Chemical Systems Biology Lab - Xie Research Group

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". Submitted.
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". Annu. Rev. Pharmacol. Toxicol. In press
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].
L. Xie, L. Xie and P.E. Bourne 2011 "Structure-based Systems Biology for Analyzing Off-target Binding". Curr. Opinions in Struct. Biol. 21(2):189-199 [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].

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]

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]

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]

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].

A. Kouranov, L. Xie, J. de la Cruz, L. Chen, J. Westbrook, P.E. Bourne, H.M. Berman 2006 "The RCSB PDB information portal for structural genomic". Nucleic Acids Res., 34(Database issue):D302-305 [PDF].

L. Xie and P.E. Bourne 2005 "Functional coverage of the human genome by existing structures, structural genomics targets, and homology models". PLoS Comp. Biol., 1(3):e31 [PDF].
N. Deshpande, K.J. Addess, W.F. Bluhm, J.C. Merino-Ott, W. Townsend-Merino, Q. Zhang, C. Knezevich, L. Xie, L. Chen, Z. Feng, R.K. Green, J.L. Flippen-Anderson, J. Westbrook, H.M. Berman, P.E. Bourne 2005 " The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema". Nucleic Acids Res., 33(Database issue):D233-237 [PDF].

C.L. Tang, L. Xie, I.Y. Koh, S. Posy, E. Alexov, B. Honig 2003 "On the role of structural information in remote homology detection and sequence alignment: new methods using hybrid sequence profiles". J. Mol. Biol., 334(5):1043-1062.
D. Petrey, Z. Xiang, C.L. Tang, L. Xie, M. Gimpelev, T. Mitros, C.S. Soto, S. Goldsmith-Fischman, A. Kernytsky, A. Schlessinger, I.Y. Koh, E. Alexov, B. Honig 2003 " Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling". Proteins, 53(S6):430-435.