protein allostery: CAP as a model system.
Biophys Rev 7:175–182
- Dinner AR, Sˇali A, Smith LJ et al (2000)
Understanding protein folding via free-
energy surfaces from theory and experiment.
Trends Biochem Sci 25:331–339
- Kohlhoff KJ, Shukla D, Lawrenz M et al
(2014) Cloud-based simulations on Google
Exacycle reveal ligand modulation of GPCR
activation pathways. Nat Chem 6:15–21
- Sweet CR, Hampton SS, Skeel RD et al
(2009) A separable shadow Hamiltonian
hybrid Monte Carlo method. J Chem Phys
131:174106
- Levitt M (2001) The birth of computational
structural biology. Nat Struct Biol 8:392–393
- Pasi M, Lavery R, Ceres N (2013) PaLaCe: a
coarse-grain protein model for studying
mechanical properties. J Chem Theory Com-
put 9:785–793
- Kar P, Gopal SM, Cheng Y-M et al (2013)
PRIMO: a transferable coarse-grained force
field for proteins. J Chem Theory Comput
9:3769–3788
- Frembgen-Kesner T, Andrews CT, Li S et al
(2015) Parametrization of backbone flexibil-
ity in a coarse-grained force field for proteins
(COFFDROP) derived from all-atom
explicit-solvent molecular dynamics simula-
tions of all possible two-residue peptides. J
Chem Theory Comput 11:2341–2354
- Tirion M (1996) Large amplitude elastic
motions in proteins from a single-parameter,
atomic analysis. Phys Rev Lett 77:1905–1908
- Atilgan A, Durell S, Jernigan R et al (2001)
Anisotropy of fluctuation dynamics of pro-
teins with an elastic network model. Biophys
J 80:505–515
- Orellana L, Rueda M, Ferrer-Costa C et al
(2010) Approaching elastic network models
to molecular dynamics flexibility. J Chem
Theory Comput 6:2910–2923
- Leioatts N, Romo TD, Grossfield A (2012)
Elastic network models are robust to varia-
tions in formalism. J Chem Theory Comput
8:2424–2434
- Xia F, Tong D, Yang L et al (2014) Identify-
ing essential pairwise interactions in elastic
network model using the alpha shape theory.
J Comput Chem 35:1111–1121
- Borrelli K, Vitalis A, Alcantra R et al (2005)
PELE: protein energy landscape exploration.
a novel Monte Carlo based technique. J Chem
Theory Comput 1:1304–1311
- Cossins B, Hosseini A, Guallar V (2012)
Exploration of protein conformational change
with PELE and meta-dynamics. J Comp
Chem 8(3):959–965
- Edman K, Hosseini A, Bjursell MK et al
(2015) Ligand binding mechanism in steroid
receptors: from conserved plasticity to differ-
ential evolutionary constraints. Structure
23:2280–2290
- Grebner C, Lecina D, Gil V et al (2017)
Exploring binding mechanisms in nuclear
hormone receptors by Monte Carlo and X-
ray-derived motions. Biophys J
112:1147–1156
- Minary P, Levitt M (2010) Conformational
optimization with natural degrees of freedom:
a novel stochastic chain closure algorithm. J
Comput Biol 17:993–1010
- Sim AYL, Levitt M, Minary P (2012) Model-
ing and design by hierarchical natural moves.
Proc Natl Acad Sci 109(8):2890–2895
- Demharter S, Knapp B, Deane CM et al
(2016) Modeling functional motions of
biological systems by customized natural
moves. Biophys J 111:710–721
- Torrie G, Valleau J (1977) Nonphysical sam-
pling distributions in Monte Carlo free-
energy estimation: umbrella sampling. J Com-
put Phys 23(2):187–199
- Sugita Y, Okamoto Y (1999) Replica-
exchange molecular dynamics method for
protein folding. Chem Phys Lett
314:141–151
- Barducci A, Bonomi M, Parrinello M (2011)
Metadynamics. WIREs Comput Mol Sci 1
(3):826–843
- Elber R (2016) Perspective: computer simula-
tions of long time dynamics. J Chem Phys 144
(6):060901
- Kumar S, Bouzida D, Swendsen R et al
(1992) The weighted histogram analysis
method for free-energy calculations on bio-
molecules. I: the method. J Comput Chem
13:1011–1021
- Barducci A, Bussi G, Parrinello M (2008)
Well-tempered metadynamics: a smoothly
converging and tunable (free-energy)
method. Phys Rev Lett 100:020603
- Comer J, Gumbart JC, He ́nin J et al (2015)
The adaptive biasing force method: every-
thing you always wanted to know but were
afraid to ask. J Phys Chem B 119:1129–1151
- Brenner P, Sweet CR, VonHandorf D et al
(2007) Accelerating the replica exchange
method through an efficient all-pairs
exchange. J Chem Phys 126:074103
- Chodera J, Shirts M (2011) Replica exchange
and expanded ensemble simulations as Gibbs
Computational Study of Protein Conformational Transitions 359
