of elastic networks. Curr Protein Pept Sci 10
(2):128–132
28. Erman B (2013) A fast approximate method of
identifying paths of allosteric communication
in proteins. Proteins 81(7):1097–1101
29. Su JG et al (2014) Prediction of allosteric sites
on protein surfaces with an elastic-networkmodel-based thermodynamic method. Phys
Rev E Stat Nonlinear Soft Matter Phys 90
(2):022719
30. Hu G et al (2017) Comparative study of elastic
network model and protein contact network
for protein complexes: the hemoglobin case.
Biomed Res Int 2017:2483264
31. Raimondi F et al (2013) A mixed protein structure network and elastic network model
approach to predict the structural communication in biomolecular systems: the PDZ2
domain from tyrosine phosphatase 1E as a
case study. J Chem Theory Comput 9
(5):2504–2518
32. Yao XQ, Skjaerven L, Grant BJ (2016) Rapid
characterization of allosteric networks with
ensemble normal mode analysis. J Phys Chem
B 120(33):8276–8288
33. Guzel P, Kurkcuoglu O (2017) Identification
of potential allosteric communication pathways
between functional sites of the bacterial ribosome by graph and elastic network models.
Biochim Biophys Acta 1861(12):3131–3141
34. Chennubhotla C, Bahar I (2006) Markov
propagation of allosteric effects in biomolecular systems: application to GroEL-GroES. Mol
Syst Biol 2:36
35. Chennubhotla C, Bahar I (2007) Signal propagation in proteins and relation to equilibrium
fluctuations.
PLoS
Comput
Biol
3
(9):1716–1726
36. Chennubhotla C, Yang Z, Bahar I (2008) Coupling between global dynamics and signal
transduction pathways: a mechanism of allostery for chaperonin GroEL. Mol BioSyst 4
(4):287–292
37. Dutta A, Bahar I (2010) Metal-binding sites
are designed to achieve optimal mechanical and
signaling
properties.
Structure
18
(9):1140–1148
38. Liang Z et al (2018) Deciphering the role of
dimer interface in intrinsic dynamics and allosteric pathways underlying the functional transformation of DNMT3A. Biochim Biophys Acta
1862(7):1667–1679
39. Park SY et al (2006) 1.25 A resolution crystal
structures of human haemoglobin in the oxy,
deoxy and carbonmonoxy forms. J Mol Biol
360(3):690–701
40. Bakan A, Meireles LM, Bahar I (2011) ProDy:
protein dynamics inferred from theory and
experiments.
Bioinformatics
27
(11):1575–1577
41. Bahar I, Atilgan AR, Erman B (1997) Direct
evaluation of thermal fluctuations in proteins
using a single-parameter harmonic potential.
Fold Des 2(3):173–181
42. Sumbul F, Acuner-Ozbabacan SE, Haliloglu T
(2015) Allosteric dynamic control of binding.
Biophys J 109(6):1190–1201
43. Rodgers TL et al (2013) Modulation of global
low-frequency motions underlies allosteric regulation: demonstration in CRP/FNR family
transcription factors. PLoS Biol 11(9):
e1001651
44. Atilgan AR et al (2001) Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys J 80(1):505–515
45. Hub JS, Kubitzki MB, de Groot BL (2010)
Spontaneous quaternary and tertiary T-R transitions of human hemoglobin in molecular
dynamics simulation. PLoS Comput Biol 6
(5):e1000774
46. Panjkovich A, Daura X (2012) Exploiting protein flexibility to predict the location of allosteric sites. BMC Bioinformatics 13:273
47. Goncearenco A et al (2013) SPACER: Server
for predicting allosteric communication and
effects of regulation. Nucleic Acids Res 41
(Web Server issue):W266–W272
48. Greener JG, Sternberg MJ (2015) AlloPred:
prediction of allosteric pockets on proteins
using normal mode perturbation analysis.
BMC Bioinformatics 16:335
49. Li H et al (2017) DynOmics: dynamics of
structural proteome and beyond. Nucleic
Acids Res 45(W1):W374–W380
Identification of Allosteric Effects in Proteins by Elastic Network Models
35
(2):128–132
28. Erman B (2013) A fast approximate method of
identifying paths of allosteric communication
in proteins. Proteins 81(7):1097–1101
29. Su JG et al (2014) Prediction of allosteric sites
on protein surfaces with an elastic-networkmodel-based thermodynamic method. Phys
Rev E Stat Nonlinear Soft Matter Phys 90
(2):022719
30. Hu G et al (2017) Comparative study of elastic
network model and protein contact network
for protein complexes: the hemoglobin case.
Biomed Res Int 2017:2483264
31. Raimondi F et al (2013) A mixed protein structure network and elastic network model
approach to predict the structural communication in biomolecular systems: the PDZ2
domain from tyrosine phosphatase 1E as a
case study. J Chem Theory Comput 9
(5):2504–2518
32. Yao XQ, Skjaerven L, Grant BJ (2016) Rapid
characterization of allosteric networks with
ensemble normal mode analysis. J Phys Chem
B 120(33):8276–8288
33. Guzel P, Kurkcuoglu O (2017) Identification
of potential allosteric communication pathways
between functional sites of the bacterial ribosome by graph and elastic network models.
Biochim Biophys Acta 1861(12):3131–3141
34. Chennubhotla C, Bahar I (2006) Markov
propagation of allosteric effects in biomolecular systems: application to GroEL-GroES. Mol
Syst Biol 2:36
35. Chennubhotla C, Bahar I (2007) Signal propagation in proteins and relation to equilibrium
fluctuations.
PLoS
Comput
Biol
3
(9):1716–1726
36. Chennubhotla C, Yang Z, Bahar I (2008) Coupling between global dynamics and signal
transduction pathways: a mechanism of allostery for chaperonin GroEL. Mol BioSyst 4
(4):287–292
37. Dutta A, Bahar I (2010) Metal-binding sites
are designed to achieve optimal mechanical and
signaling
properties.
Structure
18
(9):1140–1148
38. Liang Z et al (2018) Deciphering the role of
dimer interface in intrinsic dynamics and allosteric pathways underlying the functional transformation of DNMT3A. Biochim Biophys Acta
1862(7):1667–1679
39. Park SY et al (2006) 1.25 A resolution crystal
structures of human haemoglobin in the oxy,
deoxy and carbonmonoxy forms. J Mol Biol
360(3):690–701
40. Bakan A, Meireles LM, Bahar I (2011) ProDy:
protein dynamics inferred from theory and
experiments.
Bioinformatics
27
(11):1575–1577
41. Bahar I, Atilgan AR, Erman B (1997) Direct
evaluation of thermal fluctuations in proteins
using a single-parameter harmonic potential.
Fold Des 2(3):173–181
42. Sumbul F, Acuner-Ozbabacan SE, Haliloglu T
(2015) Allosteric dynamic control of binding.
Biophys J 109(6):1190–1201
43. Rodgers TL et al (2013) Modulation of global
low-frequency motions underlies allosteric regulation: demonstration in CRP/FNR family
transcription factors. PLoS Biol 11(9):
e1001651
44. Atilgan AR et al (2001) Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys J 80(1):505–515
45. Hub JS, Kubitzki MB, de Groot BL (2010)
Spontaneous quaternary and tertiary T-R transitions of human hemoglobin in molecular
dynamics simulation. PLoS Comput Biol 6
(5):e1000774
46. Panjkovich A, Daura X (2012) Exploiting protein flexibility to predict the location of allosteric sites. BMC Bioinformatics 13:273
47. Goncearenco A et al (2013) SPACER: Server
for predicting allosteric communication and
effects of regulation. Nucleic Acids Res 41
(Web Server issue):W266–W272
48. Greener JG, Sternberg MJ (2015) AlloPred:
prediction of allosteric pockets on proteins
using normal mode perturbation analysis.
BMC Bioinformatics 16:335
49. Li H et al (2017) DynOmics: dynamics of
structural proteome and beyond. Nucleic
Acids Res 45(W1):W374–W380
Identification of Allosteric Effects in Proteins by Elastic Network Models
35