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. Author manuscript; available in PMC: 2008 Dec 5.
Published in final edited form as: J Am Chem Soc. 2006 Mar 22;128(11):3728–3736. doi: 10.1021/ja057216r

Table 1.

Representative successful ab initio folding simulations using all-atom or united-atom (explicit polar hydrogens) physics-based models

Peptide PDB ID Structure Length Force Fields References
(AAQAA)3 N/A α (50%a) 15 CHARMM19/SAS
CHARMM22/SCP-ISM
Amber84/m-GBSAd 		56
70
71
GB1p 3gb1 (41-56) β (30-80%b) 16 OPLS/GBSA
OPLS-AA/SGB
OPLS-AA/AGBNP
CHARMM19/cGBSTILL
 72
73
57
74
GB1m1 N/A β (6%c) 16 Irbäck and Mohanty 60
HP5A N/A β (21%c) 16 N/A N/A
GB1m3 N/A β (86%c) 16 Irbäck and Mohanty 60
trpzip2 1le1 β (90%d) 12 Amber99-m1e/GBSA
OPLS-AA/GBSA
Amber96/GBSA		 49
58
75
Trp-cage 1l2y α/coil 20 Amber99-m2f/GBSA
Amber94/GBSA
Amber-m3g/GBSA
CHARMM19/(ACE,EEF1,SASA)
CHARMM22/ACE
CHARMM22/CMAP/ACE
PFF01
Irbäck and Mohanty		 76
77,78
79
80
80
80
81
60
a

helicity measured by NMR chemical shifts at 270K.82

b

population estimated from multiple NMR chemical shift probes (∼30% at 298 K69 or 42% at 278 K83) and from the tryptophan fluorescence experiment (∼80% at 273 K).84

c

folded population estimated by NMR chemical shifts at 298K;69

d

population estimated from thermal unfolding analysis.85

e

with modified backbone dihedral energetics.

f

with modified backbone dihedral energetics.

g

with a new but unreferenced Amber force field.