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Downloadable Softwares

• This program is to predict the homotypic binding status of Ig-Fold domain using multiple machine learning algorithms. ( documentation, download)
• Reference: 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.
   

• 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 and Databases

• The online database covers a large portion of cell surface proteins and the interactions between their ectodomains in human. Predicted interactions in the database are determined using a combines structural, functional, evolutionary and expression information. Currently, EXECSP contains 13877 PPIs for extracellular cell surface interactome of the human proteome. The database utilized computational modeling tools to generate interactome of cell surface proteins and structural models of associated interactions in the network. Comparing with time-consuming and resource-intensive experimental techniques, computational approaches offers possess of unique advantage in detecting protein-protein interactions and modeling structure of protein complexes. The EXCESP database also contains experimentally determined interactions compiled from a set of publicly available databases that curate interactions from the literature, e.g., Uniprot, PrePPI, SPRING, etc.. ( Link)
• Reference: K. Dhusia, M. Carlos and Y. Wu , "EXCESP: A Structure-based Online Database for Extracellular Interactome of Cell Surface Proteins in Human ." in Preparation.

• 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.

Datasets

• 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.

TNFDB database:

In this dataset, a TNFSF-TNFRSF interactome was constructed in this study by searching the database which consists of both experimentally measured and computationally predicted protein-protein interactions (PPIs). The interactome contains a total number of 194 interactions between 18 TNFSF ligands and 29 TNFRSF receptors in human. We modeled the structure for each ligand-receptor interaction in the network. Their binding affinities were further computationally estimated based on modeled structures.

All relevant information of the TNFSF-TNFRSF interactome can be found in our GitHub repository https://github.com/wulab-github/TNFDB