Feny? D. (Ed.) Computational Biology
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Co m p u t a t i o n a l Bi o l o g y
Index
ProteinInfo ............................................................ 233, 235
Proteomics
dynamic range ......................................................... 226
experimental design ......................................... 223–229
post-translational modifications .............................. 223
protein characterization ........................................... 236
protein identification ............................................... 223
protein quantitation ................................................. 223
success rate ....................................................... 226, 227
Proteotypic peptides .............................................. 194, 195
Pseudoknot ...............................................20–24, 27, 29–33
Pseudo-node ...........................................243, 246, 249, 250
Pseudo-vertex collapse (PVC) ................242–246, 249–250
PSI-BLAST ................................... 69–71, 75, 77, 232, 234
PSIPRED ................................................................ 75, 233
PTMs. See Post-translational modifications
p-value .............................195, 255, 256, 265–268, 270, 288
PyMOL ..................................................135, 149, 151, 152
PyroBayes ........................................................................ 13
454 Pyrosequencing ....................................................... 2–3
Q
Quantitation ...........................................211–221, 223, 225
Quorum sensing .................................................... 253–280
R
Ramachandran plot ................ 117, 139, 143, 145, 148, 150
Read mapping ......................................................1, 6, 7, 13
Receiver operating characteristic (ROC) .............. 269–271,
274, 275
Recombination .............................................................. 177
Recombination as a shortest-path problem
(RASPP) .....................................177, 180–184, 186
Reconstruction ................................................................81
Refinement ...............82, 131, 138, 139, 141–143, 145–148,
151, 159, 164–169, 171, 312
Regularization ................................................258–260, 268
Relative dynamic range (RDR) ............................. 227, 228
Relaxation matrix ...................................112, 114–117, 122
Reproduction ..........................................300, 309, 312, 313
Resequencing ............................................................. 2, 3, 6
Resonance assignment ............ 100, 105, 106, 112, 117, 118
Reverse engineering ........................................253–280, 293
R-factor .............................. 78, 87, 100, 117–119, 138, 146
PWAUR .................................................................. 118
Rho-diagram ......................................................... 196, 198
Rho-score .............................................................. 196, 198
RNA
mRNA expression .....................................................13
secondary structure .............................................. 19–34
Robust multichip analysis (RMA) ............38, 39, 42, 47–49
ROC. See Receiver operating characteristic
Root mean squared deviation (RMSD) ................... 84, 88,
110, 111, 114, 117, 150
Rosetta ............................................................65, 66, 70, 85
R-value .................................................................. 146, 147
S
Schema ........................................... 176, 177, 180, 184–186
Secondary structure prediction ............ 19–34, 86, 136, 233,
235–236
Selection ................. 44, 59, 78, 80, 82, 83, 87, 97, 104, 130,
137, 162, 163, 176, 180, 185, 194, 196, 260,
283–293, 299, 300, 308, 309, 312, 313
Sequence analysis .......................................................... 2, 4
Sequence-to-structure alignment .............................. 79–80
Sequencing technologies ..............................1–5, 10–14, 63
Shake and Bake (SnB) ................................................... 141
b-Sheet .................................................................. 145, 236
SHELX ................................................................. 135, 141
SHRiMP ........................................................................... 8
Side chain modeling ............................................ 75–76, 81
Signaling pathway ...........239, 247, 264, 271, 280, 283–293
Signal peptide ............................................................ 53–60
SIGNALP-HMM .......................................................... 58
SIGNALP-NN ............................................................... 58
Signal-to-noise ratio .................97, 102, 119, 122, 198, 213,
220, 269
Signal transduction .........................................239–250, 289
Significance testing ................................................ 266, 287
Simulation ....................33, 65, 84, 105, 112, 114–116, 122,
146, 193, 224, 225, 227–229, 268–271, 298, 307,
308, 311, 312, 317, 319
Single particle analysis ........................................... 157–172
SISDC ............................................................177, 178, 185
SnB. See Shake and Bake
SOAP ............................................................................... 8
Solexa sequencing .......................................................... 3–4
SOLiD sequencing .................................................. 4, 7, 14
SOLVE/RESOLVE.............................................. 144, 152
SOMA ............................................................................ 12
Spacial restraints .............................................81, 82, 85, 87
Sparse Bayesian regression .............258, 261–262, 267–269,
272–276, 279
Spectral counting ............................................................. 99
Spectral library ............................... 189, 190, 192, 194, 199
Spectrum database ..................................101–103, 204, 207
SPOCTOPUS .....................................................54, 58, 59
ssahaSNP ......................................................................... 13
Stable isotope labeling ....................................194, 211–213
Statistical inference ........................................................ 284
Stereochemical restraint .......................................... 81, 145
Stochastic ............................28, 29, 264, 285, 289, 293, 303
Stochastic context free grammars ........................ 28–30, 32
Structural alignment .................................................. 77, 84
Structural biology .............................................96, 130, 157
Structural disruption.......................................176–182, 184
Structural genomics ..................................74, 130, 132, 152
Co m p u t a t i o n a l Bi o l o g y
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Index
Structure determination
automated ..................... 96–97, 100, 103, 105, 119, 122
homology modeling ................................... 64, 100–101
NMR ................................................63, 81, 86, 95–123
prediction ..................................................19–34, 63, 64
X-ray crystallography ..............................63, 86, 96, 129
Success rate ............................................................ 226–228
Superfamily ............................................................... 67, 70
Support vector machines ........................................... 54, 58
SVMTOP ....................................................................... 54
SwissProt ......................................................66, 67, 71, 176
Systems biology ..............................................231, 258, 263
T
Tandem MS .................................................................. 217
Target selection.....................................................78, 80, 97
T-Coffee .................................................................... 75, 77
TEM. See Transmission electron microscopy
Template-based modeling ................................... 70, 73–88
Template selection ................................................78, 82, 87
Tertiary structure ............................................................. 63
TMHMM ............................................................55, 56, 58
Topology....................................... 21, 30, 55, 56, 59, 64, 65
TOPPRED ..................................................................... 54
TOPSPIN ............................................................. 103, 120
Transcriptomics ............................................................. 254
Transmembrane topology .......................................... 53–60
Transmission electron microscopy (TEM) ............ 160, 172
Transposon mutagenesis .................................254, 276, 279
Trypanosoma brucei ..................................................231–237
t-Test.............................................................................. 255
U
Ubiquitination ....................................................... 204, 290
V
Validation .................97, 100, 112, 117–119, 123, 131, 134,
139, 143, 145, 146, 148–149, 152, 186, 193–198,
260, 268
Variability ..............................13, 37, 39, 40, 44–46, 57, 312
Velvet... ...................................................................... 10–12
Vertex...................................... 241–243, 245, 246, 249, 250
Volume probability distributions ........................... 106, 107
X
XDS.... ................................................................... 133, 135
X! Hunter .............................................................. 194, 200
X-ray crystallography..................... 63, 74, 86, 96, 129, 130,
149, 157, 171
Xtalview ......................................................................... 145
X! Tandem ...................................... 193, 194, 200, 204, 207
Z
ZPRED ........................................................................... 57
Zuker–Sankoff algorithm .................................... 24–26, 30