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Recent papers

[Since 2014]


• J. Chen and Y. Wu , "A Multiscale Computational Model for Simulating the Kinetics of Protein Complex Assembly". Methods Mol Biol. (2018) 1764:401-411.
• J. Chen, B. Wang and Y. Wu , "Structural Characterization and Function Prediction of Immunoglobulin-like Fold in Cell Adhesion and Cell Signaling". Journal of Chemical Information and Modeling (2018) Feb 26;58(2):532-542.
• J. Chen, S. C. Almo and Y. Wu , "General principles of binding between cell surface receptors and multi-specific ligands: A computational study". PLoS Computational Biology (2017) Oct 10;13(10):e1005805. doi: 10.1371/journal.pcbi.1005805.
• Z. Xie J. Chen and Y. Wu , "Predicting Protein-protein Association Rates using Coarse-grained Simulation and Machine Learning". Scientific Reports (2017)  Apr 18;7:46622. doi: 10.1038/srep46622.
• J. Chen and Y. Wu , "Understanding the Functional Roles of Multiple Extracellular Domains in Cell Adhesion Molecules with a Coarse-Grained Model". Journal of Molecular Biology (2017) Apr 7;429(7):1081-1095. 
• J. Chen, Z. Xie and Y. Wu , "Understand protein functions by comparing the similarity of local structural environments". Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics (2017) Feb. PMID: 27884635 
• J. Chen, Z. Xie and Y. Wu , "Elucidating the Functional Roles of Spatial Organization in Cross-Membrane Signal Transduction by a Hybrid Simulation Method". Journal of Computational Biology (2016) Mar 30. PMID: 27028148
• Z. Xie, J. Chen and Y. Wu , "Multiscale Model for the Assembly Kinetics of Protein Complexes". J. Physical Chemistry B (2016) 120(4):621-32. doi: 10.1021/acs.jpcb.5b08962.
• J. Chen, Z. Xie and Y. Wu , "Elucidating the general principles of cell adhesion with a coarse-grained simulation model". Molecular BioSystems (2016) 12(1):205-18. doi: 10.1039/c5mb00612k.
• J. Chen, Z. Xie and Y. Wu , "Study of protein structural deformations under external mechanical perturbations by a coarse-grained simulation method". Biomechanics and Modeling in Mechanobiology (2016) 12(1):205-18. doi: 10.1039/c5mb00612k.
• Z. Xie, J. Chen, Y. Zhao and Y. Wu , "Decomposing the space of protein quaternary structures with the interface fragment pair library". BMC Bioinformatics (2015) 16: 14. doi:10.1186/s12859-014-0437-4
• Z. Xie, J. Chen and Y. Wu , "Linking 3D and 2D binding kinetics of membrane proteins by multi-scale simulations". Protein Science (2014) doi: 10.1002/pro.2574.
• J. Chen, Z. Xie and Y. Wu , "Computational Modeling of the Interplay between Cadherin-Mediated Cell Adhesion and Wnt Signaling Pathway". PLoS ONE (2014) 9(6): e100702. doi:10.1371/journal.pone.0100702.
• J. Chen, Z. Xie and Y. Wu , "A multiscale model for simulating binding kinetics of proteins with flexible linkers". Proteins: Structure, Function, and Bioinformatics (2014) Oct; 82(10):2512-22.
• Z. Xie, J. Chen and Y. Wu , "A coarse-grained model for the simulations of biomolecular interactions in cellular environments". Journal of Chemical Physics (2014) 140: 054112.


[2008-2013]


• Y. Wu, B. Honig and A. Ben-Shaul , "Theory and simulations of adhesion receptor dimerization on membrane surfaces". Biophysical Journal (2013) 104: 1221-1229.
• Y. Wu, J. Vendome, L. Shapiro, A. Ben-Shaul and B. Honig, "Transforming Binding Affinities from Three Dimension to Two With Application to Cadherin Clustering". Nature (2011) 475: 510-513.
• O. Harrison, X. Jin, S. Hong, F. Bahna1, G. Ahlsen, J. Brasch, Y. Wu, J. Vendome, K. Felsovalyi, etc. "The extracellular architecture of adherens junctions revealed by crystal structures of type I cadherins". Structure (2011) 19:244-256.
• Y. Wu, X. Jin, O. Harrison, L. Shapiro, B. Honig and A. Ben-Shaul, "Cooperativity between trans and cis interactions in cadherin-mediated junction formation". P.N.A.S. (2010) 107 (41) 17592-17597.
• Y. Wu, AD. Dousis, M. Chen, J. Li, and J. Ma, "OPUS-Dom: Applying the Folding-Based Method VECFOLD to Determine Protein Domain Boundaries". J. Mol. Biol. (2009) 385, 1314-1329.
• M. Chen, AD. Dousis, Y. Wu, and J. Ma, "Predicting protein folding cores by empirical potential functions". Archives of Biochemistry and Biophysics (2009) 483, 16-22.


[2007 or earlier]


• Y. Wu, M. Lu, M. Chen, J. Li, and J. Ma, "OPUS-Ca: A knowledge-based potential function requiring only C-alpha Positions". Protein Science (2007) 16, 1449-1463.
• M. Chen, C.J. Wilson, Y. Wu, P. Wittung-Stafshede, and J. Ma, "Correlation between Protein Stability Cores and Protein Folding Kinetics: A Case Study on Pseudomonas aeruginosa Apo-Azurin". Structure (2006) 14, 1-10.
• Y. Wu, X. Tian, M. Lu, M. Chen, Q. Wang and J. Ma, "Folding of Small Helical Proteins Assisted by Small-Angle X-Ray Scattering Profiles". Structure (2005) 13, 1587-1597.
• Y. Yuan, Y. Wu and J. Zi, "Heat Capacities of Globular Proteins". J. of Phys.: Condensed Matter, (2005) 17, 469-473.
• Y. Wu, M. Chen, M. Lu, Q. Wang and J. Ma, "Determining Protein Topology from Skeletons of Secondary Structures". J. Mol. Biol. (2005) 350, 571-586.
• Y. Wu and J. Ma, "Refinement of F-actin Model against Fiber Diffraction Data by Long-Range Normal Modes". Biophysical J. (2004) 86, 116-124.
• Y. Wu and J. Ma, "Normal-mode-based Refinement of an F-actin Model Against Fiber Diffraction Data". Fiber Diffraction Review, (2004) 12, 25-28.
• D. Ming, Y. Kong, Y. Wu and J. Ma, "Simulation of F-actin filaments of Several Microns". Biophysical J. (2003) 85, 27-35.
• Y. Kong, D. Ming, Y. Wu, J. Stoops, H. Zhou and J. Ma, "Conformational Flexibility of Pyruvate Dehydrogenase Complexes: A Computational Analysis by QEDM". J. Mol. Biol. (2003) 330, 129-135.
• D. Ming, Y. Kong, Y. Wu and J. Ma, "Substructure Synthesis Method for Simulating Large Molecular Complexes". P.N.A.S. (2003) 100, 104-109.
• Y. Wu and J. Zi, "Universal Behavior of Localization of Residue Fluctuations in Globular Proteins". Physical Reviews E. (2003) 67, 041909-041912.

Invited talks

Conference and Poster Presentations