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2011

        L. Xie, S.L. Kinnings, L. Xie and P.E. Bourne 2011 "Predicting the Polypharmacology of Drugs: Identifying New Uses Through Bioinformatics and Cheminformatics Approaches in Drug Repurposing". M. Barrett and D. Frail (Eds.) Wiley and Sons. accepted.

        S.J. Ho Sui, R. Lo, R. Fernandes, M.DG.Caulfield, J. Lerman, L. Xie, P.E. Bourne, D.L.Baillie and F.S.L.Brinkman 2011 "Identifying Potential Drug Repurposing Opportunities: The Estrogen Receptor Modulator Raloxifene Attenuates Pseudomonas aeruginosa Pyocyanin Production and Virulence". Under Revision

        L. Xie, L. Xie, S.L. Kinnings and P.E. Bourne 2011 "Novel Computational Approaches to Polypharmacology as a Means to Define Responses to Individual Drugs". Annual Review of Pharmacology and Toxicology 52 [PDF]

        L. Xie, L. Xie and P.E.Bourne 2011 "Structure-based Systems Biology for Analyzing Off-target Binding.". Curr. Opinions. in Struct. Biol. 21:1-11 [PDF]

        L. Xie, T. Evangelidis, L. Xie and P.E. Bourne 2011 "Drug Discovery Using Chemical Systems Biology: Weak inhibition of multiple kinases may contribute to the anti-cancer effect of Nelfinavir". PLoS Comp. Biol. 7(4) e1002037 [PDF] [Science 2011 332(6030) 648-649 [PDF]]

        S.L. Kinnings, N. Liu, P.J. Tonge, R.M. Jackson, L. Xie and P.E.Bourne 2011 "A Machine Learning Based Method to Improve Docking Scoring Functions and its Application to Drug Repurposing". J. Chem. Info. Model. 51(2), 408-419. [PDF]

2010

        S.L. Kinnings, L. Xie, K.H.Fung, R.M. Jackson, L. Xie and P.E. Bourne 2010 "The Mycbacterium tuberculosis druggome and its Pharmaceutical Implications". Plos Comp. Biol. 6(11): e1000976 [PDF]

        R.L Chang, L. Xie, L. Xie, P.E. Bourne B.O. Palsson 2010 "Drug Off-Target Effects Predicted Using Structural Analysis in the Context of a Metabolic Network Model". Plos Comp. Biol. 6(9): e1000938 [PDF]

        J. Ren, L. Xie, W. Li, P. E. Bourne 2010 "SMAP-WS: A Parallel Web Service for Structural Proteome-Wide Ligand Binding Site Comparison.". Nucleic Acids Res., 38(Suppl):W441-4 [PDF]

        J. D. Durrant, R. E. Amaro, L. Xie, M. D. Urbaniak, M. A. J. Ferguson, A. Haapalainen, Z. Chen, A. M. Di Guilmi, F. Wunder, P. E. Bourne, J. A. McCammon 2010 "A Multidimensional Strategy to Detect Polypharmacological Targets in the Absence of Structural and Sequence Homology". PLoS Comp. Biol., 6(1):e1000648 [PDF]

2009

        S. Kinnings, N. Liu, N. Buchmeier, P.J. Tonge, L. Xie and P.E. Bourne 2009 "Drug discovery using chemical systems biology: repositioning the safe medicine Comtan to treat multi-drug and extensively drug resistant tuberculosis". PLoS Comp. Biol., 5(7):e1000423 [PDF]

        L. Xie, J. Li, L. Xie and P.E. Bourne 2009 "Drug Discovery Using Chemical Systems Biology: Identification of the Protein-Ligand Binding Network To Explain the Side Effects of CETP Inhibitors". PLoS Comp. Biol., 5(5):e1000387 [PDF]

        L. Xie, L. Xie and P.E. Bourne 2009 "A unified statistical model to support local sequence order independent similarity searching for ligand binding sites and its application to genome-based drug discovery". Bioinformatics, 25(12):i305-i312 [PDF]

2008

        A. Gramada and P.E.Bourne 2008 "Resolving a Distribution of Charge into Intrinsic Multipole Moments: A Rankwise Distributed Multipole Analysis". Physical Review E, 78, 066601 [PDF]

        L. Xie and P.E. Bourne 2008 "Detecting Evolutionary Relationships Across Existing Fold Space, Using Sequence Order Independent Profile-profile Alignments". PNAS, 105(14):5441 [PDF]



2007

        L. Xie, J. Wang and P.E. Bourne 2007 "In Silico Elucidation of the Molecular Mechanism Defining the Adverse Effect of Selective Esterogen Receptor Modulators". PLoS Comp. Biol., 3(11):e217 [PDF].

        L. Xie, and P.E. Bourne 2007 "A Robust and Efficient Algorithm for the Shape Description of Protein Structures and Its Application in Predicting Ligand Binding Sites". BMC Bioinformatics, 8(Suppl 4):S9 [PDF].




The FS project is supported by the National Institutes of Heath (NIH) grant number GM078596 and is located within the Skaggs School of Pharmacy and Pharmaceutical Sciences and the San Diego Supercomputer Center (SDSC) at the University of California San Diego (UCSD).

© 2008, The Regents of the University of California


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