Graduate students RA
Our new paper about simulating 2D binding kinetics of membrane proteins has been published online in Protein Science
October 10th, 2014
Dr. Wu is teaching "Introduction to Systems Biology" this semester. The lecture slides can be found
October , 2014
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
A simple Fortran program to study enzyme kinetics. Kinetic Monte-Carlo algorithm is used to simulate the diffusion-reaction process between enzymes and their substrates. (
Reference: 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.
An online server that was developed to predict the kinetic rate of protein association. Proteins are modeled by the coarse-grained representation. Molecular flexibility can be included in the conformational sampling through the integration of Elastic Network Model. (coming soon)
Reference: Manuscript in preparation
An interface fragment pair library was constructed from the current structure database of protein complexes. The library includes 459 clusters and each cluster is represented by a structural model of the corresponding interface fragment pair. We expect this new library will be useful to predict structures of unknown protein-protein interactions. (coming soon)
Reference: Z. Xie, J. Chen and Y. Wu , "Decomposing the space of protein quaternary structures with the interface fragment pair library" under review.