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Comparing Voronoi and Laguerre Tessellations in the Protein-Protein Docking Context

Thomas Bourquard, Julie Bernauer, Jérôme Azé, Anne Poupon
2009 2009 Sixth International Symposium on Voronoi Diagrams  
In our work, we have tested two different, but related, formalisms: the Voronoi and Laguerre tessellations. We present here a comparison of these two models in the context of protein-protein docking.  ...  In order to design an accurate and high-throughput prediction method for protein-protein docking, the first step was to model a protein structure using a formalism allowing fast computation, without losing  ...  Next, we compared the differences observed for parameters between non-native and native conformations for Voronoi and Laguerre tessellations.  ... 
doi:10.1109/isvd.2009.11 dblp:conf/isvd/BourquardBAP09 fatcat:2bqvxh5xynhbrah7qpjnigyhhu

Voronoi and Voronoi-related tessellations in studies of protein structure and interaction

Anne Poupon
2004 Current Opinion in Structural Biology  
The tessellation invented by Voronoi in 1908, and other tessellations of space derived from it, provide versatile representations of three-dimensional structures.  ...  In recent years, they have been used to investigate a series of issues relating to proteins: atom and residue volumes, packing, folding, interactions and binding.  ...  In the context of protein structure, the Voronoi tessellation was first used by Richards in 1974 [1] to evaluate the volumes of the atoms in a globular protein, defined as the volume of their Voronoi  ... 
doi:10.1016/j.sbi.2004.03.010 pmid:15093839 fatcat:4gccx3potfgbbcbgmppsvzrrxy

Recent Progress and Future Directions in Protein-Protein Docking

David Ritchie
2008 Current protein and peptide science  
This article gives an overview of recent progress in protein-protein docking and it identifies several directions for future research.  ...  Recent results from the CAPRI blind docking experiments show that docking algorithms are steadily improving in both reliability and accuracy.  ...  [159] used a Voronoi tesselation representation of protein shape and a SVM-based machine learning approach to re-score successfully HADDOCK predictions for 4 out of 5 CAPRI targets.  ... 
doi:10.2174/138920308783565741 pmid:18336319 fatcat:yx4gggoo6bbsbg2vr2ifl7lnce

In Silico-In Vitro Screening of Protein-Protein Interactions: Towards the Next Generation of Therapeutics

Bruno Villoutreix, Karine Bastard, Olivier Sperandio, Robin Fahraeus, Jean-Luc Poyet, Fabien Calvo, Benoit Deprez, Maria Miteva
2008 Current Pharmaceutical Biotechnology  
tessellation, Laguerre polyhedral decomposition and α-shape [46] [47] [48] [49] .  ...  Interactions at the interface are usually measured in silico in terms of accessible surface area, shape complementarity, molecular surface and the associated mathematical objects, Voronoi diagram, Delaunay  ...  Acknowledgments Supports from the Inserm institute and Inserm-Transfert are greatly appreciated.  ... 
doi:10.2174/138920108783955218 pmid:18393867 fatcat:db63x2enijagzdo34ttc4hqshy

ICOSA: A Distance-Dependent, Orientation-Specific Coarse-Grained Contact Potential for Protein Structure Modeling

Wessam Elhefnawy, Lin Chen, Yun Han, Yaohang Li
2015 Journal of Molecular Biology  
in the Rosetta and I-Tasser protein decoy sets.  ...  The relative distance and orientation in contacting residue pairs plays a significant role in protein folding and stabilization.  ...  An alternative definition of contacts is based on geometric models such as Voronoi diagram [16, 17] , Laguerre tessellation [18] , Delaunay triangulation [19, 20] , or alpha shape [21, 22] .  ... 
doi:10.1016/j.jmb.2015.05.022 pmid:26055539 fatcat:3i4tfhgf3ndzxkayt3s7tiqcjq

New insights into structure and function of bis-phosphinic acid derivatives and implications for CFTR modulation

Sara Bitam, Ahmad Elbahnsi, Geordie Creste, Iwona Pranke, Benoit Chevalier, Farouk Berhal, Brice Hoffmann, Nathalie Servel, Danielle Tondelier, Aurelie Hatton, Christelle Moquereau, Mélanie Faria Da Cunha (+9 others)
2021 Scientific Reports  
We investigated the corrector effect of c407 and its derivatives on F508del-CFTR protein.  ...  Molecular docking and dynamics simulations combined with site-directed mutagenesis suggested that c407 stabilizes the F508del-Nucleotide Binding Domain 1 (NBD1) during the co-translational folding process  ...  The contacts between ligands and CFTR/NBD1 were analyzed by VLDM (Voronoi Laguerre Delaunay for Macromolecules) which represents a complex (protein/ligand) by a Laguerre tessellation [44] [45] [46] .  ... 
doi:10.1038/s41598-021-83240-x pmid:33767236 fatcat:j34pc66aafas5fvqvam6anmqcq