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Elucidating transient protein interactions with multiple dockings
September 2007
KrBa07
Intelligent drug design requires a good understanding of protein interaction mechanisms. The rapid advance of high-throughput methods of protein structure determination gives us an exponential growth in known protein structures, but the problem of determining the structure of protein complexes is still a hard one to solve, especially for fast transient interactions, which are very common in catalysis and important targets for drugs. In this paper we present a modeling approach for trying to predict protein-protein complexes by using constraint propagation techniques to incorporate information about the mechanism, and also to speed up calculations and make it more practical to compare a large number of docking simulations with similar partners in order to overcome the difficulty of modeling very weak interactions. As an example, we tested this approach on an electron transfer interaction that is part of photosynthesis in plants.
In proceedings
Ludwig Krippahl, Pedro Barahona
Rolf Backofen, Alessandro Dal Palu, Sebastian Will
Proceedings of WCB07, Workshop on Constraint Based Methods for Bioinformatics
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Porto, Portugal
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40-47
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Ludwig Krippahl and Pedro Barahona, Elucidating transient protein interactions with multiple dockings, in: Rolf Backofen and Alessandro Dal Palu and Sebastian Will (eds), Proceedings of WCB07, Workshop on Constraint Based Methods for Bioinformatics, Porto, Portugal, Pag. 40-47, September 2007.
<a href="/people/members/view.php?code=195d68ea5904b58472fd8c8aedcae233" class="author">Ludwig Krippahl</a> and <a href="/people/members/view.php?code=7e27bc13fad97e99cd21ea6914d55659" class="author">Pedro Barahona</a>, <b>Elucidating transient protein interactions with multiple dockings</b>, in: Rolf Backofen, Alessandro Dal Palu and Sebastian Will (eds), <u>Proceedings of WCB07, Workshop on Constraint Based Methods for Bioinformatics</u>, Porto, Portugal, Pag. 40-47, September 2007.
@inproceedings {KrBa07, author = {Ludwig Krippahl and Pedro Barahona}, editor = {Rolf Backofen and Alessandro Dal Palu and Sebastian Will}, title = {Elucidating transient protein interactions with multiple dockings}, booktitle = {Proceedings of WCB07, Workshop on Constraint Based Methods for Bioinformatics}, address = {Porto, Portugal}, pages = {40-47}, abstract = {Intelligent drug design requires a good understanding of protein interaction mechanisms. The rapid advance of high-throughput methods of protein structure determination gives us an exponential growth in known protein structures, but the problem of determining the structure of protein complexes is still a hard one to solve, especially for fast transient interactions, which are very common in catalysis and important targets for drugs. In this paper we present a modeling approach for trying to predict protein-protein complexes by using constraint propagation techniques to incorporate information about the mechanism, and also to speed up calculations and make it more practical to compare a large number of docking simulations with similar partners in order to overcome the difficulty of modeling very weak interactions. As an example, we tested this approach on an electron transfer interaction that is part of photosynthesis in plants.}, month = {September}, year = {2007}, }
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