Core A

  • Feng, Z.; Pearce, L. V.; Xu, X.; Yang, X.; Yang, P.; Blumberg, P. M.; Xie, X.-Q. Structural Insight into Tetrameric hTRPV1 from Homology Modeling, Molecular Docking, Molecular Dynamics Simulation, Virtual Screening and Bioassay Validations. J. Chem. Inf. Model. 2015, In press.
  • Feng, Z.; Ma, S.; Hu, G.; Xie, X.-Q. Allosteric Binding Site and Activation Mechanism of Class C G-Protein Coupled Receptors: Metabotropic Glutamate Receptor Family. AAPS J. 2015, 1-17.
  • Rentian Feng, Qin Tong, Zhaojun Xie, Haizi Cheng, Lirong Wang, Suzanne Lentzsch, G.David Roodman and Xiang-Qun Xie*
    “Targeting cannabinoid receptor-2 pathway by phenylacetylamide suppresses the proliferation of human myeloma cells through mitotic dysregulation and cytoskeleton disruption” Molecular Carcinogenesis, DOI: 10.1002/mc.22251 16 JAN 2015
  • Feng, Zhiwei, Stanton Kochanek, David Close, LiRong Wang, Ajay Srinivasan, Abdulrahman A. Almehizia, Prema Iyer, Xiang-Qun Xie, Paul A. Johnston, and Barry Gold. “Design and activity of AP endonuclease-1 inhibitors.” Journal of Chemical Biology (2015): 1-15.
  • Yingdai Gao, Peng Yang, Hongmei Shen, Hui Yu, Xianmin Song, Liyan Zhang, Peng Zhang, Haizi Cheng, Zhaojun Xie, Sha Hao, Yahui Ding, Lirong Wang, Haibin Liu, Yanxin Li, Hui Cheng, Weimin Miao, Weiping Yuan, Youzhong Yuan, Tao Cheng, Xiang-Qun Xie* “Small-molecule inhibitors targeting INK4 protein p18 INK4C enhance ex vivo expansion of haematopoietic stem cells” Nature Communications. 02/2015; 6. DOI: 10.1038/ncomms7328
  • Feng, Z., Ma, S., Hu, G., & Xie, X. Q. (2015). Allosteric binding site and activation mechanism of class C G-protein coupled receptors: metabotropic glutamate receptor family. The AAPS journal, 17(3), 737-753.
  • Ji, Kai-Long, Ping Zhang, Xiao-Nian Li, Juan Guo, Hua-Bin Hu, Chun-Fen Xiao, Xiang-Qun Xie, and You-Kai Xu. “Cytotoxic limonoids from Trichilia americana leaves.” Phytochemistry 118 (2015): 61-67.
  • Myint, K. Z., & Xie, X. Q. (2015). Ligand Biological Activity Predictions Using Fingerprint-Based Artificial Neural Networks (FANN-QSAR). In Artificial Neural Networks (pp. 149-164). Springer New York.
  • Teramachi, J.; Silbermann, R.; Yang, P.; Zhao, W.; Mohammad, K. S.; Guo, J.; Anderson, J. L.; Zhou, D.; Feng, R.; Myint, K. Z.; Maertz, N.; Beumer, J. H.; Eiseman, J. L.; Windle, J. J.; Xie, X. Q.; Roodman, G. D.; Kurihara, N., Blocking the ZZ domain of sequestosome1/p62 suppresses myeloma growth and osteoclast formation in vitro and induces dramatic bone formation in myeloma-bearing bones in vivo. Leukemia 2015.
  • Silbermann, R., Zhou, D., Teramachi, J., Xie, X. Q., Roodman, G. D., & Kurihara, N. (2014). The p62-ZZ Domain Inhibitor XRK3F2 Alters Myeloma-Induced Suppression of Osteoblast Differentiation and Is Highly Cytotoxic to Myeloma Cells in Combination with Bortezomib. Blood, 124(21), 2083-2083.
  • Zeng, D., Ouyang, Q., Cai, Z., Xie, X. Q., & Anderson, C. J. (2014). New cross-bridged cyclam derivative CB-TE1K1P, an improved bifunctional chelator for copper radionuclides. Chemical Communications, 50(1), 43-45.
  • Zhang, S., Jia, N., Shao, P., Tong, Q., Xie, X. Q., & Bai, M. (2014). Target-Selective Phototherapy Using a Ligand-Based Photosensitizer for Type 2 Cannabinoid Receptor. Chemistry & biology, 21(3), 338-344.
  • Wang, L., & Xie, X. Q. (2014). Computational target fishing: what should chemogenomics researchers expect for the future of in silico drug design and discovery?. Future medicinal chemistry, 6(3), 247-249.
  • Liu, H., Wang, L., Su, W., & Xie, X. Q. (2014). Advances in recent patent and clinical trial drug development for Alzheimer’s disease. Pharmaceutical patent analyst, 3(4), 429-447.
  • Feng, R., Milcarek, C. A., & Xie, X. Q. (2014). Antagonism of cannabinoid receptor 2 pathway suppresses IL-6-induced immunoglobulin IgM secretion.BMC Pharmacology and Toxicology, 15(1), 30.
  • Feng, Z.; Alqarni, M. H.; Yang, P.; Tong, Q.; Chowdhury, A.; Wang, L.; Xie, X.-Q. Modeling, Molecular Dynamics Simulation and Mutation Validation for Structure of Cannabinoid Receptor 2 Based on Known Crystal Structures of GPCRs. J. Chem. Inf. Model. 2014, 54, 2483-2499.
  • Qin Ouyang, Lirong Wang, Ying Mu, Xiang-Qun Xie, “Modeling skin sensitization potential of mechanistically hard-to-be-classified aniline and phenol compounds with quantum mechanistic properties”. BMC pharmacology & toxicology 12/2014; 15(1):76. DOI: 10.1186/2050-6511-15-76

Core B

  • Chen MH, Bahar I (2015) Molecular Mechanism of Dopamine Transport by Human Dopamine Transporter, Structure 23: 2171-81
  • Gur M, Zomot E, Cheng MH, Bahar I (2015) Energy landscape of LeuT from molecular simulations J Chem Phys 143: 243134
  • Li H, Chang YY, Yang LW, Bahar I (2015) iGNM 2.0: the Gaussian network model database for biomolecular structural dynamics Nucleic Acids Res pii: gkv1236 PMID: 26582920
  • Cheng MH, Bahar I (2015) Molecular Mechanism of Dopamine Transport by Human Dopamine Transporter Structure pii: S0969-2126 PMID: 26481814
  • Hu D, Gur M, Zhou Z, Gamper A, Hung MC, Fujita N, Lan L, Bahar I, Wan Y (2015) Interplay between arginine methylation and ubiquitylation regulates KLF4-mediated genome stability and carcinogenesis Nat Commun 6: 8419 PMID: 26420673
  • Keskin O, Dyson HJ, Bahar I (2015) Biomolecular Systems Interactions, Dynamics, and Allostery: Reflections and New Directions Biophysical Journal 109: E01-2 PMID: 26377787
  • Krieger J, Bahar I, Greger IH (2015) Structure, Dynamics, and Allosteric Potential of Ionotropic Glutamate Receptor N-Terminal Domains Biophysical Journal pii: S0006-3495 PMID: 26255587
  • Dutta A, Krieger J, Lee JY, Garcia-Nafria J, Greger IH, Bahar I (2015) Cooperative Dynamics of Intact AMPA and NMDA Glutamate Receptors: Similarities and Subfamily-Specific Differences Structure pii: S0969-2126 PMID: 26256538
  • Haliloglu T, Bahar I (2015) Adaptability of protein structures to enable functional interactions and evolutionary implications Current Opinion in Structural Biology 35: 17-23 PMID: 26254902
  • Bahar I, Cheng MH, Lee JY, Kaya C, Zhang S (2015) Structure-Encoded Global Motions and Their Role in Mediating Protein-Substrate Interactions Biophys J pii: S0006-3495 PMID: 26143655Cheng, M. H., F. Hu, E. Block, A. Sorkin, and I. Bahar. 2015. Insights into the mechanisms of dopamine transporter function modulation by emphetamine, orphenadrine and cocaine binding. In revision
  • Cheng, M. H., F. Hu, E. Block, A. Sorkin, and I. Bahar. 2015. Insights into the mechanisms of dopamine transporter function modulation by emphetamine, orphenadrine and cocaine binding. In revision
  • Eyal E, Lum G, Bahar I (2015) The Anisotropic Network Model web server at 2015 (ANM 2.0) Bioinformatics 2015: 1-3 PMID: 25568280 [Epub ahead of print]
  • Cheng MH, Bahar I (2014) Complete Mapping of Substrate Translocation Highlights the Role of LeuT N-terminal Segment in Regulating Transport Cycle PLoS Comput Biol 10: e1003879 PMID: 25299050; PMC4191883
  • Cobanoglu MC, Oltvai ZN, Taylor DL, Bahar I (2014) BalestraWeb: Efficient, online evaluation of drug-target interactions Bioinformatics 31:131-3 PMID: 25192741; PMC4271144
  • Bahar I (2014) Coupling between Neurotransmitter Translocation and Protonation State of a Titratable Residue during Na(+)-Coupled Transport Biophys J 106: 2547-8 PMID: 24940770; PMC4070272
  • Bakan A,* Dutta A,* Mao W, Liu Y, Chennubhotla C, Lezon TR, Bahar I (2014) Evol and ProDy for Bridging Protein Sequence Evolution and Structural Dynamics Bioinformatics 30: 2681-3 PMID: 24849577; PMC4155247
  • Das A, Gur M,* Cheng MH,* Jo S, Bahar I, Roux B (2014) Exploring the conformational transitions of biomolecular systems using a simple two-state anisotropic network model PLoS Comput Biol 10: e1003521 PMID: 24699246; PMC397464
  • Cheng, M. H., F. Hu, E. Block, A. Sorkin, and I. Bahar. 2015. Insights into the mechanisms of dopamine transporter function modulation by emphetamine, orphenadrine and cocaine binding. In revision.
  • Eyal E, Lum G, Bahar I (2015) The Anisotropic Network Model web server at 2015 (ANM 2.0) Bioinformatics 2015: 1-3 PMID: 25568280 [Epub ahead of print]
  • Cheng MH, Bahar I (2014) Complete Mapping of Substrate Translocation Highlights the Role of LeuT N-terminal Segment in Regulating Transport Cycle PLoS Comput Biol 10: e1003879 PMID: 25299050; PMC4191883
  • Cobanoglu MC, Oltvai ZN, Taylor DL, Bahar I (2014) BalestraWeb: Efficient, online evaluation of drug-target interactions Bioinformatics 31:131-3 PMID: 25192741; PMC4271144
  • Bahar I (2014) Coupling between Neurotransmitter Translocation and Protonation State of a Titratable Residue during Na(+)-Coupled Transport Biophys J 106: 2547-8 PMID: 24940770; PMC4070272
  • Bakan A,* Dutta A,* Mao W, Liu Y, Chennubhotla C, Lezon TR, Bahar I (2014) Evol and ProDy for Bridging Protein Sequence Evolution and Structural Dynamics Bioinformatics 30: 2681-3 PMID: 24849577; PMC4155247
  • Das A, Gur M,* Cheng MH,* Jo S, Bahar I, Roux B (2014) Exploring the conformational transitions of biomolecular systems using a simple two-state anisotropic network model PLoS Comput Biol 10: e1003521 PMID: 24699246; PMC3974643

Core C

  • S. Lee, A. Lozano, P. Kambadur, and E. P. Xing, An Efficient Nonlinear Regression Approach for Genome-Wide Detection of Marginal and Interacting Genetic Variations, to appear in the 19th International Conference on Research in Computational Molecular Biology (RECOMB 2015)
  • S. Lee, J. K. Kim, X. Zheng, Q. Ho, G. A. Gibson, and E. P. Xing, On Model Parallelization and Scheduling Strategies for Distributed Machine Learning, Advances in Neural Information Processing Systems 28 (eds. Corinna Cortes and Neil Lawrence), MIT Press, 2014. (NIPS 2014).
  • Wu, W.*, Bleecker, E., Moore, W., Busse, W. W., Jarjour, N., Castro, M., Chung, K. F., Calhoun, W. J., Erzurum, S., Gaston, B., Israel, E., Curran-Everett, D., Wenzel, S. E.* (2014) “Unsupervised phenotyping of Severe Asthma Research Program participants using expanded lung data.” Journal of Allergy and Clinical Immunology 133(5):1280-1288. NIHMS562128. (PMCID: PMC4038417).
  • E. P. Xing, R. Curtis, G. Schoenherr, S. Lee, J. Yin, K. Puniyani, W. Wu, P. Kinnaird, GWAS in a Box: Statistical and Visual Analytics of Structured Associations via GenAMap, PLoS One, Volume 9, Issue 6, e97524, 2014.