Papers+Conferences
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2013. Comprehensive Experimental and Computational Analysis of Binding Energy Hot Spots at the NF-κB Essential Modulator (NEMO)/IKKβ Protein-Protein Interface. Journal of the American Chemical Society. :130318121200001. Download: PDF (3.15 MB)
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2012. A First-Generation Multi-Functional Cytokine for Simultaneous Optical Tracking and Tumor Therapy. PLoS ONE. 7(7):e40234. Download: PDF (1.67 MB)
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2012. Relationship between Hot Spot Residues and Ligand Binding Hot Spots in Protein-Protein Interfaces.. Journal of chemical information and modeling. Download: PDF (3.75 MB)
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2012. Rigid Body Energy Minimization on Manifolds for Molecular Docking. Journal of Chemical Theory and Computation. :120821123549006. Download: PDF (317.26 KB)
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2012. FTMAP: extended protein mapping with user-selected probe molecules. Nucleic Acids Research. 40(W1):W271-W275. Download: PDF (1.33 MB)
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2012. Minimal ensembles of side chain conformers for modeling protein-protein interactions. Proteins: Structure, Function, and Bioinformatics. 80(2):591-601. Download: PDF (1.57 MB)
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2012. FTSite: high accuracy detection of ligand binding sites on unbound protein structures. Bioinformatics. 28(2):286-287. Download: PDF (268.3 KB)
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2012. Hot Spot Analysis for Driving the Development of Hits into Leads in Fragment-Based Drug Discovery. Journal of Chemical Information and Modeling. 52(1):199-209. Download: PDF (1.92 MB)
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2012. Analysis of Protein Binding Sites by Computational Solvent Mapping. Methods in Molecular Biology. 819:13-27. Download: PDF (1.71 MB)
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2011. Robust Identification of Binding Hot Spots Using Continuum Electrostatics: Application to Hen Egg-White Lysozyme. Journal of the American Chemical Society. 133(51):20668-20671. Download: PDF (3.55 MB)
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2011. Analysis of Binding Site Hot Spots on the Surface of Ras GTPase. Journal of Molecular Biology. 413(4):773-789.
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2011. Structural conservation of druggable hot spots in protein-protein interfaces. Proceedings of the National Academy of Sciences. 108(33):13528-13533. Download: PDF (7.25 MB)
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2011. Blocking eIF4E-eIF4G Interaction as a Strategy To Impair Coronavirus Replication. Journal of Virology. 85(13):6381-6389. Download: PDF (2.21 MB)
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2011. Reversing chemoresistance by small molecule inhibition of the translation initiation complex eIF4F.. Proceedings of the National Academy of Sciences of the United States of America. 108(3):1046-51. Abstract
Download: PDF (2.42 MB)
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2010. Domain motion and inter-domain hot spots in a multi-domain enzyme. Protein Science. Download: PDF (403.54 KB)
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2010. Achieving reliability and high accuracy in automated protein docking: Cluspro, PIPER, SDU, and stability analysis in CAPRI rounds 13-19. Proteins: Structure, Function, and Bioinformatics. 78(15):3124-3130. Download: PDF (297.68 KB)
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2010. Where does amantadine bind to the influenza virus M2 proton channel? Trends in Biochemical Sciences. Download: PDF (263.58 KB)
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2009. The Structural Basis of Pregnane X Receptor Binding Promiscuity. Biochemistry. 48(48):11572-11581. Download: PDF (3.14 MB)
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2009. Structural insights into recognition of β2-glycoprotein I by the lipoprotein receptors. Proteins: Structure, Function, and Bioinformatics. 77(4):940-949. Download: PDF (419.27 KB)
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2009. Binding Hot Spots and Amantadine Orientation in the Influenza A Virus M2 Proton Channel. Biophysical Journal. 97(10):2846-2853. Download: PDF (514.97 KB)
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2009. Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to DJ-1 and glucocerebrosidase. Journal of Computer-Aided Molecular Design. 23(8):491-500. Download: PDF (574.15 KB)
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2009. Convergence and combination of methods in protein–protein docking. Current Opinion in Structural Biology. 19(2):164-170. Download: PDF (250.8 KB)
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2009. Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques. Bioinformatics. 25(5):621-627. Download: PDF (412.04 KB)
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2009. Identification of Druggable Hot Spots on Proteins and in Protein Protein Interfaces. Computational Protein-Protein Interactions.
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2008. DARS (Decoys As the Reference State) Potentials for Protein-Protein Docking. Biophysical Journal. 95(9):4217-4227. Download: PDF (317.38 KB)
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2008. Discrimination of near‐native structures in protein–protein docking by testing the stability of local minima. Proteins: Structure, Function, and Bioinformatics. 72(3):993-1004. Download: PDF (328.1 KB)
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2008. Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions. Bioinformatics. 24(17):1865-1873. Download: PDF (328.1 KB)
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2007. ClusPro: Performance in CAPRI rounds 6–11 and the new server. Proteins: Structure, Function, and Bioinformatics. 69(4):781-785. Download: PDF (213.15 KB)
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2007. Docking with PIPER and refinement with SDU in rounds 6–11 of CAPRI. Proteins: Structure, Function, and Bioinformatics. 69(4):734-742. Download: PDF (274.39 KB)
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2006. PIPER: An FFT-based protein docking program with pairwise potentials. Proteins: Structure, Function, and Bioinformatics. 65(2):392-406. Download: PDF (385.54 KB)
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2005. Optimal Clustering for Detecting Near-Native Conformations in Protein Docking. Biophysical Journal. 89(2):867-875. Download: PDF (326.16 KB)
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2005. Optimal Clustering for Detecting Near-Native Conformation in Protein Docking. CAPRI Meeting. Download: PPT (5.34 MB)