dynamics
simulations
and
analytical
approaches: application to alpha-amylase inhibitor. Proteins 40:512–524
18. Bernardi RC, Melo MCR, Schulten K (2015)
Enhanced sampling techniques in molecular
dynamics simulations of biological systems.
Biochim Biophys Acta 1850:872–877.
https://doi.org/10.1016/j.bbagen.2014.10.
019
19. Lu S, Ji M, Ni D, Zhang J (2018) Discovery of
hidden allosteric sites as novel targets for allosteric drug design. Drug Discov Today
23:359–365.
https://doi.org/10.1016/j.
drudis.2017.10.001
20. Dror RO, Pan AC, Arlow DH, Borhani DW,
Maragakis P, Shan Y, Xu H, Shaw DE (2011)
Pathway and mechanism of drug binding to Gprotein-coupled receptors. Proc Natl Acad Sci
U S A 108:13118–13123. https://doi.org/
10.1073/pnas.1104614108
21. Yang C-Y (2015) Identification of potential
small molecule allosteric modulator sites on
IL-1R1 ectodomain using accelerated conformational sampling method. PLoS One 10:
e0118671. https://doi.org/10.1371/journal.
pone.0118671
22. Wang J, Wang Y, Cui W-W, Huang Y, Yang Y,
Liu Y, Zhao W-S, Cheng X-Y, Sun W-S, Cao P,
Zhu MX, Wang R, Hattori M, Yu Y (2018)
Druggable negative allosteric site of P2X3
receptors. Proc Natl Acad Sci U S A
115:4939–4944. https://doi.org/10.1073/
pnas.1800907115
23. Das A, Gur M, Cheng MH, Jo S, Bahar I, Roux
B (2014) Exploring the conformational transitions of biomolecular systems using a simple
two-state anisotropic network model. PLoS
Comput Biol 10:e1003521. https://doi.org/
10.1371/journal.pcbi.1003521
24. Karasawa A, Kawate T (2016) Structural basis
for subtype-specific inhibition of the P2X7
receptor. elife 5:e22153. https://doi.org/10.
7554/eLife.22153
254
Chiara Bianca Maria Platania and Claudio Bucolo
simulations
and
analytical
approaches: application to alpha-amylase inhibitor. Proteins 40:512–524
18. Bernardi RC, Melo MCR, Schulten K (2015)
Enhanced sampling techniques in molecular
dynamics simulations of biological systems.
Biochim Biophys Acta 1850:872–877.
https://doi.org/10.1016/j.bbagen.2014.10.
019
19. Lu S, Ji M, Ni D, Zhang J (2018) Discovery of
hidden allosteric sites as novel targets for allosteric drug design. Drug Discov Today
23:359–365.
https://doi.org/10.1016/j.
drudis.2017.10.001
20. Dror RO, Pan AC, Arlow DH, Borhani DW,
Maragakis P, Shan Y, Xu H, Shaw DE (2011)
Pathway and mechanism of drug binding to Gprotein-coupled receptors. Proc Natl Acad Sci
U S A 108:13118–13123. https://doi.org/
10.1073/pnas.1104614108
21. Yang C-Y (2015) Identification of potential
small molecule allosteric modulator sites on
IL-1R1 ectodomain using accelerated conformational sampling method. PLoS One 10:
e0118671. https://doi.org/10.1371/journal.
pone.0118671
22. Wang J, Wang Y, Cui W-W, Huang Y, Yang Y,
Liu Y, Zhao W-S, Cheng X-Y, Sun W-S, Cao P,
Zhu MX, Wang R, Hattori M, Yu Y (2018)
Druggable negative allosteric site of P2X3
receptors. Proc Natl Acad Sci U S A
115:4939–4944. https://doi.org/10.1073/
pnas.1800907115
23. Das A, Gur M, Cheng MH, Jo S, Bahar I, Roux
B (2014) Exploring the conformational transitions of biomolecular systems using a simple
two-state anisotropic network model. PLoS
Comput Biol 10:e1003521. https://doi.org/
10.1371/journal.pcbi.1003521
24. Karasawa A, Kawate T (2016) Structural basis
for subtype-specific inhibition of the P2X7
receptor. elife 5:e22153. https://doi.org/10.
7554/eLife.22153
254
Chiara Bianca Maria Platania and Claudio Bucolo