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PROVAT: a tool for Voronoi tessellation analysis of protein structures and complexes

S. P. Gore, D. F. Burke, T. L. Blundell
2005 Bioinformatics  
Voronoi tessellation has proved to be a useful tool in protein structure analysis.  ...  But a versatile, public-domain tool for calculating and visualizing tessellations at various levels of granularities is not available.  ...  Introduction Voronoi tessellation has proved to be a useful tool (Poupon, 2004) for estimating atomic volumes, detecting cavities, analysis of secondary structure and fold, derivation of statistical  ... 
doi:10.1093/bioinformatics/bti523 pmid:15932902 fatcat:573nasx745h6vgtr5nkxxmmv6m

PROVAT – a versatile tool for Voronoi tessellation analysis of protein structures and complexes

Swanand P Gore, David F Burke, Tom L Blundell
2005 BMC Bioinformatics  
A major feature of the tool is flexible definition of sites required as input to tessellation calculation.  ...  If 3 atoms are specified for determining local reference frame for a site, PROVAT can compute orientations of each Voronoi neighbour in that frame.  ... 
doi:10.1186/1471-2105-6-s3-p12 fatcat:tuxivuudnfa6diotaadqmepbem

The Symmetric Difference Distance: A New Way to Evaluate the Evolution of Interfaces along Molecular Dynamics Trajectories;Application to Influenza Hemagglutinin

Valentin Ozeel, Aurélie Perrier, Anne Vanet, Michel Petitjean
2019 Symmetry  
We propose a new and easy approach to evaluate structural dissimilarities between frames issued from molecular dynamics, and we test this methodology on human hemagglutinin.  ...  This protein is responsible for the entry of the influenza virus into the host cell by endocytosis, and this virus causes seasonal epidemics of infectious disease, which can be estimated to result in hundreds  ...  Its input is the tridimensional structure of a protein-protein complex or of a protein-ligand complex. This complex has two parts (molecule or macromolecule), named A and B.  ... 
doi:10.3390/sym11050662 fatcat:dwa6yficsna7dn3ktcfny3adbe

Structural deformation upon protein-protein interaction: A structural alphabet approach

Juliette Martin, Leslie Regad, Hélène Lecornet, Anne-Claude Camproux
2008 BMC Structural Biology  
Acknowledgements We are grateful to INRA for awarding a Fellowship to JM and to Ministère de l'Enseignement Supérieur et de la Recherche for awarding a Fellowship to LR.  ...  We thank two anonymous referees for their remarks that helped us to improve the manuscript.  ...  Interfaces are detected using Voronoi tessellations. Voronoi tessellations are a way to divide the space around a given set of points into cells.  ... 
doi:10.1186/1472-6807-8-12 pmid:18307769 pmcid:PMC2315654 fatcat:7njveh23pzdltiyn36xadjlysi

Functional region prediction with a set of appropriate homologous sequences-an index for sequence selection by integrating structure and sequence information with spatial statistics

Wataru Nemoto, Hiroyuki Toh
2012 BMC Structural Biology  
The detection of conserved residue clusters on a protein structure is one of the effective strategies for the prediction of functional protein regions.  ...  An objective and general method to select appropriate homologous sequences is desired for the efficient prediction of functional regions.  ...  Computational resources were supplied by the University of Cambridge (Biochemistry Department), Kyoto University (Institute for Chemical Research, Bioinformatics Center), and the Computational Biology  ... 
doi:10.1186/1472-6807-12-11 pmid:22643026 pmcid:PMC3533907 fatcat:6enrveq46nepddm5dyddm6xj5m