Publications

Journal Publications

  • D.W. Ritchie, A.W. Ghoorah, L. Mavridis, V. Venkatraman. Fast Protein Structure Alignment using Gaussian Overlap Scoring of Backbone Peptide Fragment Similarity. Bioinformatics 28(24) 3274-3281, 2012. Full Text.
  • P. Popov, D.W. Ritchie, and S. Grudinin. DockTrina: Docking triangular protein trimers. Proteins, 2013.  Full Text.
  • Thai V. Hoang, Xavier Cavin, and David W. Ritchie, gEMfitter: A highly parallel FFT-based 3D density fitting tool with GPU texture memory acceleration. Journal of Structural Biology, 2013.  Full Text.
  • Thai V. Hoang, Xavier Cavin, Patrick Schultz, and David W. Ritchie. gEMpicker: A highly parallel GPU-accelerated particle picking tool for cryo-electron microscopy. BMC Structural Biology, 2013.  Full Text.
  • A.W. Ghoorah, M. Smail-Tabbone, M.-D. Devignes, D.W. Ritchie, (2013). KBDOCK 2013: A spatial classification of 3D protein domain family interactions. Nucleic Acids Research, in press.  Full Text.
  • P. Popov and S. Grudinin. Rapid determination of RMSDs corresponding to macromolecular rigid body motions. Journal of Computational Chemistry 2014, DOI: 10.1002/jcc.23569. Full Text.
  • I Sutkeviciute et. al. Unique DC-SIGN Clustering Activity of a Small Glycomimetic: A Lesson for Ligand Design. ACS Chemical Biology 2014, DOI:10.1021/cb500054h. Full Text.
  • G. Derevyanko and S. Grudinin. HermiteFit: fast-fitting atomic structures into a low-resolution density map using three-dimensional orthogonal Hermite functions. Acta Crystallographica Section D 2014, DOI:10.1107/S1399004714011493. 

Conference Proceedings

  • D. W. Ritchie and S. Grudinin. Some Recent Progress on Generating Symmetric Protein Complexes Using Spherical Polar Fourier Docking Correlations. In Proceedings of the 14th Open Days in Biology, Computer Science and Mathematics (JOBIM), July 1 - 4, 2013, Toulouse (France), 2013. 

Conference Presentations

  • D. W. Ritchie and S. Grudinin presented a poster on "Prediction Of Complexes With Point Group Symmetry Using Spherical Polar Fourier Docking Correlations" at the Structural Bioinformatics and Computational Biophysics 3Dsig 2013, Berlin, 2013.
  • Petr Popov, David W. Ritchie and Sergei Grudinin presented "DockTrina, a novel protein docking algorithm for modeling the 3D structures of non- symmetrical triangular trimers" at CAPRI 2013, Uttrecht, Netherlands, 17-19 Apr 2013.
  • D. W. Ritchie and S. Grudinin presented a poster on "Some Recent Progress on Generating Symmetric Protein Complexes Using Spherical Polar Fourier Docking Correlations" at CAPRI 2013, Uttrecht, Netherlands, 17-19 Apr 2013.
  • Sergei Grudinin presented "Fast Fitting of Atomic Structures into Cryo-EM Density Maps Using Hermite Orthogonal Functions" at Computational Challenges in Structural Biology CCSB 2012, Nov 14-15, Strasbourg, France, 2012.
  • S. Grudinin and D. W. Ritchie presented "Predicting Multi Protein Assemblies" at Second workshop on Computational Structural Biology: Integrative Approaches for Modeling Biomolecular Complexes, IAMB 2013, May 29-31, Nice, France, 2013.
  • S. Grudinin and G. Derevyanko presented a poster on "Hermite-Fourier formalism for fitting protein structures into electron density maps" at Analysis of Diffraction Data in Real Space, ADD2013, Mar 18-22, Grenoble, France, 2013.
  • S. Grudinin and D. W. Ritchie presented a poster on "DockTrina: Docking of Triangular Trimers" at XVIIIe congrès du Groupe de Graphisme et Modélisation Molèculaire, GGMM 2013, May 21-23, St Pierre d‘Oléron, France, 2013.
  • D. W. Ritchie and S. Grudinin presented a poster on "Some Recent Progress on Generating Symmetric Protein Complexes Using Spherical Polar Fourier Docking Correlations" at XVIIIe congrès du Groupe de Graphisme et Modélisation Molèculaire, GGMM 2013, May 21-23, St Pierre d‘Oléron, France, 2013.
  • D. W. Ritchie did an oral and a poster presentation on “Homology modeling of protein-protein interactions”, BBC-11 (BeneLux Bioinformatics Conference) in Luxembourg, 12/2011.
  • Thai van Hoang presented "Using Graphics Processors to Accelerate EM Particle Picking Calculations" at Computational Challenges in Structural Biology CCSB 2012, Nov 14-15, Strasbourg, France, 2012.
  • D. W. Ritchie presented "Modeling 3D Protein Complexes Using Case-Based Reasoning" at Second workshop on Computational Structural Biology: Integrative Approaches for Modeling Biomolecular Complexes, IAMB 2013, May 29-31, Nice, France, 2013.