Easy DNA Modeling and More with GraphiteLifeExplorer

The GraphiteLifeExplorer tool enables biologists to reconstruct 3D cellular complexes built from proteins and DNA molecules. Models of DNA molecules can be drawn in an intuitive way and assembled to proteins or others globular structures. Real time navigation and immersion offer a unique view to the reconstructed biological machinery.

[1]  Ivan Junier,et al.  Spatial and Topological Organization of DNA Chains Induced by Gene Co-localization , 2010, PLoS Comput. Biol..

[2]  大野 義夫,et al.  Computer Graphics : Principles and Practice, 2nd edition, J.D. Foley, A.van Dam, S.K. Feiner, J.F. Hughes, Addison-Wesley, 1990 , 1991 .

[3]  David S Goodsell,et al.  Filling in the Gaps: Artistic License in Education and Outreach , 2007, PLoS biology.

[4]  M. Sternberg,et al.  Protein structure prediction on the Web: a case study using the Phyre server , 2009, Nature Protocols.

[5]  Michael E. Taylor,et al.  Differential Geometry I , 1994 .

[6]  Ben M. Webb,et al.  Putting the Pieces Together: Integrative Modeling Platform Software for Structure Determination of Macromolecular Assemblies , 2012, PLoS biology.

[7]  Gaël McGill,et al.  Molecular Movies… Coming to a Lecture near You , 2008, Cell.

[8]  David A. Case,et al.  Modeling Unusual Nucleic Acid Structures , 1998 .

[9]  Bert Jüttler,et al.  Computation of rotation minimizing frames , 2008, TOGS.

[10]  M. Schofield,et al.  Interaction of Escherichia coli MutS and MutL at a DNA Mismatch* , 2001, The Journal of Biological Chemistry.

[11]  D. Goodsell.  Miniseries : Illustrating the Machinery of Life Escherichia coli * , 2010 .

[12]  Frédéric Cazals,et al.  ESBTL: efficient PDB parser and data structure for the structural and geometric analysis of biological macromolecules , 2010, Bioinform..

[13]  J. Andrew Grant,et al.  A fast method of molecular shape comparison: A simple application of a Gaussian description of molecular shape , 1996, J. Comput. Chem..

[14]  Damien Larivière,et al.  An inventory of the bacterial macromolecular components and their spatial organization. , 2011, FEMS microbiology reviews.

[15]  O. Espéli,et al.  Long-Range Chromosome Organization in E. coli: A Site-Specific System Isolates the Ter Macrodomain , 2012, PLoS genetics.

[16]  F. Harold,et al.  Molecules into Cells: Specifying Spatial Architecture , 2005, Microbiology and Molecular Biology Reviews.

[17]  J. A. Grant,et al.  A fast method of molecular shape comparison: A simple application of a Gaussian description of molecular shape , 1996, J. Comput. Chem..

[18]  Paolo Cignoni,et al.  Ambient Occlusion and Edge Cueing for Enhancing Real Time Molecular Visualization , 2006, IEEE Transactions on Visualization and Computer Graphics.

[19]  Holger Gohlke,et al.  The Amber biomolecular simulation programs , 2005, J. Comput. Chem..

[20]  Frank Alber,et al.  Integrating diverse data for structure determination of macromolecular assemblies. , 2008, Annual review of biochemistry.

[21]  Anne E Carpenter,et al.  Visualization of image data from cells to organisms , 2010, Nature Methods.

[22]  David S. Goodsell,et al.  ePMV embeds molecular modeling into professional animation software environments. , 2011, Structure.

[23]  D. Kirsch,et al.  Identifying an interaction site between MutH and the C-terminal domain of MutL by crosslinking, affinity purification, chemical coding and mass spectrometry , 2006, Nucleic acids research.

[24]  T. Kunkel,et al.  Direct visualization of asymmetric adenine-nucleotide-induced conformational changes in MutL alpha. , 2008, Molecular cell.

[25]  J. Rappsilber.  The beginning of a beautiful friendship: Cross-linking/mass spectrometry and modelling of proteins and multi-protein complexes , 2011, Journal of structural biology.

[26]  Xiang-Jun Lu,et al.  3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures , 2008, Nature Protocols.

[27]  Peter Friedhoff,et al.  Chemical Trapping of the Dynamic MutS-MutL Complex Formed in DNA Mismatch Repair in Escherichia coli* , 2011, The Journal of Biological Chemistry.

[28]  Leonardo G. Trabuco,et al.  Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. , 2008, Structure.

[29]  Xiang-Jun Lu,et al.  Web 3DNA—a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures , 2009, Nucleic Acids Res..

[30]  F. Harold.  Bacterial morphogenesis: learning how cells make cells. , 2007, Current opinion in microbiology.

[31]  Steve Oudot,et al.  Provably good sampling and meshing of surfaces , 2005, Graph. Model..

[32]  Roland L Dunbrack,et al.  Outcome of a workshop on applications of protein models in biomedical research. , 2009, Structure.