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Submitted. EFICAz2.5: Application of a high-precision enzyme function predictor to 373 proteomes. BMC Bioinformatics.
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Submitted. FINDSITEX: A structure based, small molecule virtual screening approach with application to all identified human GPCRs. Molecular Pharmaceutics .
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Submitted. Importance of excluded volume and hydrodynamic interactions on macromolecular diffusion in vivo. Proceedings of the International Conference of the Quantum Bio-Informatics IV.
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Submitted. SUNPRO: Structure and function predictions of proteins from representative organisms. BMC Bioinformatics.
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In Press. Further evidence for the likely completeness of the library of solved single domain protein structures. Journal of Physical Chemistry, B. 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. 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
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2008. Protein model refinement using an optimized physics-based all-atom force field. Proceedings of the National Academy of Sciences of the United States of America. 105(24):8268-73. PDF Abstract
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2008. Assessment of programs for ligand binding affinity prediction. Journal of computational chemistry. 29(8):1316-31. PDF Abstract
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2008. Q-Dock: Low-resolution flexible ligand docking with pocket-specific threading restraints. Journal of computational chemistry. 29(10):1574-88. PDF Supplementary Data Abstract
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2008. Fast procedure for reconstruction of full-atom protein models from reduced representations. Journal of computational chemistry. 29(9):1460-5. PDF Abstract
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2008. DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions. Nucleic acids research. 36(12):3978-92. PDF Supplementary Data Abstract
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2008. Structure-based classification of 45 FK506-binding proteins. Proteins. 72(1):197-208. PDF Abstract
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2008. A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation. Proceedings of the National Academy of Sciences of the United States of America. 105(1):129-34. PDF Supplementary Data Abstract
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2008. M-TASSER: an algorithm for protein quaternary structure prediction. Biophysical journal. 94(3):918-28. PDF Abstract
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2008. What is the relationship between the global structures of apo and holo proteins? Proteins. 70(2):363-77. PDF Supplementary Data Abstract
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2008. Benchmarking of TASSER_2.0: an improved protein structure prediction algorithm with more accurate predicted contact restraints. Biophysical journal. 95(4):1956-64. PDF Abstract
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2008. Development of a physics-based force field for the scoring and refinement of protein models. Biophysical journal. 94(8):3227-40. PDF Abstract