INDEX
A
Adjacent amino acid networks ............................ 113–135
Allosteric drugs .............................. 15, 62, 138, 245–253
Allosteric effects .....................21–32, 175–180, 198, 231
Allosteric sites ................................ 15, 18, 21, 22, 29, 30,
32, 62, 63, 71, 72, 137, 138, 142, 147, 249
Allostery................................... 3–5, 7–19, 21, 23, 28, 32,
38, 45, 62, 66–68, 71, 73, 74, 77, 78, 89–106,
110, 137–139, 142, 147, 148, 153, 196, 206,
221–238, 255–268
Antibody-antigen interaction ....................................... 175
Assortativity measures.......................................... 129–135
Atomic contacts............................................................. 155
B
Big data............................................................................ 61
C
Communication pathways ......................... 22, 23, 29–30,
32, 33, 90, 93, 142, 154, 164, 234
Community analysis ...................................................... 179
Commute times.................................................. 23, 28–30
Conformational changes............................ 15, 30, 62, 66,
67, 70, 71, 90, 93, 95, 96, 98, 99, 175, 176, 187,
190, 191, 196, 198, 203, 207, 213, 214, 224,
226–229, 236, 245, 258, 266
Connected components...................................... 114, 115,
121–124, 155, 157, 158, 161, 167, 234
D
Degree distribution...................... 12, 114, 115, 124–129
Degrees of freedom (DOF)................ 63–69, 71–73, 235
Dihydrofolate reductase (DHFR) ...................... 188–199,
201–214
Dimeric interfaces .....................................................82, 83
Disulfide bond...................................................... 176–178
DNA binding domain (DBD)............225–232, 236, 239
Drug discovery ................................ 15, 21, 70, 187, 213,
214, 245–253
Dynamic networks ...................................... 158, 163, 168
E
Energy transport networks .......................................37–53
F
FIRST ....................................1–4, 11, 13, 15, 21, 22, 26,
29, 32, 33, 40, 41, 50, 62, 63, 65, 82, 93, 98, 99,
115, 121, 125, 129, 131, 133, 138, 140, 156,
167, 188, 195–197, 213, 233–236, 246, 256,
258, 259
G
Global motions................................................... 23, 30–33
Graphs................................... 8, 9, 11, 14, 23, 29, 30, 64,
84, 89–105, 115, 119, 120, 131, 133, 138–140,
142–145, 148, 154–156, 160, 161, 164, 166,
167, 170, 171, 234, 249
Graph theory .................................. 14, 69, 138, 142, 234
H
Homodimers ......................... 39, 78, 80, 82, 84, 88, 195
Hot Spot Network (HSN) ................114, 115, 120–123,
125–127, 131–135
Hydrogen bonds ............................38–40, 47, 48, 50–52,
64, 65, 69, 71, 73, 98–100, 147, 156, 159–161,
163–165, 169, 170, 177, 180, 190, 193, 198,
205, 208, 209, 258, 259
I
Induced Hot Spot Networks (IHSN) ............... 114, 115,
120, 121, 123, 124, 126, 128, 131–134
L
Laplacian matrix ...............................................12, 96, 105
Long Range Network (LRN).................... 114, 115, 120,
121, 123, 124, 128, 129, 131–134
M
Metadynamics............................ 227, 228, 232, 235–237,
247, 251, 252
Molecular dynamics (MD) .......................... 7, 22, 33, 39,
40, 47, 48, 50, 52, 63, 65, 138–145, 148, 149,
154, 158–160, 166, 169, 176, 178, 179, 205,
208, 209, 226–229, 232–236, 238, 239, 247,
249, 253
Molecular theorem ...................................................64, 65
Motion correlations ............................138, 139, 141, 180
Luisa Di Paola and Alessandro Giuliani (eds.), Allostery: Methods and Protocols, Methods in Molecular Biology, vol. 2253,
https://doi.org/10.1007/978-1-0716-1154-8, © Springer Science+Business Media, LLC, part of Springer Nature 2021
273
A
Adjacent amino acid networks ............................ 113–135
Allosteric drugs .............................. 15, 62, 138, 245–253
Allosteric effects .....................21–32, 175–180, 198, 231
Allosteric sites ................................ 15, 18, 21, 22, 29, 30,
32, 62, 63, 71, 72, 137, 138, 142, 147, 249
Allostery................................... 3–5, 7–19, 21, 23, 28, 32,
38, 45, 62, 66–68, 71, 73, 74, 77, 78, 89–106,
110, 137–139, 142, 147, 148, 153, 196, 206,
221–238, 255–268
Antibody-antigen interaction ....................................... 175
Assortativity measures.......................................... 129–135
Atomic contacts............................................................. 155
B
Big data............................................................................ 61
C
Communication pathways ......................... 22, 23, 29–30,
32, 33, 90, 93, 142, 154, 164, 234
Community analysis ...................................................... 179
Commute times.................................................. 23, 28–30
Conformational changes............................ 15, 30, 62, 66,
67, 70, 71, 90, 93, 95, 96, 98, 99, 175, 176, 187,
190, 191, 196, 198, 203, 207, 213, 214, 224,
226–229, 236, 245, 258, 266
Connected components...................................... 114, 115,
121–124, 155, 157, 158, 161, 167, 234
D
Degree distribution...................... 12, 114, 115, 124–129
Degrees of freedom (DOF)................ 63–69, 71–73, 235
Dihydrofolate reductase (DHFR) ...................... 188–199,
201–214
Dimeric interfaces .....................................................82, 83
Disulfide bond...................................................... 176–178
DNA binding domain (DBD)............225–232, 236, 239
Drug discovery ................................ 15, 21, 70, 187, 213,
214, 245–253
Dynamic networks ...................................... 158, 163, 168
E
Energy transport networks .......................................37–53
F
FIRST ....................................1–4, 11, 13, 15, 21, 22, 26,
29, 32, 33, 40, 41, 50, 62, 63, 65, 82, 93, 98, 99,
115, 121, 125, 129, 131, 133, 138, 140, 156,
167, 188, 195–197, 213, 233–236, 246, 256,
258, 259
G
Global motions................................................... 23, 30–33
Graphs................................... 8, 9, 11, 14, 23, 29, 30, 64,
84, 89–105, 115, 119, 120, 131, 133, 138–140,
142–145, 148, 154–156, 160, 161, 164, 166,
167, 170, 171, 234, 249
Graph theory .................................. 14, 69, 138, 142, 234
H
Homodimers ......................... 39, 78, 80, 82, 84, 88, 195
Hot Spot Network (HSN) ................114, 115, 120–123,
125–127, 131–135
Hydrogen bonds ............................38–40, 47, 48, 50–52,
64, 65, 69, 71, 73, 98–100, 147, 156, 159–161,
163–165, 169, 170, 177, 180, 190, 193, 198,
205, 208, 209, 258, 259
I
Induced Hot Spot Networks (IHSN) ............... 114, 115,
120, 121, 123, 124, 126, 128, 131–134
L
Laplacian matrix ...............................................12, 96, 105
Long Range Network (LRN).................... 114, 115, 120,
121, 123, 124, 128, 129, 131–134
M
Metadynamics............................ 227, 228, 232, 235–237,
247, 251, 252
Molecular dynamics (MD) .......................... 7, 22, 33, 39,
40, 47, 48, 50, 52, 63, 65, 138–145, 148, 149,
154, 158–160, 166, 169, 176, 178, 179, 205,
208, 209, 226–229, 232–236, 238, 239, 247,
249, 253
Molecular theorem ...................................................64, 65
Motion correlations ............................138, 139, 141, 180
Luisa Di Paola and Alessandro Giuliani (eds.), Allostery: Methods and Protocols, Methods in Molecular Biology, vol. 2253,
https://doi.org/10.1007/978-1-0716-1154-8, © Springer Science+Business Media, LLC, part of Springer Nature 2021
273