24. Ricci CG, Silveira RL, Rivalta I, Batista VS, Skaf
MS (2016) Allosteric pathways in the pparγ-rxrα nuclear receptor complex. Sci Rep
6:19940
25. Palermo G, Ricci CG, Fernando A, Basak R,
Jinek M, Rivalta I, Batista VS, McCammon JA
(2017) Protospacer adjacent motif-induced
allostery activates crispr-cas9. J Am Chem Soc
139(45):16028–16031
26. Negre CFA, Morzan UN, Hendrickson HP,
Pal R, Lisi GP, Loria JP, Rivalta I, Ho J, Batista
VS (2018) Eigenvector centrality for characterization of protein allosteric pathways. Proc Natl
Acad Sci U S A 115(52):E12201–E12208
27. Sethi A, Eargle J, Black AA, Luthey-Schulten Z
(2009) Dynamical networks in tRNA: protein
complexes. Proc Natl Acad Sci U S A 106
(16):6620–6625
28. Gasper PM, Fuglestad B, Komives EA, Markwick PR, McCammon JA (2012) Allosteric
networks
in
thrombin
distinguish
procoagulant vs. anticoagulant activities. Proc
Natl Acad Sci U S A 109(52):21216–21222
29. Blacklock K, Verkhivker GM (2014) Computational modeling of allosteric regulation in the
hsp90 chaperones: a statistical ensemble analysis of protein structure networks and allosteric
communications. PLoS Comput Biol 10(6):
e1003679
30. Stolzenberg S, Michino M, LeVine MV,
Weinstein H, Shi L (2016) Computational
approaches to detect allosteric pathways in
transmembrane molecular machines. Biochim
Biophys Acta 1858(7 Pt B):1652–1662
31. Wagner JR, Lee CT, Durrant JD, Malmstrom
RD, Feher VA, Amaro RE (2016) Emerging
computational methods for the rational discovery of allosteric drugs. Chem Rev 116
(11):6370–6390
32. Rivalta I, Lisi GP, Snoeberger NS, Manley G,
Loria JP, Batista VS (2016) Allosteric communication disrupted by a small molecule binding
to the imidazole glycerol phosphate synthase
protein-protein interface. Biochemistry 55
(47):6484–6494
33. Chaudhuri BN, Lange SC, Myers RS, Chittur
SV, Davisson VJ, Smith JL (2001) Crystal
structure of imidazole glycerol phosphate
synthase: a tunnel through a (beta/alpha)
(8) barrel joins two active sites. Structure 9
(10):987–997
34. Breitbach K, Ko ¨hler J, Steinmetz I (2008)
Induction of protective immunity against burkholderia pseudomallei using attenuated
mutants with defects in the intracellular life
cycle. Trans R Soc Trop Med Hyg 102:
S89–S94
35. Gomez MJ, Neyfakh AA (2006) Genes
involved in intrinsic antibiotic resistance of acinetobacter baylyi. Antimicrob Agents Chemother 50(11):3562–3567
36. Berman HM, Westbrook J, Feng Z,
Gilliland G, Bhat TN, Weissig H, Shindyalov
IN, Bourne PE (2000) The protein data bank.
Nucleic Acids Res 28(1):235–242. http://
www.rcsb.org/pdb/
37. Case DA, Cheatham TE, Darden T, Gohlke H,
Luo R, Merz KM, Onufriev A, Simmerling C,
Wang B, Woods RJ (2005) The amber biomolecular simulation programs. J Comput Chem
26(16):1668–1688
38. Hess B, Kutzner C, van der Spoel D, Lindahl E
(2008) Gromacs 4: algorithms for highly efficient, load-balanced, and scalable molecular
simulation. J Chem Theory Comput 4
(3):435–447
39. Phillips JC, Braun R, Wang W, Gumbart J,
Tajkhorshid E, Villa E, Chipot C, Skeel RD,
Kale L, Schulten K (2005) Scalable molecular
dynamics with namd. J Comput Chem 26
(16):1781–1802
40. See
webpage:
https://ambermd.org/
tutorials/
41. See webpage: http://www.Ks.Uiuc.Edu/train
ing/tutorials/namd-index.Html
42. See webpage: http://www.Gromacs.Org/doc
umentation/tutorials
43. Wang J, Wolf RM, Caldwell JW, Kollman PA,
Case DA (2004) Development and testing of a
general amber force field. J Comput Chem 25
(9):1157–1174
44. Lange OF, Grubmuller H (2006) Generalized
correlation for biomolecular dynamics. Proteins 62(4):1053–1061
45. Kraskov A, Stogbauer H, Grassberger P (2004)
Estimating mutual information. Phys Rev E
Stat Nonlinear Soft Matter Phys 69(6 Pt
2):066138
46. See webpage: https://parmed.github.io/
parmed/html/parmed.html
47. Floyd RW (1962) Algorithm-97—shortest
path. Commun ACM 5(6):345–345
48. Girvan M, Newman MEJ (2002) Community
structure in social and biological networks.
Proc Natl Acad Sci U S A 99(12):7821–7826
49. Newman MEJ, Girvan M (2004) Finding and
evaluating community structure in networks.
Phys Rev E 69(2):026113
50. Lipchock J, Loria JP (2009) Millisecond
dynamics in the allosteric enzyme imidazole
150
Ivan Rivalta and Victor S. Batista
MS (2016) Allosteric pathways in the pparγ-rxrα nuclear receptor complex. Sci Rep
6:19940
25. Palermo G, Ricci CG, Fernando A, Basak R,
Jinek M, Rivalta I, Batista VS, McCammon JA
(2017) Protospacer adjacent motif-induced
allostery activates crispr-cas9. J Am Chem Soc
139(45):16028–16031
26. Negre CFA, Morzan UN, Hendrickson HP,
Pal R, Lisi GP, Loria JP, Rivalta I, Ho J, Batista
VS (2018) Eigenvector centrality for characterization of protein allosteric pathways. Proc Natl
Acad Sci U S A 115(52):E12201–E12208
27. Sethi A, Eargle J, Black AA, Luthey-Schulten Z
(2009) Dynamical networks in tRNA: protein
complexes. Proc Natl Acad Sci U S A 106
(16):6620–6625
28. Gasper PM, Fuglestad B, Komives EA, Markwick PR, McCammon JA (2012) Allosteric
networks
in
thrombin
distinguish
procoagulant vs. anticoagulant activities. Proc
Natl Acad Sci U S A 109(52):21216–21222
29. Blacklock K, Verkhivker GM (2014) Computational modeling of allosteric regulation in the
hsp90 chaperones: a statistical ensemble analysis of protein structure networks and allosteric
communications. PLoS Comput Biol 10(6):
e1003679
30. Stolzenberg S, Michino M, LeVine MV,
Weinstein H, Shi L (2016) Computational
approaches to detect allosteric pathways in
transmembrane molecular machines. Biochim
Biophys Acta 1858(7 Pt B):1652–1662
31. Wagner JR, Lee CT, Durrant JD, Malmstrom
RD, Feher VA, Amaro RE (2016) Emerging
computational methods for the rational discovery of allosteric drugs. Chem Rev 116
(11):6370–6390
32. Rivalta I, Lisi GP, Snoeberger NS, Manley G,
Loria JP, Batista VS (2016) Allosteric communication disrupted by a small molecule binding
to the imidazole glycerol phosphate synthase
protein-protein interface. Biochemistry 55
(47):6484–6494
33. Chaudhuri BN, Lange SC, Myers RS, Chittur
SV, Davisson VJ, Smith JL (2001) Crystal
structure of imidazole glycerol phosphate
synthase: a tunnel through a (beta/alpha)
(8) barrel joins two active sites. Structure 9
(10):987–997
34. Breitbach K, Ko ¨hler J, Steinmetz I (2008)
Induction of protective immunity against burkholderia pseudomallei using attenuated
mutants with defects in the intracellular life
cycle. Trans R Soc Trop Med Hyg 102:
S89–S94
35. Gomez MJ, Neyfakh AA (2006) Genes
involved in intrinsic antibiotic resistance of acinetobacter baylyi. Antimicrob Agents Chemother 50(11):3562–3567
36. Berman HM, Westbrook J, Feng Z,
Gilliland G, Bhat TN, Weissig H, Shindyalov
IN, Bourne PE (2000) The protein data bank.
Nucleic Acids Res 28(1):235–242. http://
www.rcsb.org/pdb/
37. Case DA, Cheatham TE, Darden T, Gohlke H,
Luo R, Merz KM, Onufriev A, Simmerling C,
Wang B, Woods RJ (2005) The amber biomolecular simulation programs. J Comput Chem
26(16):1668–1688
38. Hess B, Kutzner C, van der Spoel D, Lindahl E
(2008) Gromacs 4: algorithms for highly efficient, load-balanced, and scalable molecular
simulation. J Chem Theory Comput 4
(3):435–447
39. Phillips JC, Braun R, Wang W, Gumbart J,
Tajkhorshid E, Villa E, Chipot C, Skeel RD,
Kale L, Schulten K (2005) Scalable molecular
dynamics with namd. J Comput Chem 26
(16):1781–1802
40. See
webpage:
https://ambermd.org/
tutorials/
41. See webpage: http://www.Ks.Uiuc.Edu/train
ing/tutorials/namd-index.Html
42. See webpage: http://www.Gromacs.Org/doc
umentation/tutorials
43. Wang J, Wolf RM, Caldwell JW, Kollman PA,
Case DA (2004) Development and testing of a
general amber force field. J Comput Chem 25
(9):1157–1174
44. Lange OF, Grubmuller H (2006) Generalized
correlation for biomolecular dynamics. Proteins 62(4):1053–1061
45. Kraskov A, Stogbauer H, Grassberger P (2004)
Estimating mutual information. Phys Rev E
Stat Nonlinear Soft Matter Phys 69(6 Pt
2):066138
46. See webpage: https://parmed.github.io/
parmed/html/parmed.html
47. Floyd RW (1962) Algorithm-97—shortest
path. Commun ACM 5(6):345–345
48. Girvan M, Newman MEJ (2002) Community
structure in social and biological networks.
Proc Natl Acad Sci U S A 99(12):7821–7826
49. Newman MEJ, Girvan M (2004) Finding and
evaluating community structure in networks.
Phys Rev E 69(2):026113
50. Lipchock J, Loria JP (2009) Millisecond
dynamics in the allosteric enzyme imidazole
150
Ivan Rivalta and Victor S. Batista