{"id":49,"date":"2019-05-08T20:34:06","date_gmt":"2019-05-08T20:34:06","guid":{"rendered":"https:\/\/wordpress.clarku.edu\/shuo\/?page_id=49"},"modified":"2024-12-13T21:17:32","modified_gmt":"2024-12-13T21:17:32","slug":"publications","status":"publish","type":"page","link":"https:\/\/wordpress.clarku.edu\/shuo\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"

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.<\/p>\n

Waters, K. L., Rich, K. J., Schwaegerle, N. D., Yang, T.<\/u>, Huo, S., Spratt, D. E.<\/strong> (2024) \u201cThe disordered negatively charged C-terminus of the large HECT E3 ubiquitin ligase HERC2 provides structural and thermal stability to the HECT C-lobe\u201d, Protein Sci.<\/em><\/strong> 33, e5229.<\/p>\n

Yang, T.<\/u>, Han, L., and Huo, S.<\/strong> (2022) \u201cDynamics and Allosteric Information Pathways of Unphosphorylated c\u2011<\/strong>Cbl\u201d, J. Chem. Inf. Model.<\/em><\/strong> 62, 6148.<\/p>\n

Le, A.*, Xu, M., Yang, T.,<\/u> Barrows, L.*, Fontaine, D.*, Huo, S., and Jakobsche, C. E.<\/strong> (2022) \u201cContrasting solution-state properties within a family of amyloid bindingmolecular tools\u201d, Tetrahedron<\/em><\/strong> 116, 132817.<\/p>\n

Tan, Q.<\/u>, Liu, H., <\/u>Duan, M.||<\/sup>, and Huo, S<\/strong>. (2021) \u201cInterplay between Human Islet Amyloid Polypeptide Aggregates and Micro-heterogeneous Membranes\u201d, BBA – Biomembranes<\/em><\/strong> 1863, 183691.<\/p>\n

Tan, Q.<\/u>, Duan, M.,||<\/sup> Li, M.,||<\/sup> Han, L., and Huo, S<\/strong>. (2019) \u201cApproximating Dynamic Proximity with a Hybrid Geometry Energy-based Kernel for Diffusion Maps\u201d, J. Chem. Phys.<\/em><\/strong> 151, 105101.  <\/p>\n

Liu, H., Tan, Q.<\/u>, Han, L., Huo, S.<\/strong> (2017) \u201cObservations on AMBER Force Field Performance under the Conditions of Low pH and High Salt Concentrations\u201d, J. Phys. Chem. B.<\/em><\/strong> 121, 9838-9847.<\/p>\n

Reardon, M. B.<\/u>, Xu, M., Tan, Q., <\/u>Baumgartel, P. G.*, Augur, D. J.*, Huo, S., Jakobsche, C. E.<\/strong> (2016) \u201cLong-Range Reactivity Modulations in Geranyl Chloride Derivatives\u201d, J. Org. Chem.<\/em><\/strong> <\/em><\/strong>81, 10964-10974. DOI:10.1021\/acs.joc.6b01759.<\/p>\n

Liu, H<\/u>., Li, M.,||<\/sup> Fan, J.,<\/u> and Huo, S.<\/strong> (2016) \u201cInherent Structure Versus Geometric Metric for State Space Discretization\u201d, J. Compt. Chem.<\/em><\/strong> 37, 1251\u20131258. DOI:10.1002\/jcc.24315<\/a><\/p>\n

Duan, M.,||<\/sup> Liu, H.<\/u>, Li, M.,|| <\/sup>and Huo, S.<\/strong> (2015) \u201cNetwork Representation of Conformational Transitions between Hidden Intermediates of Rd-apocytochrome b562<\/sub><\/em>\u201d, J. Chem. Phys.<\/em><\/strong> 143, 135101.  <\/p>\n

Duan, M.,||<\/sup>  Han, L.<\/strong>, Rudolph, L., and Huo, S.<\/strong> (2014) \u201cGeometric Issues in Dimensionality Reduction and Protein Conformation Space\u201d, Proceeding of Robotics Methods for Structural and Dynamic Modeling of Molecular Systems.<\/em><\/strong><\/p>\n

Duan, M.,||<\/sup>  Li, M.,||<\/sup>  Han, L., and Huo, S.<\/strong> (2014) \u201cEuclidean Sections of Protein Conformation Space and Their Implications in Dimensionality Reduction\u201d, Proteins: Structure, Function, and Bioinformatics<\/em><\/strong>.<\/em> 82:2585\u20132596.<\/p>\n

Li, M.,||<\/sup> Duan, M.,||<\/sup> Fan, J.<\/u>, Han, L., and Huo, S.<\/strong> (2013) \u201cGraph Representation of Protein Free Energy Landscape\u201d, J. Chem. Phys.<\/em><\/strong> 139: 185101.<\/p>\n

Duan, M.,||<\/sup> Fan, J.<\/u> Li, M.||<\/sup>, Han, L. and Huo, S.<\/strong> (2013) \u201cEvaluation of Dimensionality-Reduction Methods from Peptide Folding\u2212Unfolding Simulations\u201d, J. Chem. Theory. Compt.<\/em><\/strong> 9(5): 2490-2497.<\/p>\n

Duan, M.||<\/sup> Fan, J.,<\/u> and Huo, S.<\/strong> (2012) \u201cConformations of Islet Amyloid Polypeptide Monomers in a Membrane Environment: Implications for Fibril Formation\u201d, PLoS<\/em><\/strong>ONE<\/em><\/strong> 7(11): e47150.<\/p>\n

Liu, H<\/u>. and Huo, S.<\/strong> (2012) “Effects of Two Solvent Conditions on the Free Energy Landscape of the BBL Peripheral Subunit Binding Domain”, J. Phys. Chem. B. <\/em><\/strong>116: 646-652.<\/p>\n

Fan, J., <\/u>Duan, M.,||<\/sup> Li, D.,||<\/sup> Wu, H., Yang, H.,<\/u> Han, L., and Huo, S.<\/strong> (2011) \u201cObservation of Two Families of Folding Pathways of BBL\u201d, Biophys. J.<\/em><\/strong> 100: 2457\u20132465.<\/p>\n

Wu, H<\/u>., Canfield, A.,* Adhikari, J<\/u>., and  Huo<\/strong>, S.<\/strong> (2010) \u201cQuantum Mechanical Studies on Model a-Pleated Sheets\u201d,  J. Compt. Chem.<\/em><\/strong> 31: 1216\u20131223.<\/p>\n

Li, D.,||<\/sup> Mohanty, S., Irb\u00e4ck, A., and Huo<\/strong>, S.<\/strong> (2008) \u201cFormation and Growth of Oligomers: A Monte Carlo Study of an Amyloid Tau Fragment\u201d, PLoS Comput. Biol.<\/em><\/strong> 4(12): e1000238.<\/p>\n

Lim, C.<\/strong>, Yang, H., Yang, M.<\/u>, Wang, C., Shi, J., Berg, E. A., Pimentel, D. R., Gwathmey, J. K., Hajjar, R. J., Helmes, M., Costello, C., Huo, S.<\/strong>, and Liao. R. (2008) \u201cA Novel   Mutant Cardiac Troponin C Disrupts Molecular Motions Critical for Calcium Binding Affinity and Cardiomyocyte Contractility\u201d, Biophys. J.<\/em><\/strong> 94, 3577-3589. (Cover).<\/p>\n

Li, D.||<\/sup>, Yang, H.<\/u>, Han, L., and Huo, S.<\/strong> (2008) \u201cPredicting the Folding Pathway of Engrailed Homeodomain with a Probabilistic Roadmap Enhanced Reaction-path Algorithm\u201d, Biophys. J.<\/em><\/strong> 94, 1622-1629.<\/p>\n

Li, D.||<\/sup>, Khanlarzadeh, M.<\/u>, Wang, J., Huo, S., <\/strong>and Bruschweiler, R. (2007) \u201cEvaluation of Configurational Entropy Methods from Peptide Folding-Unfolding Simulation\u201d, J. Phys. Chem. B. <\/em><\/strong>111, 13807-13813.<\/p>\n

Li, D.||<\/sup>, Han, L., Huo, S.<\/strong> (2007) “Structural and Pathway Complexity of \u03b2-strand Reorganization within Aggregates of Human Transthyretin(105-115) Peptide”, J. Phys. Chem. B. <\/em><\/strong>111, 5425-5433.<\/p>\n

Yang, H., Wu, H.<\/u>, Li, D. ||<\/sup>, Han, L., and Huo, S.<\/strong> (2007) \u201cTemperature-Dependent Probabilistic Roadmap: Algorithm for Calculating Variationally Optimized Conformational Transition Pathways\u201d, J. Chem. Theory Comput.<\/em><\/strong> 3, 17-25.<\/p>\n

Yang, M.<\/u>, Yordanov, B.*, Levy, Y., Br\u00fcschweiler, R., and Huo, S.<\/strong> (2006) \u201cThe Sequence-Dependent Unfolding Pathway Plays a Critical Role in the Amyloidogenicity of Transthyretin\u201d, Biochemistry.<\/em><\/strong> 45, 11992-12002.<\/p>\n

Zhao, J.<\/u>, Nelson, D. J., and Huo, S.<\/strong> (2006) \u201cPotential Influence of Asp in the Ca2+ Coordination Position 5 of Parvalbumin on the Calcium Binding Affinity: A Computational Study\u201d,  J. Inorg. Biochem.<\/em><\/strong> 100, 1879\u20131887.<\/p>\n

Yang, M.<\/u>, Lei, M.||<\/sup>, Yordanov B.*, and Huo, S<\/strong>. (2006) \u201cPeptide Plane Can Flip in Two Opposite Directions: Implication in Amyloid Formation of Transthyretin\u201d, J. Phys. Chem. B. <\/em><\/strong>110, 5829-5833.<\/p>\n

Yang, M.<\/u>, Lei, M.||<\/sup>, Bruschweiler, R., Huo, S.<\/strong> (2005)  \u201cInitial conformational changes of human transthyretin under partially denaturing conditions\u201d, Biophys. J.<\/em><\/strong> 89, 433-443.<\/p>\n

Lei, M.||<\/sup>, Yang, M.<\/u>, Huo<\/strong>, S.<\/strong> (2004) \u201cIntrinsic versus Mutation Dependent Instability\/Flexibility: A Comparative Analysis of the Structure and Dynamics of Wild-type Transthyretin and its Pathogenic Variants\u201d,  J. Struct. Biol. <\/em><\/strong>148, 153-168.<\/p>\n

Yang, M.<\/u>, Lei M.||<\/sup>, Huo, S.<\/strong> (2003)  \u201cWhy Is Leu55\u00aePro55 Transthyretin Variant the Most Amyloidogenic: Insights from Molecular Dynamics Simulations of Transthyretin Monomers\u201d,  Protein Sci.<\/em><\/strong>  12, 1222-1231.<\/p>\n

Huo, S.<\/strong>, Wang, J., Cieplak, P., Kollman P. A., Kuntz I. D. (2002) \u201cMolecular Dynamics and Free Energy Analyses of Cathepsin d-inhibitor Interactions: Insight into Structure-based Ligand Design\u201d, J. Med. Chem.<\/em><\/strong> 45, 1412-1419.<\/p>\n

Huo, S., Massova, I., Kollman, P. A.<\/strong> (2002) \u201dComputational Alanine Scanning of the 1:1 Human Growth Hormone-receptor Complex\u201d, J. Comput. Chem.<\/em><\/strong> 23, 15-27.<\/p>\n

Wang, J., Wang, W., Huo, S., Lee, M., & Kollman, P. A.<\/strong> (2001)  \u201cA Solvation Model based on Weighted Solvent Accessible Surface Area\u201d,  J. Phys. Chem. B.<\/em><\/strong> 105, 5055-5067.<\/p>\n

Kuhn, B., Domini O., Huo, S., Wang J, Kollman, P. A.<\/strong>  (2001) \u201cMM-PBSA Applied to Computer-assisted Ligand Design\u201d  in \u201cFree Energy Calculations in Rational Drug Design\u201d,  Reddy, M. R. and Erion, M. D. editors.  Kluwer Academic\/Plenum Publishers: New York.<\/p>\n

Kollman, P. A.<\/strong>, Massova, I., Reyes, C., Kuhn, B., Huo, S., et al. (2000) \u201cCalculating Structures and Free Energies of Complex Molecules: Combining Molecular Mechanics and Continuum Model\u201d, Acc. Chem. Res.<\/em><\/strong> 33, 889-897.<\/p>\n

Straub, J. E.<\/strong>, Guevara, J., Huo, S., Lee J. P. (2002)  \u201cLong Time Dynamic Simulations: Exploring the Folding Pathways of an Alzheimer\u2019s Amyloid Ab-peptide\u201d,  Acc. Chem. Res.<\/em>  35<\/strong>, 473-481.<\/p>\n

Huo, S., & Straub, J. E.<\/strong> (1999) \u201cDirect Computation of Long Time Dynamical Processes in Peptides and Proteins: Reaction Path Study of the Coil to Helix Transition in Polyalanine\u201d, Proteins: Structure, Function, and Genetics<\/em> 36<\/strong>, 249-261<\/p>\n

Huo, S., & Straub, J. E.<\/strong> (1997) \u201cThe MaxFlux Algorithm for Calculating Variationally Optimized Reaction Paths for Conformational Transitions in Many Body Systems at Finite Temperature\u201d, J. Chem. Phys.<\/em> 107<\/strong>, 5000-5006.<\/p>\n

Ma, J., Huo, S., & Straub, J. E.<\/strong> (1997) \u201cMolecular Dynamics Simulation Study of the B-States of Solvated Carbon Monoxymyoglobin\u201d, J. Am. Chem. Soc.<\/em> 119<\/strong>, 2541-2551.<\/p>\n

Huo<\/strong>, S.<\/strong>, Wang, H., & Chen, J. (1995) \u201cOnline Control and Spectral Drawing Software for Fluorescence Spectrophotometer\u201d, Computers and Applied Chem.<\/em><\/strong> 12<\/strong>, 233-236.<\/p>\n

Xiao, G., Huo, S., Tang, R., Ma, Z., & Cao, T. <\/strong>(1992) \u201cStudy of the Abnormal Effects of Rare Earth Elements on Tetrahymena\u201d, China Environ. Sci.<\/em><\/strong> 12<\/strong>, 292-297.<\/p>\n","protected":false},"excerpt":{"rendered":"

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. […]<\/p>\n","protected":false},"author":894,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"ngg_post_thumbnail":0,"footnotes":""},"class_list":["post-49","page","type-page","status-publish","czr-hentry"],"_links":{"self":[{"href":"https:\/\/wordpress.clarku.edu\/shuo\/wp-json\/wp\/v2\/pages\/49","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/wordpress.clarku.edu\/shuo\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/wordpress.clarku.edu\/shuo\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/wordpress.clarku.edu\/shuo\/wp-json\/wp\/v2\/users\/894"}],"replies":[{"embeddable":true,"href":"https:\/\/wordpress.clarku.edu\/shuo\/wp-json\/wp\/v2\/comments?post=49"}],"version-history":[{"count":0,"href":"https:\/\/wordpress.clarku.edu\/shuo\/wp-json\/wp\/v2\/pages\/49\/revisions"}],"wp:attachment":[{"href":"https:\/\/wordpress.clarku.edu\/shuo\/wp-json\/wp\/v2\/media?parent=49"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}