References
- D.M. Ecker, S.D. Jones and H.L. Levine, mAbs 7 (1), 9–14 (2015), PMID: 25529996. doi:10.4161/19420862.2015.989042
- A.S. Rosenberg, AAPS. J. 8 (3), E501–E507 (2006). doi:10.1208/aapsj080359
- M. Holstein, J. Hung, H. Feroz, S. Ranjan, C. Du, S. Ghose and Z.J. Li, Biotechnol. Bioeng. 117 (11), 3591–3606 (2020). doi:10.1002/bit.v117.11
- R. Lumry and H. Eyring, J. Phys. Chem. 58 (2), 110–120 (1954). doi:10.1021/j150512a005
- J. Sanchez-Ruiz, Biophys J. 61 (4), 921–935 (1992). doi:10.1016/S0006-3495(92)81899-4
- S. Zale and A. Klibanov, Biotechnol. Bioeng. 25, 2221–2230 (1983). doi:10.1002/(ISSN)1097-0290
- C. Kalonia, V. Toprani, R. Toth, N. Wahome, I. Gabel, C. Russell Middaugh and D. Volkin, J. Phys. Chem. B 120 (29), 7062–7075 (2016). doi:10.1021/acs.jpcb.6b03878
- A. Lervik, F. Bresme, S. Kjelstrup, D. Bedeaux and J. Miguel Rubi, Phys. Chem. Chem. Phys. 12, 1610–1617 (2010). doi:10.1039/b918607g
- J. Jung, W. Nishima, M. Daniels, G. Bascom, C. Kobayashi, A. Adedoyin, M. Wall, A. Lappala, D. Phillips, W. Fischer, C.S. Tung, T. Schlick, Y. Sugita and K.Y. Sanbonmatsu, J. Comput. Chem. 40 (21), 1919–1930 (2019). doi:10.1002/jcc.v40.21
- K.Y. Sanbonmatsu, Curr. Opin. Struct. Biol. 55, 104–113 (2019). doi:10.1016/j.sbi.2019.03.004
- Y. Shan, E.T. Kim, M.P. Eastwood, R.O. Dror, M.A. Seeliger and D.E. Shaw, J. Am. Chem. Soc. 133 (24), 9181–9183 (2011). doi:10.1021/ja202726y
- V. Summa, A. Petrocchi, F. Bonelli, B. Crescenzi, M. Donghi, M. Ferrara, F. Fiore, C. Gardelli, O. Gonzalez Paz, D.J. Hazuda, P. Jones, O. Kinzel, R. Laufer, E. Monteagudo, E. Muraglia, E. Nizi, F. Orvieto, P. Pace, G. Pescatore, R. Scarpelli, K. Stillmock, M.V. Witmer and M. Rowley, J. Med. Chem. 51 (18), 5843–5855 (2008). doi:10.1021/jm800245z
- B. Nandy, S. Saurabh, A.K. Sahoo, N.M. Dixit and P.K. Maiti, Nanoscale 7 (44), 18628–18641 (2015). doi:10.1039/C5NR04632G
- Q. Chen, Q. Wang, Y.C. Liu, T. Wu, Y. Kang, J.D. Moore and K.E. Gubbins, J. Chem. Phys. 131 (1), 015101 (2009). doi:10.1063/1.3148025
- M. Pickholz and G. Giupponi, J. Phys. Chem. B 114 (20), 7009–7015 (2010). doi:10.1021/jp909148n
- J.P. Jambeck, E.S. Eriksson, A. Laaksonen, A.P. Lyubartsev and L.A. Eriksson, J. Chem. Theory. Comput. 10 (1), 5–13 (2014). doi:10.1021/ct400466m
- P. Singh, A. Roche, C.F. van der Walle, S. Uddin, J. Du, J. Warwicker, A. Pluen and R. Curtis, Mol. Pharmaceutics 16, 4775–4786 (2019). doi:10.1021/acs.molpharmaceut.9b00430
- M. Olsson, C. Søndergaard, M. Rostkowski and J.H. Jensen, J. Chem. Theory Comput. 7, 525–537 (2011). doi:10.1021/ct100578z
- T.J. Dolinsky, P. Czodrowski, H. Li, J.E. Nielsen, J. Jensen, G. Klebe and N.A. Baker, Nucleic. Acids. Res. 35, W522–W525 (2007). doi:10.1093/nar/gkm276
- D.E. Smith and L.X. Dang, J. Chem. Phys. 100 (5), 3757–3766 (1994). doi:10.1063/1.466363
- J. Aqvist, J. Phys. Chem. 94 (21), 8021–8024 (1990). doi:10.1021/j100384a009
- M.M. Reif and P.H. Hünenberger, J. Chem. Phys. 134 (14), 144104 (2011). doi:10.1063/1.3567022
- K. Lindorff-Larsen, S. Piana, K. Palmo, P. Maragakis, J.L. Klepeis, R.O. Dror and D.E. Shaw, Proteins: Structure, Function, and Bioinformatics 78 (8), 1950–1958 (2010). doi:10.1002/prot.22711
- N. Schmid, A. Eichenberger, A. Choutko, S. Riniker, M. Winger, A. Mark and W. Van Gunsteren, Eur. Biophys. J. 40 (7), 843–856 (2011). doi:10.1007/s00249-011-0700-9
- W. Huang, Z. Lin and W.F. van Gunsteren, J. Chem. Theory. Comput. 7 (5), 1237–1243 (2011). doi:10.1021/ct100747y
- P. Mark and L. Nilsson, J. Phys. Chem. A 105 (43), 9954–9960 (2001). doi:10.1021/jp003020w
- W.L. Jorgensen, J. Chandrasekhar, J.D. Madura, R.W. Impey and M.L. Klein, J. Chem. Phys. 79 (2), 926–935 (1983). doi:10.1063/1.445869
- R.B. Best, J. Mittal, M. Feig and A.D. MacKerell Jr, Biophys. J. 103 (5), 1045–1051 (2012). doi:10.1016/j.bpj.2012.07.042
- S.P. Kadaoluwa Pathirannahalage, N. Meftahi, A. Elbourne, A.C.G. Weiss, C.F. McConville, A. Padua, D.A. Winkler, M. Costa Gomes, T.L. Greaves, T.C. Le, Q.A. Besford and A.J. Christofferson, J. Chem. Inf. Model. 61 (9), 4521–4536 (2021). doi:10.1021/acs.jcim.1c00794
- G.A. Kaminski, R.A. Friesner, J. Tirado-Rives and W.L. Jorgensen, J. Phys. Chem. B 105 (28), 6474–6487 (2001). doi:10.1021/jp003919d
- D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A.E. Mark and H.J.C. Berendsen, J. Comput. Chem. 26, 1701–1718 (2005). doi:10.1002/(ISSN)1096-987X
- M.J. Abraham, T. Murtola, R. Schulz, S. Páll, J.C. Smith, B. Hess and E. Lindahl, SoftwareX1-2, 19–25 (2015). doi:10.1016/j.softx.2015.06.001
- G. Bussi, D. Donadio and M. Parrinello, J. Chem. Phys. 126 (1), 014101 (2007). doi:10.1063/1.2408420
- H.J.C. Berendsen, J.P.M. Postma, W.F. van Gunsteren, A. Di Nola and J.R. Haak, Science 81 (8), 3684–3690 (1984). doi:10.1063/1.448118
- M. Parrinello and A. Rahman, J. Appl. Phys. 52 (12), 7182–7190 (2007). doi:10.1063/1.328693
- T. Darden, D. York and L. Pedersen, J. Chem. Phys. 98 (12), 10089–10092 (1993). doi:10.1063/1.464397
- B. Hess, H. Bekker, H. Berendsen and J. Fraaije, J. Comput. Chem. 18 (12), 10089–10092 (1997). doi:10.1002/(ISSN)1096-987X
- J. Kästner, WIREs Comput. Molecular Sci. 1 (6), 932–942 (2011). doi:10.1002/wcms.66
- S. Kumar, J.M. Rosenberg, D. Bouzida, R.H. Swendsen and P.A. Kollman, J. Comput. Chem. 13 (8), 1011–1021 (1992). doi:10.1002/(ISSN)1096-987X
- A. Guinier, G. Fournet and K.L. Yudowitch, Small-Angle Scattering of X-rays (Wiley, New York, 1955).
- S. Yadav, T.M. Scherer, S.J. Shire and D.S. Kalonia, Anal. Biochem. 411 (2), 292–296 (2011). doi:10.1016/j.ab.2010.12.014
- S. Alamdari, S.J. Roeters, T.W. Golbek, L. Schmuser, T. Weidner and J. Pfaendtner, Langmuir 36 (40), 11855–11865 (2020). doi:10.1021/acs.langmuir.0c01881
- C. Vega and J.L.F. Abascal, Phys. Chem. Chem. Phys. 13, 19663–19688 (2011). doi:10.1039/c1cp22168j
- B. Hess and N.F. van der Vegt, J. Phys. Chem. B 110 (35), 17616–17626 (2006). doi:10.1021/jp0641029
- L.A. Abriata and M. Dal Peraro, Sci. Rep. 5 (1), 1–12 (2015). doi:10.1038/srep10549
- M. Carballo-Pacheco, A.E. Ismail and B. Strodel, J. Chem. Theory. Comput. 14 (11), 6063–6075 (2018). doi:10.1021/acs.jctc.8b00579
- S. Samantray, F. Yin, B. Kav and B. Strodel, J. Chem. Inf. Model. 60 (12), 6462–6475 (2020). doi:10.1021/acs.jcim.0c01063
- S. Piana, A.G. Donchev, P. Robustelli and D.E. Shaw, J. Phys. Chem. B 119 (16), 5113–5123 (2015). doi:10.1021/jp508971m
- P. Robustelli, S. Piana and D.E. Shaw, Proc. Natl. Acad. Sci. 115 (21), E4758–E4766 (2018). doi:10.1073/pnas.1800690115
- M. Frank, R.C. Walker, W.N. Lanzilotta, J.H. Prestegard and A.W. Barb, J. Mol. Biol. 426 (8), 1799–1811 (2014). doi:10.1016/j.jmb.2014.01.011
- S.G. Remesh, A.A. Armstrong, A.D. Mahan, J. Luo and M. Hammel, Struc. 26 (7), 1007–1014 (2018). doi:10.1016/j.str.2018.03.017
- Z. Li, R. Li, C. Smith, F. Pan, M. Campana, J.R. Webster, C.F. Van Der Walle, S. Uddin, S.M. Bishop, R. Narwal, J. Warwicker and J.R. Lu, ACS. Appl. Mater. Interfaces. 9 (27), 23202–23211 (2017). doi:10.1021/acsami.7b06131
- S. Ruane, Z. Li, M. Campana, X. Hu, H. Gong, J.R. Webster, F. Uddin, C. Kalonia, S.M. Bishop, C.F. van Der Walle and J.R. Lu, Langmuir 35 (42), 13543–13552 (2019). doi:10.1021/acs.langmuir.9b02317
- H. Martínez, E. Chacón, P. Tarazona and F. Bresme, Proc. R. Soc. A: Mathematical, Physical and Engineering Sciences 467 (2131), 1939–1958 (2011). doi:10.1098/rspa.2010.0516
- F. Bresme, E. Chacón, P. Tarazona and K. Tay, Phys. Rev. Lett. 101, 056102 (2008). doi:10.1103/PhysRevLett.101.056102
- P. Bjelkmar, P. Larsson, M.A. Cuendet, B. Hess and E. Lindahl, J. Chem. Theory. Comput. 6 (2), 459–466 (2010). doi:10.1021/ct900549r
- D. Petrov and B. Zagrovic, PLoS. Comput. Biol. 10 (5), e1003638 (2014). doi:10.1371/journal.pcbi.1003638
- O. Velev, E. Kaler and A. Lenhoff, Biophys. J. 75 (6), 2682–2697 (1998). doi:10.1016/S0006-3495(98)77713-6
- B.H. Zimm, J. Chem. Phys. 16 (12), 1093–1099 (1948). doi:10.1063/1.1746738
- A.C. Stark, C.T. Andrews and A.H. Elcock, J. Chem. Theory. Comput. 9 (9), 4176–4185 (2013). doi:10.1021/ct400008p