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Path-LZerD
Allows users to determine protein complexes order of assembly. Path-LZerD is an application that performs its prediction by constructing the complex structure. It is built around two main components (i) Multi-LZerD, an approach able to predict the docking order of protein complexes by simulating the assembly process of protein complexes and; (ii) LZerD, an algorithm that starts from individual subunit structures and determines order according to the observation of the simulated assembly process of the complex.
XLink-DB
Serves as a data storage site and visualization tool for cross-linking results. XLink-DB accepts data generated with any cross-linker and stores them in a relational database. The method is a way to organize and demonstrate protein interaction data with topological information. It allows compilation and analysis of large-scale cross-linking data. It will not only help the cross-linking community to store, share and process their data but also share the data with other scientists with interests in protein interactions and topologies.
SPRING / Single-chain-based prediction of interactions and geometries
A template-base algorithm for protein-protein structure prediction. It first threads one chain of the protein complex through the PDB library with the binding partners retrieved from the original oligomer entries. The complex models associated with another chain is deduced from a pre-calculated look-up table, with the best orientation selected by the SPRING-score which is a combination of threading Z-score, interface contacts, and TM-align match between monomer-to-dimer templates.
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