Graduate students RA
Our new paper about mathematical modeling of Wnt signaling pathway has just been published on PLOS ONE
June 26th, 2014
Our new paper has been published on Proteins
June 10th, 2014
Our new paper has been featured on Global Medical Discovery
April 8th, 2014
Our rigid-body simulation paper has been published on J. Chem. Phys.
February 7th, 2014
Zhong-Ru and Jiawen have joined the lab, welcome aboard!
June 1st, 2013
Dr. Wu will give a talk at ACS meeting in New Orleans
April 1st, 2013
J. Chen, Z. Xie and
, "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
, "A multiscale model for simulating binding kinetics of proteins with flexible linkers". Proteins: Structure, Function, and Bioinformatics (2014) doi: 10.1002/prot.24614.
Z. Xie, J. Chen and
, "A coarse-grained model for the simulations of biomolecular interactions in cellular environments". Journal of Chemical Physics (2014) 140: 054112.
, B. Honig and A. Ben-Shaul , "Theory and simulations of adhesion receptor dimerization on membrane surfaces". Biophysical Journal (2013) 104: 1221-1229.
, 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,
, J. Vendome, K. Felsovalyi, etc. "The extracellular architecture of adherens junctions revealed by crystal structures of type I cadherins". Structure (2011) 19:244-256.
, 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.
, 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,
, and J. Ma, "Predicting protein folding cores by empirical potential functions". Archives of Biochemistry and Biophysics (2009) 483, 16-22.
[2007 or earlier]
, 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,
, 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.
, 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.
and J. Zi, "Heat Capacities of Globular Proteins". J. of Phys.: Condensed Matter, (2005) 17, 469-473.
, M. Chen, M. Lu, Q. Wang and J. Ma, "Determining Protein Topology from Skeletons of Secondary Structures". J. Mol. Biol. (2005) 350, 571-586.
and J. Ma, "Refinement of F-actin Model against Fiber Diffraction Data by Long-Range Normal Modes". Biophysical J. (2004) 86, 116-124.
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,
and J. Ma, "Simulation of F-actin filaments of Several Microns". Biophysical J. (2003) 85, 27-35.
Y. Kong, D. Ming,
, 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,
and J. Ma, "Substructure Synthesis Method for Simulating Large Molecular Complexes". P.N.A.S. (2003) 100, 104-109.
and J. Zi, "Universal Behavior of Localization of Residue Fluctuations in Globular Proteins". Physical Reviews E. (2003) 67, 041909-041912.
Conference and Poster Presentations