Downloadable Softwares


EnzymSimulator:
  • 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. ( documentation, download)
  • 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.



Online Servers


FlexBind:
  • 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: Z. Xie, J. Chen and Y. Wu , "Coarse-grained simulation of protein association: application to rate prediction and implication for association mechanisms." Submitted to PloS Comput Bio.



Databases


FragPairLib:
  • 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. ( download )
  • Reference: Z. Xie, J. Chen 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.


 

 
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