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Submitted. Investigation of the possible screening of long-range hydrodynamic interactions in concentrated macromolecular solutions. Journal of Chemical Physics.
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In Press. Are predicted protein structures of any value for binding site prediction and virtual ligand screening? Current Opinion in Structural Biology. PDF
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In Press. Interplay of physics and evolution in the likely origin of protein biochemical function. Proc Natl Acad Science.
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2013. Restricted N-glycan Conformational Space in the PDB and Its Implication in Glycan Structure Modeling. PLoS Computational Biology. 9(3):e1002946. PDF
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2013. Segment assembly, structure alignment and iterative simulation in protein structure prediction. BMC Biology. 11(1):44. PDF
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2013. On the Importance of Hydrodynamic Interactions in Lipid Membrane Formation. Biophysical Journal. 104(1):96-105. PDF
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2013. APoc: large-scale identification of similar protein pockets. Bioinformatics. 29(5):597-604. PDF
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2013. FINDSITEcomb: A Threading/Structure-Based, Proteomic-Scale Virtual Ligand Screening Approach. Journal of Chemical Information and Modeling. 53(1):230-240. PDF
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2013. Importance of excluded volume and hydrodynamic interactions on macromolecular diffusion in vivo. International Conference of the Quantum Bio-Informatics IV. 30:378-387.
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2012. EFICAz2.5: application of a high-precision enzyme function predictor to 396 proteomes. Bioinformatics. 28(20):2687-2688. PDF
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2012. Krylov subspace methods for computing hydrodynamic interactions in Brownian dynamics simulations. The Journal of Chemical Physics. 137:064106. PDF
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2012. Biography of Harold A. Scheraga. The Journal of Physical Chemistry B. 116(23):6572-6572. PDF
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2012. Career Accomplishments of Harold A. Scheraga. The Journal of Physical Chemistry B. 116(23):6569-6571. PDF
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2012. FINDSITEX: A Structure-Based, Small Molecule Virtual Screening Approach with Application to All Identified Human GPCRs. Molecular Pharmaceutics. 9(6):1775-1784. PDF
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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
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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
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2012. Template-based protein structure modeling using TASSERVMT. Proteins: Structure, Function, and Bioinformatics. 80(2):352-361. PDF
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2011. GOAP: A Generalized Orientation-Dependent, All-Atom Statistical Potential for Protein Structure Prediction. Biophysical Journal. 101(8):2043-2052. PDF
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2011. New benchmark metrics for protein-protein docking methods. Proteins: Structure, Function, and Bioinformatics. 79(5):1623-1634. PDF
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2011. Editorial overview. Current Opinion in Structural Biology. 21:147-149. PDF
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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
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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
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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
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2011. Learning Protein Folding Energy Functions. 2011 IEEE 11th International Conference on Data Mining (ICDM)2011 IEEE 11th International Conference on Data Mining. :1062-1067. PDF
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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
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2010. 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
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2010. iAlign: a method for the structural comparison of protein-protein interfaces. Bioinformatics (Oxford, England). 26(18):2259-65. PDF Supplementary Data Abstract
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2010. PSiFR: an integrated resource for prediction of protein structure and function. Bioinformatics (Oxford, England). 26(5):687-8. PDF Abstract
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2010. Improving threading algorithms for remote homology modeling by combining fragment and template comparisons. Proteins. 78(9):2041-8. PDF Abstract
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2010. Comparison of structure-based and threading-based approaches to protein functional annotation. Proteins. 78(1):118-34. PDF Supplementary Data Abstract
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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 Abstract
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2010. Q-Dock(LHM): Low-resolution refinement for ligand comparative modeling. Journal of computational chemistry. 31(5):1093-105. PDF Abstract
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2010. Cross-Reactivity Virtual Profiling of the Human Kinome by X-ReactKIN: A Chemical Systems Biology Approach. Molecular Pharmaceutics. 7(6):2324–2333. PDF
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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
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2010. TASSER-based protein structure prediction. Introduction to Protein Structure Prediction: Methods and Algorithms. 14:219-242. PDF
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2010. TASSER_low-zsc: An approach to improve structure prediction using low z-score ranked templates. Protiens. 78(13):2769-2080. PDF
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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 Abstract
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2009. Novel computational approaches to drug discovery. Proceedings of the International Conference of the Quantum Bio-Informatics III. PDF
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2009. 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 Abstract
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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 Abstract
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2009. Protein structure prediction by pro-Sp3-TASSER. Biophysical journal. 96(6):2119-27. PDF Abstract
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2009. From nonspecific DNA-protein encounter complexes to the prediction of DNA-protein interactions. PLoS computational biology. 5(3):e1000341. PDF Abstract
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2009. FINDSITE: a threading-based approach to ligand homology modeling. PLoS computational biology. 5(6):e1000405. PDF Abstract
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2009. FINDSITE: a combined evolution/structure-based approach to protein function prediction. Briefings in bioinformatics. 10(4):378-91. PDF Abstract
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2009. Theory and Simulation (Editorial overview). Current opinion in structural biology. 19(2):117-9. PDF Abstract
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2009. EFICAz2: enzyme function inference by a combined approach enhanced by machine learning. BMC bioinformatics. 10:107. PDF Abstract
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2009. Reply to Zimmerman et al: The space of single domain protein structures is continuous and highly connected. Proc Natl Acad Science 2009:106(51): E138. PDF Abstract
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2008. Marker metabolites can be therapeutic targets as well. Nature. 456(7221):443. PDF
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2008. Protein model quality assessment prediction by combining fragment comparisons and a consensus C(alpha) contact potential. Proteins. 71(3):1211-8. PDF Abstract