CHARMM36m: an improved force field for folded and intrinsically disordered proteins

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Huang, Jing, Rauscher, Sarah, Nawrocki, Grzegorz, Ran, Ting, Feig, Michael, de Groot, Bert L, Grubmüller, Helmut, MacKerell, Alexander D·2017·Nature Methods

DOI 10.1038/nmeth.4067

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Abstract

The all-atom additive CHARMM36 protein force field is widely used in molecular modeling and simulations. We present its refinement, CHARMM36m (http://mackerell.umaryland.edu/charmm_ff.shtml), with improved accuracy in generating polypeptide backbone conformational ensembles for intrinsically disordered peptides and proteins.

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Wright, P.E. & Dyson, H.J. Nat. Rev. Mol. Cell Biol. 16, 18–29 (2015). · DOI · Paper page
Brucale, M., Schuler, B. & Samorì, B. Chem. Rev. 114, 3281–3317 (2014). · DOI
Mackerell, A.D. Jr. J. Comput. Chem. 25, 1584–1604 (2004). · DOI · Paper page
Rauscher, S. et al. J. Chem. Theory Comput. 11, 5513–5524 (2015). · DOI · Paper page
Best, R.B., Zheng, W. & Mittal, J. J. Chem. Theory Comput. 10, 5113–5124 (2014). · DOI · Paper page
Piana, S., Donchev, A.G., Robustelli, P. & Shaw, D.E. J. Phys. Chem. B 119, 5113–5123 (2015). · DOI · Paper page
Best, R.B. et al. J. Chem. Theory Comput. 8, 3257–3273 (2012). · DOI · Paper page
MacKerell, A.D. Jr., Feig, M. & Brooks, C.L. III. J. Am. Chem. Soc. 126, 698–699 (2004). · DOI · Paper page
Fitzkee, N.C., Fleming, P.J. & Rose, G.D. Proteins 58, 852–854 (2005). · DOI
Fesinmeyer, R.M., Hudson, F.M. & Andersen, N.H. J. Am. Chem. Soc. 126, 7238–7243 (2004). · doi:10.1021/ja0379520
Fluitt, A.M. & de Pablo, J.J. Biophys. J. 109, 1009–1018 (2015). · DOI
Walters, R.H. & Murphy, R.M. J. Mol. Biol. 393, 978–992 (2009). · DOI
Lapidus, L.J., Eaton, W.A. & Hofrichter, J. Proc. Natl. Acad. Sci. USA 97, 7220–7225 (2000). · DOI · Paper page
Buscaglia, M., Lapidus, L.J., Eaton, W.A. & Hofrichter, J. Biophys. J. 91, 276–288 (2006). · DOI
Lovell, S.C. et al. Proteins 50, 437–450 (2003). · DOI · Paper page
Meng, W., Shan, B., Tang, Y. & Raleigh, D.P. Protein Sci. 18, 1692–1701 (2009). · DOI
Baltzis, A.S. & Glykos, N.M. Protein Sci. 25, 587–596 (2016). · doi:10.1002/pro.2850
Jensen, M.R. & Blackledge, M. Proc. Natl. Acad. Sci. USA 111, E1557–E1558 (2014). · doi:10.1073/pnas.1323876111
Müller-Späth, S. et al. Proc. Natl. Acad. Sci. USA 107, 14609–14614 (2010). · DOI · Paper page
Chen, P.C. & Hub, J.S. Biophys. J. 107, 435–447 (2014). · DOI · Paper page
Vorobyov, I.V., Anisimov, V.M. & MacKerell, A.D. Jr. J. Phys. Chem. B 109, 18988–18999 (2005). · DOI · Paper page
Mukrasch, M.D. et al. J. Am. Chem. Soc. 129, 5235–5243 (2007). · doi:10.1021/ja0690159
Mantsyzov, A.B. et al. Protein Sci. 23, 1275–1290 (2014). · DOI
Gibson, K.D. & Scheraga, H.A. Proc. Natl. Acad. Sci. USA 83, 5649–5653 (1986). · DOI
Brooks, B.R., Pastor, R.W. & Carson, F.W. Proc. Natl. Acad. Sci. USA 84, 4470–4474 (1987). · doi:10.1073/pnas.84.13.4470
Roterman, I.K., Gibson, K.D. & Scheraga, H.A. J. Biomol. Struct. Dyn. 7, 391–419 (1989). · DOI
Li, D.-W. & Brüschweiler, R. Angew. Chem. Int. Ed. Engl. 49, 6778–6780 (2010). · DOI · Paper page
Di Pierro, M. & Elber, R. J. Chem. Theory Comput. 9, 3311–3320 (2013). · DOI
Wang, L.-P. et al. J. Phys. Chem. B 117, 9956–9972 (2013). · DOI · Paper page
Piana, S., Lindorff-Larsen, K. & Shaw, D.E. Biophys. J. 100, L47–L49 (2011). · DOI · Paper page
Debiec, K.T., Gronenborn, A.M. & Chong, L.T. J. Phys. Chem. B 118, 6561–6569 (2014). · DOI
Jorgensen, W.L., Chandrasekhar, J., Madura, J.D., Impey, R.W. & Klein, M.L. J. Chem. Phys. 79, 926–926 (1983). · DOI · Paper page
Hess, B., Kutzner, C., van der Spoel, D. & Lindahl, E. J. Chem. Theory Comput. 4, 435–447 (2008). · DOI · Paper page
Brooks, B.R. et al. J. Comput. Chem. 30, 1545–1614 (2009). · DOI · Paper page
Eastman, P. et al. J. Chem. Theory Comput. 9, 461–469 (2013). · DOI · Paper page
Huang, J. & MacKerell, A.D. Jr. J. Comput. Chem. 34, 2135–2145 (2013). · DOI · Paper page
Boonstra, S., Onck, P.R. & van der Giessen, E. J. Phys. Chem. B 120, 3692–3698 (2016). · doi:10.1021/acs.jpcb.6b01316

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Guo, H.-B., Perminov, A., Bekele, S., Kedziora, G., Farajollahi, S., Varaljay, V., Hinkle, K., Molinero, V., Meister, K., Hung, C., et al. (2022) · Scientific Reports · doi:10.1038/s41598-022-14382-9 · Cited by 248
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Pandi, A., Adam, D., Zare, A., Trinh, V. T., Schaefer, S. L., Burt, M., Klabunde, B., Bobkova, E., Kushwaha, M., Foroughijabbari, Y., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-42434-9 · Cited by 173
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Lazar, T., Martínez-Pérez, E., Quaglia, F., Hatos, A., Chemes, L. B., Iserte, J. A., Méndez, N. A., Garrone, N. A., Saldaño, T. E., Marchetti, J., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa1021 · Cited by 142
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(2022) · doi:10.1126/sciadv.add1436 · Cited by 49
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Cook, A. S. I., Chen, M., Nguyen, T. N., Cabezudo, A. C., Khuu, G., Rao, S., Garcia, S. N., Yang, M., Iavarone, A. T., Ren, X., et al. (2025) · Science · doi:10.1126/science.adl3787 · Cited by 34
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Authors: Huang, J., Rauscher, S., Nawrocki, G., Ran, T., Feig, M., de Groot, B. L., Grubmüller, H., & MacKerell, A. D.
Venue: Nature Methods
Publisher: Springer Science and Business Media LLC
Published: 2016-11-07
Volume: 14
Issue: 1
Pages: 71-73
ISSN: 1548-7091 (ISSN-L)
1548-7105
DOI: 10.1038/nmeth.4067
OpenAlex: W2555870966
Cited by: 7,285
References: 0
FWCI: 78.25
Type: journal article
Language: en
Open access: bronze
Licence: www.springer.com/tdm (tdm)

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CHARMM36m: an improved force field for folded and intrinsically disordered proteins

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