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Protein-protein structure detection software tools

Recent technical advancements of the chemical cross-linking methods achieved in a number of labs have allowed this technique to be extended to complex systems. Successful applications of chemical cross-linking to studies of intact virus particles, cell lysates, and even intact bacterial and human cells suggest that in the future, cross-linking methods may provide a majority of structural and topological data on protein complexes as they exist in cells or other complex samples. Many fundamental cellular processes are mediated by protein-protein interactions. Protein interactions support most biological function and are directed by shapes or topologies of the interacting proteins. The rate of solving complex structures, which constitutes an important step toward a mechanistic understanding of these processes, by experimental methods has been slow. Improved measurements of protein interaction topologies in cells are needed to increase our understanding of how protein interactions carryout their life supporting functions. By examining the sequence space of protein complexes, scientists estimated the total number of unique interaction types to be around 10,000. Most prior applications have been limited to either purified proteins or complexes due to the complexity and wide dynamic range presented by complex biological samples. Thus, at the current rate of structure determination of unique protein complexes, it would take at least two decades before a complete set of protein complex structures is available. These data highlight the urgent need for developing efficient computational methods for protein complex structure prediction, especially when the structures of homologous proteins are not available.

Source text:
(Murkherjee and Zhang, 2011) Protein-protein complex structure predictions by multimeric threading and template recombination. Structure.

(Zheng et al, 2013) XLink-DB: database and software tools for storing and visualizing protein interaction topology data. J Proteome Res.

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