References
- Bahl, A., Brunk, B., Crabtree, J., Fraunholz, M. J., Gajria, B., Grant, G. R., … Whetzel, P. (2003). PlasmoDB: The Plasmodium genome resource. A database integrating experimental and computational data. Nucleic Acids Research, 31(1), 212–215.10.1093/nar/gkg081
- Becker, K., Tilley, L., Vennerstrom, J. L., Roberts, D., Rogerson, S., & Ginsburg, H. (2004). Oxidative stress in malaria parasite-infected erythrocytes: Host-parasite interactions. International Journal for Parasitology, 34(2), 163–189. doi:10.1016/j.ijpara.2003.09.011
- Buchan, D. W., Minneci, F., Nugent, T. C., Bryson, K., & Jones, D. T. (2013). Scalable web services for the PSIPRED protein analysis workbench. Nucleic Acids Research, 41(W1), W349–W357. doi:10.1093/nar/gkt381
- Case, D. A., Cheatham, T. E., 3rd, Darden, T., Gohlke, H., Luo, R., Merz, K. M., Jr., … Woods, R. J. (2005). The Amber biomolecular simulation programs. Journal of Computational Chemistry, 26(16), 1668–1688. doi:10.1002/jcc.20290
- Cohen, P. (2002). Protein kinases–the major drug targets of the twenty-first century? Nature Reviews Drug Discovery, 1(4), 309–315. doi:10.1038/nrd773
- Colovos, C., & Yeates, T. O. (1993). Verification of protein structures: Patterns of nonbonded atomic interactions. Protein Science, 2(9), 1511–1519. doi:10.1002/pro.5560020916
- Cosconati, S., Forli, S., Perryman, A. L., Harris, R., Goodsell, D. S., & Olson, A. J. (2010). Virtual screening with AutoDock: Theory and practice. Expert Opinion on Drug Discovery, 5(6), 597–607. doi:10.1517/17460441.2010.484460
- Doerig, C., Baker, D., Billker, O., Blackman, M. J., Chitnis, C., Dhar Kumar, S., … Alano, P. (2009). Signalling in malaria parasites. The MALSIG consortium. Parasite, 16(3), 169–182.10.1051/parasite/2009163169
- Dvorin, J. D., Bei, A. K., Coleman, B. I., & Duraisingh, M. T. (2010). Functional diversification between two related Plasmodium falciparum merozoite invasion ligands is determined by changes in the cytoplasmic domain. Molecular Microbiology, 75(4), 990–1006. doi:10.1111/j.1365-2958.2009.07040.x
- Franceschini, A., Szklarczyk, D., Frankild, S., Kuhn, M., Simonovic, M., Roth, A., … Jensen, L. J. (2012). STRING v9.1: Protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Research, 41(D1), D808–D815. doi:10.1093/nar/gks1094
- Gardner, M. J., Hall, N., Fung, E., White, O., Berriman, M., Hyman, R. W., … Barrell, B. (2002). Genome sequence of the human malaria parasite Plasmodium falciparum. Nature, 419(6906), 498–511. doi:10.1038/nature01097
- Gaulton, A., Bellis, L. J., Bento, A. P., Chambers, J., Davies, M., Hersey, A., … Overington, J. P. (2012). ChEMBL: A large-scale bioactivity database for drug discovery. Nucleic Acids Research, 40(D1), D1100–D1107. doi: 10.1093/nar/gkr777
- Guttery, D. S., Poulin, B., Ramaprasad, A., Wall, R. J., Ferguson, D. J., Brady, D., … Tewari, R. (2014). Genome-wide functional analysis of Plasmodium protein phosphatases reveals key regulators of parasite development and differentiation. Cell Host & Microbe, 16(1), 128–140. doi:10.1016/j.chom.2014.05.020
- He, R. J., Yu, Z. H., Zhang, R. Y., & Zhang, Z. Y. (2014). Protein tyrosine phosphatases as potential therapeutic targets. Acta Pharmacologica Sinica, 35(10), 1227–1246. doi:10.1038/aps.2014.80
- Hunter, T. (1995). Protein kinases and phosphatases: The Yin and Yang of protein phosphorylation and signaling. Cell, 80(2), 225–236.10.1016/0092-8674(95)90405-0
- Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., … Higgins, D. G. (2007). Clustal W and Clustal X version 2.0. Bioinformatics, 23(21), 2947–2948. doi:10.1093/bioinformatics/btm404
- Laskowski, R. A., & Swindells, M. B. (2011). LigPlot+: Multiple ligand–protein interaction diagrams for drug discovery. Journal of Chemical Information and Modeling, 51(10), 2778–2786. doi:10.1021/ci200227u
- Le Guilloux, V., Schmidtke, P., & Tuffery, P. (2009). Fpocket: An open source platform for ligand pocket detection. BMC Bioinformatics, 10, 168. doi:10.1186/1471-2105-10-168
- Li, L., Stoeckert, C. J., Jr., & Roos, D. S. (2003). OrthoMCL: Identification of ortholog groups for eukaryotic genomes. Genome Research, 13(9), 2178–2189. doi:10.1101/gr.1224503
- Long, H. Y., Lell, B., Dietz, K., & Kremsner, P. G. (2001). Plasmodium falciparum: In vitro growth inhibition by febrile temperatures. Parasitology Research, 87(7), 553–555.
- Marchler-Bauer, A., Lu, S., Anderson, J. B., Chitsaz, F., Derbyshire, M. K., DeWeese-Scott, C., … Bryant, S. H. (2011). CDD: A conserved domain database for the functional annotation of proteins. Nucleic Acids Research, 39(Database issue), D225–D229. doi: 10.1093/nar/gkq1189
- McConnell, J. L., & Wadzinski, B. E. (2009). Targeting protein serine/threonine phosphatases for drug development. Molecular Pharmacology, 75(6), 1249–1261. doi:10.1124/mol.108.053140
- Moon, R. W., Taylor, C. J., Bex, C., Schepers, R., Goulding, D., Janse, C. J., … Billker, O. (2009). A cyclic GMP signalling module that regulates gliding motility in a malaria parasite. PLoS Pathogens, 5(9), e1000599. doi:10.1371/journal.ppat.1000599
- Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., … Olson, A. J. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30(16), 2785–2791. doi:10.1002/jcc.21256
- Nayyar, G. M., Breman, J. G., Newton, P. N., & Herrington, J. (2012). Poor-quality antimalarial drugs in southeast Asia and sub-Saharan Africa. Lancet Infectious Diseases, 12(6), 488–496. doi:10.1016/S1473-3099(12)70064-6
- Nguyen, L. K., Matallanas, D., Croucher, D. R., von Kriegsheim, A., & Kholodenko, B. N. (2013). Signalling by protein phosphatases and drug development: A systems-centred view. FEBS Journal, 280(2), 751–765. doi:10.1111/j.1742-4658.2012.08522.x
- Pandey, R., Mohmmed, A., Pierrot, C., Khalife, J., Malhotra, P., & Gupta, D. (2014). Genome wide in silico analysis of Plasmodium falciparum phosphatome. BMC Genomics, 15, 1024. doi:10.1186/1471-2164-15-1024
- Pendyala, P. R., Ayong, L., Eatrides, J., Schreiber, M., Pham, C., Chakrabarti, R., … Chakrabarti, D. (2008). Characterization of a PRL protein tyrosine phosphatase from Plasmodium falciparum. Molecular and Biochemical Parasitology, 158(1), 1–10. doi:10.1016/j.molbiopara.2007.11.006
- Sapay, N., & Tieleman, D. P. (2011). Combination of the CHARMM27 force field with united-atom lipid force fields. Journal of Computational Chemistry, 32(7), 1400–1410. doi:10.1002/jcc.21726
- Si, X., Zeng, Q., Ng, C. H., Hong, W., & Pallen, C. J. (2001). Interaction of farnesylated PRL-2, a protein-tyrosine phosphatase, with the beta-subunit of geranylgeranyltransferase II. Journal of Biological Chemistry, 276(35), 32875–32882. doi:10.1074/jbc.M010400200
- Singh, M., Mukherjee, P., Narayanasamy, K., Arora, R., Sen, S. D., Gupta, S., … Malhotra, P. (2009). Proteome analysis of Plasmodium falciparum extracellular secretory antigens at asexual blood stages reveals a cohort of proteins with possible roles in immune modulation and signaling. Molecular & Cellular Proteomics, 8(9), 2102–2118. doi:10.1074/mcp.M900029-MCP200
- Tamura, K., Stecher, G., Peterson, D., Filipski, A., & Kumar, S. (2013). MEGA6: molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution, 30(12), 2725–2729. doi:10.1093/molbev/mst197
- Treeck, M., Sanders, J. L., Elias, J. E., & Boothroyd, J. C. (2011). The phosphoproteomes of Plasmodium falciparum and Toxoplasma gondii reveal unusual adaptations within and beyond the parasites’ boundaries. Cell Host & Microbe, 10(4), 410–419. doi:10.1016/j.chom.2011.09.004
- Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26(16), 1701–1718. doi:10.1002/jcc.20291
- Ward, P., Equinet, L., Packer, J., & Doerig, C. (2004). Protein kinases of the human malaria parasite Plasmodium falciparum: The kinome of a divergent eukaryote. BMC Genomics, 5, 79. doi:10.1186/1471-2164-5-79
- World Health Organization. (2016). World malaria report 2016. Geneva: Author.
- Wiesner, J., & Seeber, F. (2005). The plastid-derived organelle of protozoan human parasites as a target of established and emerging drugs. Expert Opinion on Therapeutic Targets, 9(1), 23–44. doi:10.1517/14728222.9.1.23
- Zeng, Q., Si, X., Horstmann, H., Xu, Y., Hong, W., & Pallen, C. J. (2000). Prenylation-dependent association of protein-tyrosine phosphatases PRL-1, -2, and -3 with the plasma membrane and the early endosome. Journal of Biological Chemistry, 275(28), 21444–21452. doi:10.1074/jbc.M000453200
- Zhang, Y. (2008). I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 9, 40. doi:10.1186/1471-2105-9-40