Henry van den Bedem

 



Interests:
Computational Structural Biology, in particular methods and algorithms for interpreting structure and dynamics of macromolecules from experimental (crystallography) data, and physics-based refinement of comparative protein models.

Recent Projects:

 

Protein Model Completion: Xpleo

 

Xpleo inserts missing fragments (loops) into a partially complete protein model, given an 2mF_o-DF_c (or similar) electron density map. It is available as a web service: Xpleo Web Server. Xpleo software binaries and source are also available for download:

 

Linux x86_64 (RHEL5)

Xpleo-0.9.0.2-x86_64.tbz

OS X Snow Leopard

Xpleo-0.9.0.2-OSX.tbz

Source

Xpleo-0.9.0.2-src.tbz

 
Xpleo in action: movie

Consensus Modeler: an algorithm to automatically combine structural models.

Consensus Modeler provides an optimal starting model for manual structure refinement from combining traces obtained from different strategies in automated data processing.

Modeling Structural Heterogeneity: qFit

qFit automatically identifies and models discrete heterogeneity in electron density maps with a convex optimization algorithm. A beta version of the software is available as a web service: qFit Web Server.

 

Selected Publications:

James Fraser, Henry van den Bedem, Avi Samelson, P. Therese Lang, James Holton, Nathaniel Echols and Tom Alber Accessing protein conformational ensembles by room-temperature X-ray crystallography. PNAS (in press)

H. van den Bedem, G. Wolf, Q. Xu and A.M. Deacon (2011) Distributed structure determination at the JCSG. Acta Cryst. D67:368-375

H. van den Bedem, A. Dhanik, J.-C. Latombe and A.M. Deacon (2009) Modeling discrete heterogeneity in X-ray diffraction data by fitting multi-conformers Acta Cryst. D65:1107-1117

P. Yao, A. Dhanik, N. Marz, R. Propper, C. Kou, G. Liu, H. van den Bedem, J-C Latombe, I. Halperin Landsberg, R. Altman. (2008) Efficient Algorithms to Explore Conformation Spaces of Flexible Protein Loops. IEEE/ACM Transaction on Computational Biology and Bioinformatics. 5:534-545

A. Dhanik, H. van den Bedem, A. Deacon, and J-C Latombe. Modeling Structural Heterogeneity in Proteins From X-Ray Data. (2008) Proc. 8th Workshop on Algorithmic Foundations of Robotics (WAFR `08). Guanajuato, Mexico.

A. Dhanik, P. Yao, N. Marz, R. Propper, C. Kou, G. Liu, H. van den Bedem and J-C Latombe. (2007) Efficient Algorithms to Sample Closed Clash-Free Conformations of Protein Loops. In Algorithms in Bioinformatics. Lecture Notes in Computer Science. (Springer Berlin) 4645:265-276.

Zhang, Z., van den Bedem, H., Sauter, N. K., Snell, G. and Deacon, A. (2006) Automated diffraction image analysis and spot searching for high-throughput crystal screening. J. Appl. Cryst.  39:112-119

H. van den Bedem, I. Lotan, J.-C Latombe and A.M. Deacon. (2005). Real-Space Protein-Model Completion: an Inverse-Kinematics Approach. Acta Cryst.  D61:2-13

I. Lotan, H. van den Bedem, A.M. Deacon and J.-C Latombe, Computing Protein Structures from Electron Density Maps: The Missing Loop Problem. 6th Workshop on Algorithmic Foundations of Robotics (WAFR `04). Published in Algorithmic Foundations of Robotics VI, M. Erdmann, M. Overmars, D. Hsu, F. van der Stappen (eds.), Springer Tracts in Advanced Robotics, Vol. 17, Springer-Verlag GmbH, 2005.

van den Bedem, H., Miller, M. and Wolf, G. (2003). Towards Automated Data Collection at the Stanford Synchrotron Radiation Laboratory, Synchrotron Radiat. News 16:15-19.

van den Bedem, H., Chernov, N., (2002) Expanding maps of an interval with holes. Ergod. Th. & Dynam. Sys. 22:637–654

van den Bedem, H., (2001) Statistical properties of hyperbolic systems with tangential singularities, Nonlinearity 14:1393–1410