyloid Formation of Transthyretin”, J. Phys. Chem. B. 110, 5829-5833.
Yang, M., Lei, M.||, Bruschweiler, R., Huo, S. (2005) “Initial conformational changes of human transthyretin under partially denaturing conditions”, Biophys. J. 89, 433-443.
Lei, M.||, Yang, M., Huo, S. (2004) “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.
Yang, M., Lei M.||, Huo, S. (2003) “Why Is Leu55®Pro55 Transthyretin Variant the Most Amyloidogenic: Insights from Molecular Dynamics Simulations of Transthyretin Monomers”, Protein Sci. 12, 1222-1231.
Huo, S., Wang, J., Cieplak, P., Kollman P. A., Kuntz I. D. (2002) “Molecular Dynamics and Free Energy Analyses of Cathepsin d-inhibitor Interactions: Insight into Structure-based Ligand Design”, J. Med. Chem. 45, 1412-1419.
Huo, S., Massova, I., Kollman, P. A. (2002) ”Computational Alanine Scanning of the 1:1 Human Growth Hormone-receptor Complex”, J. Comput. Chem. 23, 15-27.
Wang, J., Wang, W., Huo, S., Lee, M., & Kollman, P. A. (2001) “A Solvation Model based on Weighted Solvent Accessible Surface Area”, J. Phys. Chem. B. 105, 5055-5067.
Kuhn, B., Domini O., Huo, S., Wang J, Kollman, P. A. (2001) “MM-PBSA Applied to Computer-assisted Ligand Design” in “Free Energy Calculations in Rational Drug Design”, Reddy, M. R. and Erion, M. D. editors. Kluwer Academic/Plenum Publishers: New York.
Kollman, P. A., Massova, I., Reyes, C., Kuhn, B., Huo, S., et al. (2000) “Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Mechanics and Continuum Model”, Acc. Chem. Res. 33, 889-897.
Straub, J. E., Guevara, J., Huo, S., Lee J. P. (2002) “Long Time Dynamic Simulations: Exploring the Folding Pathways of an Alzheimer’s Amyloid Ab-peptide”, Acc. Chem. Res. 35, 473-481.
Huo, S., & Straub, J. E. (1999) “Direct Computation of Long Time Dynamical Processes in Peptides and Proteins: Reaction Path Study of the Coil to Helix Transition in Polyalanine”, Proteins: Structure, Function, and Genetics 36, 249-261
Huo, S., & Straub, J. E. (1997) “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.
Ma, J., Huo, S., & Straub, J. E. (1997) “Molecular Dynamics Simulation Study of the B-States of Solvated Carbon Monoxymyoglobin”, J. Am. Chem. Soc. 119, 2541-2551.
Huo, S., Wang, H., & Chen, J. (1995) “Online Control and Spectral Drawing Software for Fluorescence Spectrophotometer”, Computers and Applied Chem. 12, 233-236.
Xiao, G., Huo, S., Tang, R., Ma, Z., & Cao, T. (1992) “Study of the Abnormal Effects of Rare Earth Elements on Tetrahymena”, China Environ. Sci. 12, 292-297.