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additive CHARMM all-atom protein force field targeting improved sampling of the backbone
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Wang L, Abel R, Friesner RA, Harder ED (2019) OPLS3e: extending force field coverage for
drug-like small molecules. J Chem Theory Comput 15(3):1863–1874. https://doi.org/10.1021/
acs.jctc.8b01026
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39. Paul F, Meng Y, Roux B (2020) Identification of druggable kinase target conformations using
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for a kinase subfamily. Nat Chem 10:903–909. https://doi.org/10.1038/s41557-018-0077-9
41. Sultan MM, Denny RA, Unwalla R, Lovering F, Pande VS (2017) Millisecond dynamics of
BTK reveal kinome-wide conformational plasticity within the apo kinase domain. Sci Rep
7:15604. https://doi.org/10.1038/s41598-017-10697-0
42. Friesner RA, Murphy RB, Repasky MP, Frye LL, Greenwood JR, Halgren TA, Sanschagrin
PC, Mainz DT (2006) Extra precision glide: docking and scoring incorporating a model of
hydrophobic enclosure for protein-ligand complexes. J Med Chem 49:6177–6196. https://doi.
org/10.1021/jm051256o
43. Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, Mainz DT, Repasky MP, Knoll EH,
Shelley M, Perry JK, Shaw DE, Francis P, Shenkin PS (2004) Glide: a new approach for rapid,
accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem
47:1739–1749. https://doi.org/10.1021/jm0306430
Molecular Modeling of Protein Kinases: Current Status and Challenges
39
Science 254:1598–1603. https://doi.org/10.1126/science.1749933
29. Pisani P, Caporuscio F, Carlino L, Rastelli G (2016) Molecular dynamics simulations and
classical multidimensional scaling unveil new metastable states in the conformational landscape
of CDK2. PLoS One 11:e0154066. https://doi.org/10.1371/journal.pone.0154066
30. Pande VS, Beauchamp K, Bowman GR (2010) Everything you wanted to know about Markov
State Models but were afraid to ask. Methods 52:99–105. https://doi.org/10.1016/j.ymeth.2010.
06.002
31. Meng Y, Gao C, Clawson DK, Atwell S, Russell M, Vieth M, Roux B (2018) Predicting the
conformational variability of Abl tyrosine kinase using molecular dynamics simulations and
Markov state models. J Chem Theory Comput 14:2721–2732. https://doi.org/10.1021/acs.jctc.
7b01170
32. Maier JA, Martinez C, Kasavajhala K, Wickstrom L, Hauser KE, Simmerling C (2015) ff14SB:
improving the accuracy of protein side chain and backbone parameters from ff99SB. J Chem
Theory Comput 11:3696–3713. https://doi.org/10.1021/acs.jctc.5b00255
33. Best RB, Zhu X, Shim J, Lopes PE, Mittal J, Feig M, MacKerell AD (2012) Optimization of the
additive CHARMM all-atom protein force field targeting improved sampling of the backbone
ϕ, ψ and side-chain χ1 and χ2 dihedral angles. J Chem Theory Comput 8:3257–3273. https://
doi.org/10.1021/ct300400x
34. Vanommeslaeghe K, MacKerell AD (2014) CHARMM additive and polarizable force fields for
biophysics and computer-aided drug design. Biochim Biophys Acta 1850:861–871. https://doi.
org/10.1016/j.bbagen.2014.08.004
35. Harder E, Damm W, Maple J, Wu C, Reboul M, Xiang J, Wang L, Lupyan D, Dahlgren MK,
Knight JL, Kaus JW, Cerutti DS, Krilov G, Jorgensen WL, Abel R, Friesner RA (2016) OPLS3:
a force field providing broad coverage of drug-like small molecules and proteins. J Chem
Theory Comput 12:281–296. https://doi.org/10.1021/acs.jctc.5b00864
36. Roos K, Wu C, Damm W, Reboul M, Stevenson JM, Lu C, Dahlgren MK, Mondal S, Chen W,
Wang L, Abel R, Friesner RA, Harder ED (2019) OPLS3e: extending force field coverage for
drug-like small molecules. J Chem Theory Comput 15(3):1863–1874. https://doi.org/10.1021/
acs.jctc.8b01026
37. Asthana A, Wheeler DR (2013) A polarizable reactive force field for water to enable molecular
dynamics simulations of proton transport. J Chem Phys 138:174502. https://doi.org/10.1063/1.
4798457
38. Jing Z, Liu C, Cheng SY, Qi R, Walker BD, Piquemal J-P, Ren P (2019) Polarizable force fields
for biomolecular simulations: recent advances and applications. Annu Rev Biophys
48:371–394. https://doi.org/10.1146/annurev-biophys-070317-033349
39. Paul F, Meng Y, Roux B (2020) Identification of druggable kinase target conformations using
Markov model metastable states analysis of apo-Abl. J Chem Theory Comput 16:1896–1912.
https://doi.org/10.1021/acs.jctc.9b01158
40. Sultan MM, Kiss G, Pande VS (2018) Towards simple kinetic models of functional dynamics
for a kinase subfamily. Nat Chem 10:903–909. https://doi.org/10.1038/s41557-018-0077-9
41. Sultan MM, Denny RA, Unwalla R, Lovering F, Pande VS (2017) Millisecond dynamics of
BTK reveal kinome-wide conformational plasticity within the apo kinase domain. Sci Rep
7:15604. https://doi.org/10.1038/s41598-017-10697-0
42. Friesner RA, Murphy RB, Repasky MP, Frye LL, Greenwood JR, Halgren TA, Sanschagrin
PC, Mainz DT (2006) Extra precision glide: docking and scoring incorporating a model of
hydrophobic enclosure for protein-ligand complexes. J Med Chem 49:6177–6196. https://doi.
org/10.1021/jm051256o
43. Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, Mainz DT, Repasky MP, Knoll EH,
Shelley M, Perry JK, Shaw DE, Francis P, Shenkin PS (2004) Glide: a new approach for rapid,
accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem
47:1739–1749. https://doi.org/10.1021/jm0306430
Molecular Modeling of Protein Kinases: Current Status and Challenges
39