References
- Aguilar, H. C., Ataman, Z. A., Aspericueta, V., Fang, A. Q., Stroud, M., Negrete, O. A., … Lee, B. (2009). A novel receptor-induced activation site in the Nipah virus attachment glycoprotein (G) involved in triggering the fusion glycoprotein (F). Journal of Biological Chemistry, 284(3), 1628–1635. doi:10.1074/jbc.M807469200
- Ali, M. H., Anwar, S., Kumar Roy, P., & Ashrafuzzaman, M. (2018). Virtual screening for identification of small lead compound inhibitors of Nipah virus attachment glycoprotein. Journal of Pharmacogenomics & Pharmacoproteomics, 9(2), 1000180. doi:10.4172/2153-0645.1000180
- Antoine, T. E., Park, P. J., & Shukla, D. (2013). Glycoprotein targeted therapeutics: A new era of anti-herpes simplex virus-1 therapeutics. Reviews in Medical Virology, 23(3), 194–208. doi:10.1002/rmv.1740
- Banerjee, N., & Mukhopadhyay, S. (2016). Viral glycoproteins: Biological role and application in diagnosis. VirusDisease, 27(1), 1–11. doi:10.1007/s13337-015-0293-5
- Berendsen, H. J. C. (1991). Computer simulation in materials science. Dordrecht: Springer. doi:10.1007/978-94-011-3546-7
- Berendsen, H. J. C., van der Spoel, D., & van Drunen, R. (1995). GROMACS: A message-passing parallel molecular dynamics implementation. Computer Physics Communications, 91(1–3), 43–56. doi:10.1016/0010-4655(95)00042-E
- Bolcato, G., Cuzzolin, A., Bissaro, M., Moro, S., & Sturlese, M. (2019). Can we still trust docking results? An extension of the applicability of DockBench on PDBbind database. International Journal of Molecular Sciences, 20(14), 3558. doi:10.3390/ijms20143558
- Bonaparte, M. I., Dimitrov, A. S., Bossart, K. N., Crameri, G., Mungall, B. A., Bishop, K. A., … Broder, C. C. (2005). From the cover: Ephrin-B2 ligand is a functional receptor for Hendra virus and Nipah virus. Proceedings of the National Academy of Sciences of the United States of America, 102(30), 10652–10657. doi:10.1073/pnas.0504887102
- Burley, S. K., Berman, H. M., Bhikadiya, C., Bi, C., Chen, L., Di Costanzo, L., … & Feng, Z. (2018). RCSB Protein Data Bank: Biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy. Nucleic Acids Research, 47(D1), D464–D474. doi:10.1093/nar/gky1004
- Chen, D., Oezguen, N., Urvil, P., Ferguson, C., Dann, S. M., & Savidge, T. C. (2016). Regulation of protein-ligand binding affinity by hydrogen bond pairing. Science Advances, 2(3), e1501240. doi:10.1126/sciadv.1501240
- Chen, L., Cruz, A., Ramsey, S., Dickson, C. J., Duca, J. S., & Hornak, V. (2019). Hidden bias in the DUD-E dataset leads to misleading performance of deep learning in structure-based virtual screening. ChemRxiv, Preprint. doi:10.26434/chemrxiv.7886165.v1
- Danishuddin, A. A., Maryam, L., Srivastava, G., Sharma, A., & Khan, A. U. (2018). Designing of inhibitors against CTX-M-15 type β-lactamase: Potential drug candidate against β-lactamases-producing multi-drug-resistant bacteria. Journal of Biomolecular Structure and Dynamics, 36, 1806–1821. doi:10.1080/07391102.2017.1335434
- Danishuddin, M., Khan, A., Faheem, M., Kalaiarasan, P., Baig, M. H., Subbarao, N., & Khan, A. U. (2014). Structure-based screening of inhibitors against KPC-2: Designing potential drug candidates against multidrugresistant bacteria. Journal of Biomolecular Structure and Dynamics, 32(5), 741–750. doi:10.1080/07391102.2013.789988
- Dar, A. M., & Mir, S. (2017). Molecular docking: Approaches, types, applications and basic challenges. Journal of Analytical & Bioanalytical Techniques, 8(2), 8–10. doi:10.4172/2155-9872.1000356
- Dawes, B. E., Kalveram, B., Ikegami, T., Juelich, T., Smith, J. K., Zhang, L., … & Freiberg, A. N. (2018). Favipiravir (T-705) protects against Nipah virus infection in the hamster model. Scientific Reports, 8(1), 7604. doi:10.1038/s41598-018-25780-3
- De Vivo, M., Masetti, M., Bottegoni, G., & Cavalli, A. (2016). Role of molecular dynamics and related methods in drug discovery. Journal of Medicinal Chemistry, 59(9), 4035–4061. doi:10.1021/acs.jmedchem.5b01684
- Dorigo, M., & Stützle, T. (2004). Ant colony optimization. Cambridge, MA: MIT Press.
- Epstein, J. H., Field, H. E., Luby, S., Pulliam, J. R. C., & Daszak, P. (2006). Nipah virus: Impact, origins, and causes of emergence. Current Infectious Disease Reports, 8(1), 59–65. doi:10.1007/s11908-006-0036-2
- Giangaspero, M. (2013). Nipah virus. Tropical Medicine & Surgery, 1, 1–4. doi:10.4172/2329-9088
- Hadži, D., Kidrič, J., Koller, J., & Mavri, J. (1990). The role of hydrogen bonding in drug-receptor interactions. Journal of Molecular Structure, 237, 139–150. doi:10.1016/0022-2860(90)80136-8
- Hess, B., Bekker, H., Berendsen, H. J. C., & Fraaije, J. G. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18(12), 1463–1472. doi:10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
- Hess, B., Kutzner, C., van der Spoel, D., & Lindahl, E. (2008). GRGMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation, 4(3), 435–447. doi:10.1021/ct700301q
- Hospital, A., Goñi, J. R., Orozco, M., & Gelpí, J. L. (2015). Molecular dynamics simulations: Advances and applications. Advances and Applications in Bioinformatics and Chemistry, 8, 37–47. doi:10.2147/AABC.S70333
- Huey, R., Morris, G. M., Olson, A. J., & Goodsell, D. S. (2007). A semiempirical free energy force field with charge-based desolvation. Journal of Computational Chemistry, 28(6), 1145–1152. doi:10.1002/jcc.20634
- Kamthania, M., & Sharma, D. K. (2015). Screening and structure-based modeling of T-cell epitopes of Nipah virus proteome: An immunoinformatic approach for designing peptide-based vaccine. 3 Biotech, 5(6), 877–882. doi:10.1007/s13205-015-0303-8
- Khamis, M. A., & Gomaa, W. (2015). Comparative assessment of machine-learning scoring functions on PDBbind 2013. Engineering Applications of Artificial Intelligence, 45, 136–151. doi:10.1016/j.engappai.2015.06.021
- Korb, O., Stützle, T., & Exner, T. E. (2006). PLANTS: Application of ant colony optimization to structure-based drug design. In M. Dorigo, L. M. Gambardella, M. Birattari, A. Martinoli, R. Poli, & T. Stützle (Eds.), Ant colony optimization and swarm intelligence: 5th International Workshop, Ants 2006, Brussels, Belgium, September 4–7, 2006. Proceedings (pp. 247–258). Berlin: Springer. doi:10.1007/11839088_22
- Korb, O., Stützle, T., & Exner, T. E. (2009). Empirical scoring functions for advanced protein–ligand docking with plants. Journal of Chemical Information and Modeling, 49(1), 84–96. doi:10.1021/ci800298z
- Martinez-Gil, L., Vera-Velasco, N. M., & Mingarro, I. (2017). Exploring the human-Nipah virus protein-protein interactome. Journal of Virology, 91(23), e01461–17. doi:10.1128/JVI.01461-17
- Meagher, K. L., & Carlson, H. A. (2005). Solvation influences flap collapse in HIV-1 protease. Proteins: Structure, Function, and Bioinformatics, 58(1), 119–125. doi:10.1002/prot.20274
- Minyi, S., Qifan, Y., Yu, D., Guoqin, F., Zhihai, L., Yan, L., & Renxiao, W. (2019). Comparative assessment of scoring functions: The CASF-2016 update. Journal of Chemical Information and Modeling, 59, 895–913. doi:10.1021/acs.jcim.8b00545
- Morris, G. M., Goodsell, D. S., Halliday, R. S., Huey, R., Hart, W. E., Belew, R. K., & Olson, A. J. (1998). Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. Journal of Computational Chemistry, 19(14), 1639–1662. doi:10.1002/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B
- 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.AutoDock4
- Niedermeier, S., Singethan, K., Rohrer, S. G., Matz, M., Kossner, M., Diederich, S., … Holzgrabe, U. (2009). A small-molecule inhibitor of Nipah virus envelope protein-mediated membrane fusion. Journal of Medicinal Chemistry, 52(14), 4257–4265. doi:10.1021/jm900411s
- O’Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., & Hutchison, G. R. (2011). Open Babel: An open chemical toolbox. Journal of Cheminformatics, 3(1), 33. doi:10.1186/1758-2946-3-33
- Parrinello, M., & Rahman, A. (1981). Polymorphic transitions in single crystals: A new molecular dynamics method. Journal of Applied Physics, 52(12), 7182–7190. doi:10.1063/1.328693
- Pascoini, A. L., Federico, L. B., Arêas, A. L. F., Verde, B. A., Freitas, P. G., & Camps, I. (2019). In silico development of new acetylcholinesterase inhibitors. Journal of Biomolecular Structure and Dynamics, 37(4), 1007–1021. doi:10.1080/07391102.2018.1447513
- Petersen, H. G. (1995). Accuracy and efficiency of the particle mesh Ewald method. The Journal of Chemical Physics, 103(9), 3668–3679. doi:10.1063/1.470043
- Ravichandran, L., Venkatesan, A., & Febin Prabhu Dass, J. (2018). Epitope-based immunoinformatics approach on RNA&-dependent RNA polymerase (RdRp) protein complex of Nipah virus (NiV). Journal of Cell Biology, 120(5), 7082–7095. doi:10.1002/jcb.27979
- Shi, B. X., Chen, F. R., & Sun, X. (2017). Structure-based modelling, scoring, screening, and in vitro kinase assay of anesthetic pkc inhibitors against a natural medicine library. SAR and QSAR in Environmental Research, 28(2), 151–163. doi:10.1080/1062936X.2017.1292406
- Schüttelkopf, A. W., & Van Aalten, D. M. F. (2004). PRODRG: A tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallographica Section D Biological Crystallography, 60(8), 1355–1363. doi:10.1107/S0907444904011679
- Stierand, K., & Rare, M. (2010). Drawing the PDB: Protein–ligand complexes in two dimensions. ACS Medicinal Chemistry Letters, 1(9), 540–545. doi:10.1021/ml100164p
- Tigabu, B., Rasmussen, L., White, E. L., Tower, N., Saeed, M., Bukreyev, A., … Noah, J. W. (2014). A BSL-4 high-throughput screen identifies sulfonamide inhibitors of Nipah virus. Assay and Drug Development Technologies, 12(3), 155–161. doi:10.1089/adt.2013.567
- Trott, O., & Olson, A. J. (2010). AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading. Journal of Computational Chemistry, 31(2), 455–461. doi:10.1002/jcc.21334
- Van Gunsteren, W. F., & Berendsen, H. J. C. (1988). A leap-frog algorithm for stochastic dynamics. Molecular Simulation, 1, 173–185. doi:10.1080/08927028808080941
- Veerappan, K., Natarajan, S., Ethiraj, P., Vetrivel, U., & Samuel, S. (2017). Inhibition of IKKβ by celastrol and its analogues – An in silico and in vitro approach. Pharmaceutical Biology, 55(1), 368–373. doi:10.1080/13880209.2016.1241809
- Wang, R., Lai, L., & Wang, S. (2002). Further development and validation of empirical scoring functions for structure based binding affinity prediction. Journal of Computer Aided Molecular Design, 16(1), 11–26. doi:10.1023/A:1016357811882
- Xu, K., Rajashankar, K. R., Chan, Y.-P., Himanen, J. P., Broder, C. C., & Nikolov, D. B. (2008). Host cell recognition by the henipaviruses: Crystal structures of the Nipah G attachment glycoprotein and its complex with ephrin-B3. Proceedings of the National Academy of Sciences of the United States of America, 105(29), 9953–9958. doi:10.1073/pnas.0804797105
- Xu, W., Lucke, A. J., & Fairlie, D. P. (2015). Comparing sixteen scoring functions for predicting biological activities of ligands for protein targets. Journal of Molecular Graphics and Modelling, 57, 76–88. doi:10.1016/j.jmgm.2015.01.009
- Yan, L., Su, M., Liu, Z., Li, J., Liu, J., Han, L., & Wang, R. (2018). Assessing protein–ligand interaction scoring functions with the CASF-2013 benchmark. Nature Protocols, 13, 666–680. doi:10.1038/nprot.2017.114