N
Non-bonded networks (NBN) ......................... 41, 43, 44
Non-covalent interaction................................................ 92
Normal mode analysis............................................ 22, 247
P
P53........................................................................ 221–240
Pebble game algorithms ...........................................65, 69
Pharmacology....................................................... 245–252
Point-mutation..........................................................39, 62
Protein contact network (PCN).......................15, 22, 84,
114, 115, 117, 119–121, 123, 124, 126–129,
131–134, 247–250, 253
Protein flexibility .................................................... 63, 249
Protein motions ............................ 63, 65, 138, 139, 141,
144, 212–214, 247
Protein-protein interaction........................................... 131
Protein structure networks (PSNs) ................90–98, 105,
153–156
Protein structures........................ 3, 8–13, 22, 23, 30, 50,
62, 67, 68, 71, 90, 92, 94, 95, 102, 106, 110, 114,
134, 139, 143, 154–157, 161, 163, 167, 185,
201, 227, 228, 230
Protein topology ............................................................. 78
R
Rigidity theory .............................................62–64, 66, 71
Rigidity-transmission allostery (RTA) ................... 62, 63,
67–71, 74
RNA cooperativity ............................................... 255–268
RTA algorithm .............................................62, 67, 69–71
S
Salt-bridge ...........................................39, 41, 43–45, 156
Side-chain interactions........................90, 94, 98, 99, 106
Spectral decomposition........................... 12, 96, 102, 105
Structural communication ......................... 154, 155, 158,
161, 167, 168, 229
Subnetworks ......................................................... 124, 129
T
Thermodynamics............................. 10, 22, 85, 175, 208,
210, 225, 256–259, 261–263, 266, 268
Topology of graphs associated with proteins .............. 117
Transcription factors ................................... 223, 228, 231
W
Water clusters ...............................................39, 41, 43–45
Weighted networks ..............................44, 90, 91, 94, 95,
106, 110, 140, 142–144, 156, 179
274
ALLOSTERY: METHODS AND PROTOCOLS
Index
Non-bonded networks (NBN) ......................... 41, 43, 44
Non-covalent interaction................................................ 92
Normal mode analysis............................................ 22, 247
P
P53........................................................................ 221–240
Pebble game algorithms ...........................................65, 69
Pharmacology....................................................... 245–252
Point-mutation..........................................................39, 62
Protein contact network (PCN).......................15, 22, 84,
114, 115, 117, 119–121, 123, 124, 126–129,
131–134, 247–250, 253
Protein flexibility .................................................... 63, 249
Protein motions ............................ 63, 65, 138, 139, 141,
144, 212–214, 247
Protein-protein interaction........................................... 131
Protein structure networks (PSNs) ................90–98, 105,
153–156
Protein structures........................ 3, 8–13, 22, 23, 30, 50,
62, 67, 68, 71, 90, 92, 94, 95, 102, 106, 110, 114,
134, 139, 143, 154–157, 161, 163, 167, 185,
201, 227, 228, 230
Protein topology ............................................................. 78
R
Rigidity theory .............................................62–64, 66, 71
Rigidity-transmission allostery (RTA) ................... 62, 63,
67–71, 74
RNA cooperativity ............................................... 255–268
RTA algorithm .............................................62, 67, 69–71
S
Salt-bridge ...........................................39, 41, 43–45, 156
Side-chain interactions........................90, 94, 98, 99, 106
Spectral decomposition........................... 12, 96, 102, 105
Structural communication ......................... 154, 155, 158,
161, 167, 168, 229
Subnetworks ......................................................... 124, 129
T
Thermodynamics............................. 10, 22, 85, 175, 208,
210, 225, 256–259, 261–263, 266, 268
Topology of graphs associated with proteins .............. 117
Transcription factors ................................... 223, 228, 231
W
Water clusters ...............................................39, 41, 43–45
Weighted networks ..............................44, 90, 91, 94, 95,
106, 110, 140, 142–144, 156, 179
274
ALLOSTERY: METHODS AND PROTOCOLS
Index
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