Deciphering the mechanism behind the varied binding activities of COXIBs through Molecular Dynamic Simulations, MM-PBSA binding energy calculations and per-residue energy decomposition studies

References

• Abelson, R., & Gardiner, H. (2004) Pfizer warns of risks from its painkiller. The New York Times, 204: B1.
   Google Scholar
• Agarwal, S., Reddy, G. V., & Reddanna, P. (2009). Eicosanoids in inflammation and cancer: the role of COX-2. Expert Review of Clinical Immunology, 5, 145–165.10.1586/1744666X.5.2.145
   PubMed Web of Science ®Google Scholar
• Allison, M. C., Howatson, A. G., Torrance, C. J., Lee, F. D., & Russell, R. I. (1992). Gastrointestinal damage associated with the use of nonsteroidal antiinflammatory drugs. New England Journal of Medicine, 327, 749–754.10.1056/NEJM199209103271101
   PubMed Web of Science ®Google Scholar
• Aparoy, P., Reddy, K. K., & Reddanna, P. (2012). Structure and ligand based drug design strategies in the development of novel 5- LOX inhibitors. Current Medicinal Chemistry, 19, 3763–3778.10.2174/092986712801661112
   PubMed Web of Science ®Google Scholar
• Bayly, C. I., Cieplak, P., Cornell, W., & Kollman, P. A. (1993). A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: The RESP model. The Journal of Physical Chemistry, 97, 10269–10280.10.1021/j100142a004
   Web of Science ®Google Scholar
• Berendsen, H. J. C., van der Spoel, D., & van Drunen, R. (1995). GROMACS: A message-passing parallel molecular dynamics implementation. Computer Physics Communications, 91, 43–56.10.1016/0010-4655(95)00042-E
   Web of Science ®Google Scholar
• Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., … Bourne, P. E. (2000). The protein data bank. Nucleic Acids Research, 28, 235–242.10.1093/nar/28.1.235
   PubMed Web of Science ®Google Scholar
• Bhattacharyya, D. K., Lecomte, M., Rieke, C. J., Garavito, M., & Smith, W. L. (1996). Involvement of arginine 120, glutamate 524, and tyrosine 355 in the binding of arachidonate and 2-phenylpropionic acid inhibitors to the cyclooxygenase active site of ovine prostaglandin endoperoxide H synthase-1. The Journal of Biological Chemistry, 271, 2179–2184.
   PubMed Web of Science ®Google Scholar
• Blobaum, A. L., & Marnett, L. J. (2007). Molecular determinants for the selective inhibition of cyclooxygenase-2 by lumiracoxib. Journal of Biological Chemistry, 282, 16379–16390.10.1074/jbc.M609883200
   PubMed Web of Science ®Google Scholar
• Bolton, E. E., Wang, Y., Thiessen, P. A., & Bryant, S. H. (2008). Chapter 12 – PubChem: Integrated platform of small molecules and biological activities. In A. W. Ralph & C. S. David (Eds.), Annual reports in computational chemistry (Vol. 4, pp. 217–241). Bethesda, USA: Elsevier.
   Google Scholar
• Bombardier, C., Laine, L., Reicin, A., Shapiro, D., Burgos-Vargas, R., Davis, B., … Schnitzer, T. J. (2000). Comparison of upper gastrointestinal toxicity of rofecoxib and naproxen in patients with rheumatoid arthritis. New England Journal of Medicine, 343, 1520–1528. 10.1056/NEJM200011233432103
   PubMed Web of Science ®Google Scholar
• Bouaziz-Terrachet, S., Toumi-Maouche, A., Maouche, B., & Taïri-Kellou, S. (2010). Modeling the binding modes of stilbene analogs to cyclooxygenase-2: A molecular docking study. Journal of Molecular Modeling, 16, 1919–1929.10.1007/s00894-010-0679-7
   PubMed Web of Science ®Google Scholar
• Bresalier, R. S., Sandler, R. S., Quan, H., Bolognese, J. A., Oxenius, B., Horgan, K., … Baron, J. A. (2005). Cardiovascular events associated with rofecoxib in a colorectal adenoma chemoprevention trial. New England Journal of Medicine, 352, 1092–1102.10.1056/NEJMoa050493
   PubMed Web of Science ®Google Scholar
• Chandrasekharan, N. V., Dai, H., Roos, K. L., Evanson, N. K., Tomsik, J., Elton, T. S., & Simmons, D. L. (2002). COX-3, a cyclooxygenase-1 variant inhibited by acetaminophen and other analgesic/antipyretic drugs: Cloning, structure, and expression. Proceedings of the National Academy of Sciences of the United States of America, 99, 13926–13931.10.1073/pnas.162468699
   PubMed Web of Science ®Google Scholar
• Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems. The Journal of Chemical Physics, 98, 10089–10092.10.1063/1.464397
   Web of Science ®Google Scholar
• Dupradeau, F. Y., Pigache, A., Zaffran, T., Savineau, C., Lelong, R., Grivel, N., … Cieplak, P. (2010). The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building. Physical Chemistry Chemical Physics, 12, 7821–7839.10.1039/c0cp00111b
   PubMed Web of Science ®Google Scholar
• FitzGerald, G. A. (2003). COX-2 and beyond: Approaches to prostaglandin inhibition in human disease. Nature Reviews Drug Discovery, 2, 879–890.10.1038/nrd1225
   PubMed Web of Science ®Google Scholar
• FitzGerald, G. A., & Patrono, C. (2001). The coxibs, selective inhibitors of cyclooxygenase-2. The New England Journal of Medicine, 345, 433–442.
   PubMed Web of Science ®Google Scholar
• García-Nieto, R., Pérez, C., & Gago, F. (2000). Automated docking and molecular dynamics simulations of nimesulide in the cyclooxygenase active site of human prostaglandin-endoperoxide synthase-2 (COX-2). Journal of Computer-Aided Molecular Design, 14, 147–160.10.1023/A:1008110924479
   PubMed Web of Science ®Google Scholar
• Gohlke, H., Kiel, C., & Case, D. A. (2003). Insights into protein–protein binding by binding free energy calculation and free energy decomposition for the Ras–Raf and Ras–RalGDS Complexes. Journal of Molecular Biology, 330, 891–913.10.1016/S0022-2836(03)00610-7
   PubMed Web of Science ®Google Scholar
• Herschman, H. R. (1996). Prostaglandin synthase 2. Biochim Biophys Acta, 1299, 125–140.10.1016/0005-2760(95)00194-8
   PubMed Web of Science ®Google Scholar
• Hess, B., Bekker, H., Berendsen, H. J. C., & Fraaije, J. G. E. M. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18, 1463–1472.10.1002/(ISSN)1096-987X
   Web of Science ®Google Scholar
• Hess, B., Kutzner, C., van der Spoel, D., & Lindahl, E. (2008). GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation, 4, 435–447.10.1021/ct700301q
   PubMed Web of Science ®Google Scholar
• Homeyer, N., & Gohlke, H. (2012). Free energy calculations by the molecular mechanics Poisson−Boltzmann surface area method. Molecular Informatics, 31, 114–122.10.1002/minf.v31.2
   PubMed Web of Science ®Google Scholar
• Honarparvar, B., Govender, T., Maguire, G. E. M., Soliman, M. E. S., & Kruger, H. G. (2014). Integrated approach to structure-based enzymatic drug design: Molecular modeling, spectroscopy, and experimental bioactivity. Chemical Reviews, 114, 493–537.10.1021/cr300314q
   PubMed Web of Science ®Google Scholar
• Hood, W. F., Gierse, J. K., Isakson, P. C., Kiefer, J. R., Kurumbail, R. G., Seibert, K., & Monahan, J. B. (2003). Characterization of celecoxib and valdecoxib binding to cyclooxygenase. Molecular Pharmacology, 63, 870–877.10.1124/mol.63.4.870
   PubMed Web of Science ®Google Scholar
• Hou, T., Li, N., Li, Y., & Wang, W. (2012). Characterization of domain–peptide interaction interface: Prediction of SH3 domain-mediated protein–protein interaction network in yeast by generic structure-based models. Journal of Proteome Research, 11, 2982–2995.10.1021/pr3000688
   PubMed Web of Science ®Google Scholar
• Hou, T., Wang, J., Li, Y., & Wang, W. (2011a). Assessing the performance of the MM/PBSA and MM/GBSA methods: I. The accuracy of binding free energy calculations based on molecular dynamics simulations. Journal of Chemical Information and Modeling, 51, 69–82.10.1021/ci100275a
   PubMed Web of Science ®Google Scholar
• Hou, T., Wang, J., Li, Y., & Wang, W. (2011b). Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking. Journal of Computational Chemistry, 32, 866–877.10.1002/jcc.v32.5
   PubMed Web of Science ®Google Scholar
• Hünenberger, P. (2005). Thermostat algorithms for molecular dynamics simulations. In C. Holm & K. Kremer (Eds.), Advanced computer simulation (Vol. 173, pp. 105–149). Berlin: Springer.10.1007/b98052
   Google Scholar
• Inc., A. S. (2013). Discovery studio modeling environment, release 4.0. San Diego, CA: Accelrys Software Inc.
   Google Scholar
• Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics, 79, 926–935.10.1063/1.445869
   Web of Science ®Google Scholar
• Kargman, S., Charleson, S., Cartwright, M., Frank, J., Riendeau, D., Mancini, J., … O’Neill, G. (1996). Characterization of prostaglandin G/H synthase 1 and 2 in rat, dog, monkey, and human gastrointestinal tracts. Gastroenterology, 111, 445–454.10.1053/gast.1996.v111.pm8690211
   PubMed Web of Science ®Google Scholar
• Konecny, R., Baker, N. A., & McCammon, J. A. (2012). iAPBS: a programming interface to Adaptive Poisson–Boltzmann Solver (APBS). Computational Science & Discovery, 5, 015005.
   Google Scholar
• Kothekar, V., Sahi, S., & Mishra, J. (2001). Molecular dynamics simulation of the interaction of 5-keto substituted 7-tert-butyl-2, 3-dihydro-3, 3-dimethylbenzofuran derivatives with cyclooxygenase-2. Current Science-Bangalore, 80, 764–769.
   Web of Science ®Google Scholar
• Kujubu, D. A., & Herschman, H. R. (1992). Dexamethasone inhibits mitogen induction of the TIS10 prostaglandin synthase/cyclooxygenase gene. The Journal of Biological Chemistry, 267, 7991–7994.
   PubMed Web of Science ®Google Scholar
• Kumari, R., Kumar, R., & Lynn, A. (2014). g_mmpbsa – A GROMACS tool for high-throughput MM-PBSA calculations. Journal of Chemical Information and Modeling, 54, 1951–1962.10.1021/ci500020m
   PubMed Web of Science ®Google Scholar
• Kurumbail, R. G., Stevens, A. M., Gierse, J. K., McDonald, J. J., Stegeman, R. A., Pak, J. Y., … Stallings, W. C. (1996). Structural basis for selective inhibition of cyclooxygenase-2 by anti-inflammatory agents. Nature, 384, 644–648.10.1038/384644a0
   PubMed Web of Science ®Google Scholar
• Lee, M. S., & Olson, M. A. (2013). Comparison of volume and surface area nonpolar solvation free energy terms for implicit solvent simulations. The Journal of Chemical Physics, 139, 044119.10.1063/1.4816641
   Web of Science ®Google Scholar
• Lemkul, J. A. (2008/2015). GROMACS tutorials. Baltimore, MD: Department of Pharmaceutical Sciences, University of Maryland.
   Google Scholar
• Limongelli, V., Bonomi, M., Marinelli, L., Gervasio, F. L., Cavalli, A., Novellino, E., & Parrinello, M. (2010). Molecular basis of cyclooxygenase enzymes (COXs) selective inhibition. Proceedings of the National Academy of Sciences of the United States of America, 107, 5411–5416.10.1073/pnas.0913377107
   PubMed Web of Science ®Google Scholar
• Lindahl, E., Hess, B., & van der Spoel, D. (2001). GROMACS 3.0: A package for molecular simulation and trajectory analysis. Molecular Modeling Annual, 7, 306–317.
   Web of Science ®Google Scholar
• Luong, C., Miller, A., Barnett, J., Chow, J., Ramesha, C., & Browner, M. F. (1996). Flexibility of the NSAID binding site in the structure of human cyclooxygenase-2. Nature Structural Biology, 3, 927–933.10.1038/nsb1196-927
   PubMedGoogle Scholar
• Mancini, J. A., Vickers, P. J., O’Neill, G. P., Boily, C., Falgueyret, J. P., & Riendeau, D. (1997). Altered sensitivity of aspirin-acetylated prostaglandin G/H synthase-2 to inhibition by nonsteroidal anti-inflammatory drugs. Molecular Pharmacology, 51, 52–60.
   PubMed Web of Science ®Google Scholar
• Masferrer, J. L., Zweifel, B. S., Seibert, K., & Needleman, P. (1990). Selective regulation of cellular cyclooxygenase by dexamethasone and endotoxin in mice. Journal of Clinical Investigation, 86, 1375–1379.10.1172/JCI114850
   PubMed Web of Science ®Google Scholar
• Melnikova, I. (2005). Future of COX2 inhibitors. Nature Reviews Drug Discovery, 4, 453–454.10.1038/nrd1755
   PubMed Web of Science ®Google Scholar
• 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, 2785–2791.10.1002/jcc.v30:16
   PubMed Web of Science ®Google Scholar
• Neeraja, S., Sreenath, A. S., Reddy, P. R., & Reddanna, P. (2003). Expression of cyclooxygenase-2 in rat testis. Reproductive BioMedicine Online, 6, 302–309.10.1016/S1472-6483(10)61849-4
   PubMedGoogle Scholar
• Neophytou, N., Leonis, G., Stavrinoudakis, N., Simcic, M., Golic Grdadolnik, S., Papavassilopoulou, E., … Mavromoustakos, T. (2011). Docking and molecular dynamics calculations of pyrrolidinone analog MMK16 bound to COX and LOX enzymes. EuroQSAR 2010, 30, 473–486.
   Google Scholar
• Ong, C. K., Lirk, P., Tan, C. H., & Seymour, R. A. (2007). An evidence-based update on nonsteroidal anti-inflammatory drugs. Clinical Medicine & Research, 5, 19–34.10.3121/cmr.2007.698
   PubMedGoogle Scholar
• Oostenbrink, C., Villa, A., Mark, A. E., & Van Gunsteren, W. F. (2004). A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6. Journal of Computational Chemistry, 25, 1656–1676.10.1002/(ISSN)1096-987X
   PubMed Web of Science ®Google Scholar
• Otto, J. C., & Smith, W. L. (1995). Prostaglandin endoperoxide synthases-1 and -2. Journal of Lipid Mediators and Cell Signalling, 12, 139–156.10.1016/0929-7855(95)00015-I
   PubMedGoogle Scholar
• Penning, T. D., Talley, J. J., Bertenshaw, S. R., Carter, J. S., Collins, P. W., Docter, S., … Isakson, P. C. (1997). Synthesis and biological evaluation of the 1,5-diarylpyrazole class of cyclooxygenase-2 inhibitors: identification of 4-[5-(4-methylphenyl)-3-(trifluoromethyl)-1H-pyrazol-1-yl] benze nesulfonamide (SC-58635, celecoxib). Journal of Medicinal Chemistry, 40, 1347–1365.10.1021/jm960803q
   PubMed Web of Science ®Google Scholar
• Picot, D., Loll, P. J., & Garavito, R. M. (1994). The X-ray crystal structure of the membrane protein prostaglandin H2 synthase-1. Nature, 367, 243–249.10.1038/367243a0
   PubMed Web of Science ®Google Scholar
• Plount Price, M. L., & Jorgensen, W. L. (2000). Analysis of binding affinities for celecoxib analogues with COX-1 and COX-2 from combined docking and monte carlo simulations and insight into the COX-2/COX-1 selectivity. Journal of the American Chemical Society, 122, 9455–9466.10.1021/ja001018c
   Web of Science ®Google Scholar
• Prasit, P., Wang, Z., Brideau, C., Chan, C. C., Charleson, S., Cromlish, W., & Zamboni, R. (1999). The discovery of rofecoxib, [MK 966, Vioxx, 4-(4’-methylsulfonylphenyl)-3-phenyl-2(5H)-furanone], an orally active cyclooxygenase-2-inhibitor. Bioorganic & Medicinal Chemistry Letters, 9, 1773–1778.10.1016/S0960-894X(99)00288-7
   PubMed Web of Science ®Google Scholar
• Rao, P., & Knaus, E. E. (2008). Evolution of nonsteroidal anti-inflammatory drugs (NSAIDs): cyclooxygenase (COX) inhibition and beyond. Journal of Pharmacy & Pharmaceutical Sciences, 11, 81s–110s.
   PubMed Web of Science ®Google Scholar
• Reddy, R. N., Mutyala, R., Aparoy, P., Reddanna, P., & Reddy, M. R. (2007). Computer aided drug design approaches to develop cyclooxygenase based novel anti-inflammatory and anti-cancer drugs. Current Pharmaceutical Design, 13, 3505–3517.10.2174/138161207782794275
   PubMed Web of Science ®Google Scholar
• Reddy, M. R., Reddy, C. R., Rathore, R. S., Erion, M. D., Aparoy, P., Reddy, R. N., & Reddanna, P. (2014). Free energy calculations to estimate ligand-binding affinities in structure-based drug design. Current Pharmaceutical Design, 20, 3323–3337.10.2174/13816128113199990604
   PubMed Web of Science ®Google Scholar
• Rowlinson, S. W., Kiefer, J. R., Prusakiewicz, J. J., Pawlitz, J. L., Kozak, K. R., Kalgutkar, A. S., … Marnett, L. J. (2003). A novel mechanism of cyclooxygenase-2 inhibition involving interactions with Ser-530 and Tyr-385. Journal of Biological Chemistry, 278, 45763–45769.10.1074/jbc.M305481200
   PubMed Web of Science ®Google Scholar
• Sai Ram, K. V., Rambabu, G., Sarma, J. A., & Desiraju, G. R. (2006). Ligand coordinate analysis of SC-558 from the active site to the surface of COX-2: A molecular dynamics study. Journal of Chemical Information and Modeling, 46, 1784–1794.10.1021/ci050142i
   PubMed Web of Science ®Google Scholar
• Schnitzer, T. J., Burmester, G. R., Mysler, E., Hochberg, M. C., Doherty, M., Ehrsam, E., … Hawkey, C. J. (2004). Comparison of lumiracoxib with naproxen and ibuprofen in the Therapeutic Arthritis Research and Gastrointestinal Event Trial (TARGET), reduction in ulcer complications: randomised controlled trial. The Lancet, 364, 665–674.10.1016/S0140-6736(04)16893-1
   PubMed Web of Science ®Google Scholar
• Silverstein, F. E., Faich, G., Goldstein, J. L., Simon, L. S., Pincus, T., Whelton, A., … Geis, G. S. (2000). Gastrointestinal toxicity with celecoxib vs nonsteroidal anti-inflammatory drugs for osteoarthritis and rheumatoid arthritis: The CLASS study: A randomized controlled trial. Celecoxib Long-term Arthritis Safety Study. JAMA, 284, 1247–1255.
   PubMed Web of Science ®Google Scholar
• Singh, O., Kakularam, K. R., Reddanna, P., & Aparoy, P. (2015). Understanding the dual inhibition of COX-2 and carbonic anhydrase-II by celecoxib and CG100649 using density functional theory calculations and other molecular Modelling approaches. Protein & Peptide Letters, 22, 903–912.
   PubMed Web of Science ®Google Scholar
• Solomon, S. D., McMurray, J. J., Pfeffer, M. A., Wittes, J., Fowler, R., Finn, P., … Bertagnolli, M. (2005). Cardiovascular risk associated with celecoxib in a clinical trial for colorectal adenoma prevention. New England Journal of Medicine, 352, 1071–1080.10.1056/NEJMoa050405
   PubMed Web of Science ®Google Scholar
• Solomon, D. H., Schneeweiss, S., Glynn, R. J., Kiyota, Y., Levin, R., Mogun, H., & Avorn, J. (2004). Relationship between selective cyclooxygenase-2 inhibitors and acute myocardial infarction in older adults. Circulation, 109, 2068–2073.10.1161/01.CIR.0000127578.21885.3E
   PubMed Web of Science ®Google Scholar
• Srinivasan, J., Cheatham, T. E., Cieplak, P., Kollman, P. A., & Case, D. A. (1998). Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate−DNA Helices. Journal of the American Chemical Society, 120, 9401–9409.10.1021/ja981844+
   Web of Science ®Google Scholar
• Sun, H., Li, Y., Shen, M., Tian, S., Xu, L., Pan, P., Guan, Y., & Hou, T. (2014). Assessing the performance of MM/PBSA and MM/GBSA methods. 5. Improved docking performance using high solute dielectric constant MM/GBSA and MM/PBSA rescoring. Phys Chem Chem Phys, 16, 22035–22045.10.1039/C4CP03179B
   PubMed Web of Science ®Google Scholar
• Sun, H., Li, Y., Tian, S., Xu, L., & Hou, T. (2014). Assessing the performance of MM/PBSA and MM/GBSA methods. 4. Accuracies of MM/PBSA and MM/GBSA methodologies evaluated by various simulation protocols using PDBbind data set. Physical Chemistry Chemical Physics, 16, 16719–16729.10.1039/C4CP01388C
   PubMed Web of Science ®Google Scholar
• Vane, J. R., Bakhle, Y. S., & Botting, R. M. (1998). Cyclooxygenases 1 and 2. Annual Review of Pharmacology and Toxicology, 38, 97–120.10.1146/annurev.pharmtox.38.1.97
   PubMed Web of Science ®Google Scholar
• Vanquelef, E., Simon, S., Marquant, G., Garcia, E., Klimerak, G., Delepine, J. C., … Dupradeau, F. Y. (2011). R.E.D. Server: A web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments. Nucleic Acids Research, 39, W511–W517.10.1093/nar/gkr288
   PubMed Web of Science ®Google Scholar
• Weber, A., Casini, A., Heine, A., Kuhn, D., Supuran, C. T., Scozzafava, A., & Klebe, G. (2004). Unexpected nanomolar inhibition of carbonic anhydrase by COX-2-selective celecoxib: New pharmacological opportunities due to related binding site recognition. Journal of Medicinal Chemistry, 47, 550–557.10.1021/jm030912m
   PubMed Web of Science ®Google Scholar
• Weis, A., Katebzadeh, K., Söderhjelm, P., Nilsson, I., & Ryde, U. (2006). Ligand affinities predicted with the MM/PBSA method: Dependence on the simulation method and the force field. Journal of Medicinal Chemistry, 49, 6596–6606.10.1021/jm0608210
   PubMed Web of Science ®Google Scholar
• Xie, W. L., Chipman, J. G., Robertson, D. L., Erikson, R. L., & Simmons, D. L. (1991). Expression of a mitogen-responsive gene encoding prostaglandin synthase is regulated by mRNA splicing. Proceedings of the National Academy of Sciences, 88, 2692–2696.10.1073/pnas.88.7.2692
   PubMed Web of Science ®Google Scholar
• Xu, L., Sun, H., Li, Y., Wang, J., & Hou, T. (2013). Assessing the performance of MM/PBSA and MM/GBSA methods. 3. The impact of force fields and ligand charge models. The Journal of Physical Chemistry B, 117, 8408–8421.10.1021/jp404160y
   PubMed Web of Science ®Google Scholar
• Zoete, V., Cuendet, M. A., Grosdidier, A., & Michielin, O. (2011). SwissParam: A fast force field generation tool for small organic molecules. Journal of Computational Chemistry, 32, 2359–2368.10.1002/jcc.v32.11
   PubMed Web of Science ®Google Scholar