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On the role of physics and evolution in dictating protein structure and function. Israel Journal of Chemistry.. In Press.
Experimental validation of FINDSITEcomb virtual ligand screening results for eight proteins yields novel nanomolar and micromolar binders. Journal of Cheminformatics. 6(1):16. PDF. 2014.
Advances in GPCR Modeling Evaluated by the GPCR Dock 2013 Assessment: Meeting New Challenges. Structure. 22(8):1120-1139. PDF. 2014.
WeFold: A Coopetition for Protein Structure Prediction. Proteins: Structure, Function, and Bioinformatics. :n/a-n/a. PDF. 2014.
Restricted N-glycan Conformational Space in the PDB and Its Implication in Glycan Structure Modeling. PLoS Computational Biology. 9(3):e1002946. PDF. 2013.
Are predicted protein structures of any value for binding site prediction and virtual ligand screening? Current opinion in structural biology. 23(2):191-7. PDF. 2013.
Segment assembly, structure alignment and iterative simulation in protein structure prediction. BMC Biology. 11(1):44. PDF. 2013.
A Comprehensive Survey of Small-Molecule Binding Pockets in Proteins. PLoS Computational Biology. 9(10):e1003302. PDF. 2013.
On the Importance of Hydrodynamic Interactions in Lipid Membrane Formation. Biophysical Journal. 104(1):96-105. PDF. 2013.
Interplay of physics and evolution in the likely origin of protein biochemical function. Proceedings of the National Academy of Sciences. 110(23):9344-9349. PDF. 2013.
APoc: large-scale identification of similar protein pockets. Bioinformatics. 29(5):597-604. PDF. 2013.
FINDSITEcomb: A Threading/Structure-Based, Proteomic-Scale Virtual Ligand Screening Approach. Journal of Chemical Information and Modeling. 53(1):230-240. PDF. 2013.
Dynamic simulation of concentrated macromolecular solutions with screened long-range hydrodynamic interactions: Algorithm and limitations. Journal of Chemical Physics. 139:121922-1. PDF. 2013.
Importance of excluded volume and hydrodynamic interactions on macromolecular diffusion in vivo. International Conference of the Quantum Bio-Informatics IV. 30:378-387.. 2013.
EFICAz2.5: application of a high-precision enzyme function predictor to 396 proteomes. Bioinformatics. 28(20):2687-2688. PDF. 2012.
Krylov subspace methods for computing hydrodynamic interactions in Brownian dynamics simulations. The Journal of Chemical Physics. 137:064106. PDF. 2012.
FINDSITEX: A Structure-Based, Small Molecule Virtual Screening Approach with Application to All Identified Human GPCRs. Molecular Pharmaceutics. 9(6):1775-1784. PDF. 2012.
Further Evidence for the Likely Completeness of the Library of Solved Single Domain Protein Structures. The Journal of Physical Chemistry B. 116(23):6654-6664. PDF. 2012.
The distribution of ligand-binding pockets around protein-protein interfaces suggests a general mechanism for pocket formation. Proceedings of the National Academy of Sciences. 109(10):3784-3789. PDF. 2012.
Template-based protein structure modeling using TASSERVMT. Proteins: Structure, Function, and Bioinformatics. 80(2):352-361. PDF. 2012.
Status of GPCR Modeling and Docking as Reflected by Community-wide GPCR Dock 2010 Assessment. Structure. 19(8):1108-1126. PDF. 2011.
GOAP: A Generalized Orientation-Dependent, All-Atom Statistical Potential for Protein Structure Prediction. Biophysical Journal. 101(8):2043-2052. PDF. 2011.
New benchmark metrics for protein-protein docking methods. Proteins: Structure, Function, and Bioinformatics. 79(5):1623-1634. PDF. 2011.
FINDSITE-metal: Integrating evolutionary information and machine learning for structure-based metal-binding site prediction at the proteome level. Proteins: Structure, Function, and Bioinformatics. 79(3):735-751. PDF. 2011.
The utility of geometrical and chemical restraint information extracted from predicted ligand-binding sites in protein structure refinement. Journal of Structural Biology. 173(3):558-569. PDF. 2011.
Brownian dynamics simulation of macromolecule diffusion in a protocell. Proceedings of the International Conference of the Quantum Bio-Informatics IV. 28:413-426. PDF. 2011.
Why not consider a spherical protein? Implications of backbone hydrogen bonding for protein structure and function Physical Chemistry Chemical Physics. 13 (38):17044-17055. PDF. 2011.
Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion. Proceedings of the National Academy of Sciences of the United States of America. 107:18457-18462. PDF Supplementary Data. 2010.
iAlign: a method for the structural comparison of protein-protein interfaces. Bioinformatics (Oxford, England). 26(18):2259-65. PDF Supplementary Data. 2010.
PSiFR: an integrated resource for prediction of protein structure and function. Bioinformatics (Oxford, England). 26(5):687-8. PDF. 2010.
Structural space of protein-protein interfaces is degenerate, close to complete, and highly connected. Proceedings of the National Academy of Sciences of the United States of America. 107(52):22517-22. PDF Supplementary Data. 2010.
Q-Dock(LHM): Low-resolution refinement for ligand comparative modeling. Journal of computational chemistry. 31(5):1093-105. PDF. 2010.
Cross-Reactivity Virtual Profiling of the Human Kinome by X-ReactKIN: A Chemical Systems Biology Approach. Molecular Pharmaceutics. 7(6):2324–2333. PDF. 2010.
Comprehensive structural and functional characterization of the human kinome by protein structure modeling and ligand virtual screening. Journal of Chemical Information and Modeling. 50:1839-1854. PDF. 2010.
TASSER_low-zsc: An approach to improve structure prediction using low z-score ranked templates. Protiens. 78(13):2769-2080. PDF. 2010.
TASSER_WT: A protein structure prediction algorithm with accurate predicted contact restraints for difficult protein targets. Biophysical Journal. 99(9):3066-75. PDF Supplementary Data. 2010.
The continuity of protein structure space is an intrinsic property of proteins. Proceedings of the National Academy of Sciences of the United States of America. 106(37):15690-5. PDF. 2009.
A threading-based method for the prediction of DNA-binding proteins with application to the human genome. PLoS computational biology. 5(11):e1000567. PDF Supplementary Data. 2009.