Schlick T. Molecular Modeling and Simulation: An Interdisciplinary Guide
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Index
anti, 280f
gauche, 97f, 280f
trans, 97f, 280f
ab initio methods, 242–247
actin, 126, 127
Ada, Yonath, 4
adiabatic map, 148, 148n, 149f
agglutinin, 112f, 117
AIDS
drugs, 59f, 58–62, 62b, 522b, 523
retrovirus, 59
algorithm
definition, xvi
improvements, 2
Allinger, Norman, 7t, 10, 262
Altman, Sidney, 18
AMBER, xvii, 262, 594h
Fortran language, 388
parameter examples, 286–297
amino acids, 86f, 87f, 82–89
α-Carbon, 79f, 82
essential, 83b, 83–84
formula, 79f
nonessential, 83–84
Anfinsen, Christian B., 103, 103n
Anton, 11, 13, 239, 514
apoptosis, 222
aptamers, 220
Arber, Werner, 7t, 22
aspartame, 84f, 85
ATP synthase B chain-like, 123f
Avery, Oswald, 7t, 17
backward error analysis, 466n
bacteriorhodopsin, 106
Baltimore, David, 31q
barstar, 92, 96f
base pair
stacking, 140, 157,
166–168, 168b, 206
base pairing schemes, 206–216
Hoogsteen, 207, 209f
mismatches, 209–210
reverse Hoogsteen, 208
reverse Watson-Crick, 207
Watson-Crick, 206–207
wobbles, 209–210
bending
in-plane
rocking, 271
scissoring, 271
out-of-plane
twisting, 271
wagging, 271
710 Index
Berendsen, H.J.C., 11
Berman, Helen, 572h
Bernal, J. D., 14
Bernanke, Ben , 346q
Berne, Bruce, 474
BFGS method, 371–372
biochips, 39b, 526, 530b
bioengineering, 70, 71b
bioinformatics, 43, 65
biology
dogma, 131
machinery, 251
symmetry, 53
biopharming, 70
Black, James W., 521
BLAST, 590h
Blue Gene, 49
Blue Waters, 50
Board, John, 323
Bohr, Niels, xix, 3, 520q
Boltzmann factor, 412
Boltzmann probability, 413f
Boltzmann statistics, 387
Born-Oppenheimer approximation,
242–247, 249
bovine pancreatic trypsin inhibitor (BPTI)
calculated spectra, 271
bovine papillomavirus E2 protein
DNA binding, 168b
bovine spongiform encephalopathy
(BSE), see mad cow disease
Bragg’s law, 19
Brahe, Tycho, 429
Brenner, Sydney, 7t, 26, 29
Brown, Robert, 489
Brownian dynamics, 337–338, 428t, 430f,
487–496
algorithms, 337, 491
complexity, 495b, 494–496, 496f
Ermak-McCammon, 491
inertial, 491
random-force computation, 495b,
494
–496, 496f
biased, 509
diffusion constant, 337, 481, 490, 614h
diffusive limit, 336
DNA applications, 202f, 202, 335, 337
exercise, 614h
fluctuation/dissipation theorem, 336,
489
hydrodynamics, 337–338, 492b,
491–494
Kirkwood-Riseman approximation,
494b, 494
Oseen tensor, 492–494
Rotne-Prager tensor, 492–494
software, 343
theory and applications, 335
Brownian motion, 198, 337, 614h
Broyde, Suse, xv
bulge, 216, 218f
butane
torsional states, 280f
calcium-binding protein, 95f
calmodulin, 94, 115
Calugareanu, Grigore, 195
Carboxypeptidase inhibitor, 124f
catabolite gene-activating protein (CAP)
DNA binding, 168b, 172f
Cech, Thomas, 18
Celera Genomics, 26–27, 30–33, 33b
cellomics, 42
cellulase cela, 108f, 115
central limit theorem, 409–410, 438
CFF, 262
chaos, 441f, 440–441
Lyapunov exponent, 440n
chaperones, 51f, 50–
51, 52b, 252b
Chargaff, Erwin, 7t, 17
CHARMM, xvii, 255, 256t, 257f, 262,
594h
Fortran language, 388
Monte Carlo, 416
parameter examples, 286–297
Chase, Martha, 7t, 17
Chemical Design, 519–552
chemical libraries, 526–550
bioactivity, 529–530, 535–536
compound descriptors, 534–535
data compression and analysis, 540–550
PCA, 540–542
SVD, 542–544
problems, 526–530, 532–539
diversity, 527–528, 538–539
similarity, 527–528, 538–539
QSAR, 65
Index 711
SAR, 536
schematic illustration, 533f
chemogenomics, 523
chemoinformatics, 43, 65, 521
chimeraplast, 68b
chromatin, 184–185, 187f
model, 192f
simulation, 193b, 195f
chromosome, 182–193
classical mechanics
limitations, 432–435
collagen, 78, 91f, 91, 110
combinatorial chemistry
future, 551–552
history, 520–526
combinatorial optimization, 527, 538
computational biology, 41
computing
progress, 2, 239
Comte de Buffon, 387
configuration, 258
definition, 258
relation to conformation, 258
conjugate-gradient methods, 244,
372–374
consilience, 2
constrained dynamics, 453–455
RATTLE, 454
SHAKE, 453–454
in MTS, 482, 485b
constraints
in minimization, 428t
continuum solvation, 333–342, 428t
Poisson-Boltzmann approach, 338–343
potential of mean force, 334–335
convergence (of a sequence), 352b
linear, 352b
quadratic, 352b
superlinear, 352b
Copernicus, Nicolas, 429
Corey, Robert, 7t, 15
Coronavirus NSP10-like, 124f
cosmeceuticals, 74
counterion condensation theory, 177, 180b
Course Syllabus, 557–558
Creutzfeld-Jacob disease (CJD), see mad
cow disease
Crick, Francis, 7t, 17–18, 130, 135, 150,
155
Crigler-Najjar (CN) syndrome, 67, 68b
Critical Assessment of Techniques for
Protein Structure Prediction
(CASP), 48–49
Crothers, Don, 170
Crowfoot-Hodgkin, Dorothy, 14
cruciform, 218f
cryoelectron microscopy (cryo-EM), 23
illustration, 5f
crystallography
direct lattice, 315b
electron density, 314, 315b
indices of reflection, 315b
reciprocal lattice, 315b
structure factor, 314, 315b, 322
unit cell, 314b
cube, see periodic boundary conditions
cutoff schemes, 302–310
force switch, 308–309
general formulation, 306–307
in multiple timesteps, 305, 308, 309f,
323
potential switch, 307–308, 309f
shift functions, 309f, 309–310
CVFF, 262, 287
cystic fibrosis, 67
cytochrome, 92, 96f, 114
, 115
databases
analysis, 41–44
growth, 44f, 45t, 572h
NDB, 133, 135, 165, 206, 572h, 582h,
584h, 589, 590h
NRPR, 44f, 45t
PDB, 43, 45t, 165, 206, 572h, 589,
590h
PIR, 44f, 45t
RCSB, 44, 45t, 165, 206, 572h, 590h,
592h
sequence, 44f, 45t, 572h
structure, 44f, 45t, 572h
Debye-H¨uckel theory, 177, 193b, 341f,
340–342
Debye length, 340, 341f
Delbr¨uck, Max, 17
DelPhi, 342, 343
density functional theory, 243
derivatives
gradient vector, 352, 435–436
712 Index
Hessian matrix, 353
positive-definite, 353
descent direction, 359–360
detailed balance, 411–412
dielectric constant, 316, 317, 334,
338–340, 342, 343f
dielectric function, 338–339
diffusion constant, 337, 481, 490
dihedral angle
anti, 280f
gauche, 97f, 280f
trans, 97f, 280f
definition, 97b, 98f
relation to torsion angle, 97b
Dirac, Paul, 241
Dirac, Paul Adrien Maurice, 431q
directed molecular evolution, 68
disulfide bonds, 89
divergence operator, 319b
Djerassi, Carl, 521
DNA
London Times quote, 130q
A-form, 158f, 156–158, 159, 160f
A-tracts, 169–173, 173f, 174b, 178,
201b
adducts, xv
B-form, 155–157, 158–160f
base-pair step analysis, 167t
bending, 166, 171f, 169–173, 173f,
174b
canonical forms, 155–161, 582h, 584h
cellular organization, 187f, 182–193
chips, 39b, 526, 530b
chromosome, 182
–193
computing, 134, 165, 240
double helix, 136f
diameter, 150
grooves, 150
helix sense, 150, 150n
pitch, 136f, 150
residues per turn, 150
rise, 150
twist, 136f, 150
dynamics, 9t, 12, 15, 16f, 133–134,
179f, 193b, 195f, 198, 202b, 202f,
203f, 200–204, 215b
fundamental processes, 132–133
genome content, 184f, 182–184, 185t
geometry, 195–197
histone, 187f
hydration, 172, 174–180
ion patterns, 174–180
junk, 28
linking number, 196f, 195–196
Maddox quote, 240q
microarrays, 39b, 42
mimics, 212f, 212–213
model forms, 151, 152t, 158–160f
nucleosome, 189f, 186–193
overstretched, 215b, 214–216
persistence length, 187f, 198–202
polymer model, 198–202
quadruplexes, 211–212
S-DNA, 214
sequence effects, 165–174
Ascona Consortium, 169
site juxtaposition, 201, 202b, 202, 203f
supercoil, 156
supercoiling, 200b, 184–204
elastic approximation, 200b, 201b,
199–202
simulation, 197–204
TATA-box, 169b, 172f, 179f, 182, 207
telomeres, 211–212
topology, 195–197
triplexes, 211
twist, 196f, 196–197
understretched, 214–216
Watson and Crick’s seminal paper, 164q
writhe, 196f, 197
Z-form, 156, 158–160f, 160–161
DNA topoisomerase I, 121f
DNA-binding leucine zipper protein, 114
DNA/protein interactions, 181t, 180–182
helix-turn-helix (HTH) motif, 584h
Down’s syndrome, 31
Doyle, Arthur Conan, 346q
drugs, 58–67
abacavir, 531b
AIDS, 59f
biologics, 524
chlorpromazine, 527f
codeine, 531b
COX-2 inhibitors, 529b
cyclosporin, 58, 522b
for chronic pain, 529b
future, 552
herceptin, 530, 531b
Index 713
lead generation, 530
lead optimization, 530
mevacor, 522b
Natural, 522b
neuropeptide inhibitors, 523
PDE-5 inhibitors, 523
prilosec, 58
quinacrine, 527f
raloxifene, 527f
rational, 58, 521–526
tamoxifen, 527f
taxol, 522b
thrombin inhibitors, 523
viagra, 58, 525f
viracept, 525f
warfarin, 531b
zomig, 525f
dyad, 152, 154
ECEPP, xvii, 262, 594h
Einstein, Albert, 490
Elber, Ron, 517
Elion, Gertrude, 58
elongated dodecahedron, see periodic
boundary conditions
Engels, Friedrich, 77q
Englund, Paul, 170
ensembles, 412–413, 439, 455–461
canonical (NVT), 412–418, 455–457,
459–460
generalized, 421
isothermal-isobaric (NPT), 412, 455,
457–458, 460–461
microcanonical (NVE), 412, 439, 455
weak barostat coupling, 457–458
weak thermostat coupling, 456–457
epigenetics, 222
ergodicity, 411–412
error bars, 388, 409–410
ester, 138n
Ewald method, 314b, 311–324
complexity, 320–321
direct space term, 321–322
Ewald’s trick, 316–319
finite-dielectric correction, 320–322
Gaussian masking, 319f, 317–319
nonbonded-exclusion correction,
321–322
reciprocal space term, 321–322
roots in crystallography, 314–316
self-interactions correction, 321–322
experimental progress, 14–23, 239
cryoelectron microscopy, 5f, 23
NMR, 20–23
X-ray crystallography, 14–20, 22–23
experimental triumphs, 4
face-centered cube, see periodic boundary
conditions
fatty acid binding protein, 111f, 116, 117
ferritin, 114
Fibonacci series, 396n
fibronectin, 111f, 116, 117
Finch, John, 189
Fixman, Marshall, 338, 494, 495b
flagellin, 126
flavodoxin, 118, 120f
fluctuation/dissipation theorem, 336
, 489
Fokker-Planck equation, 337, 489
foods
amino acid sources, 83, 83b
designed, 71b, 69–72
vegetarian diet, 83b
force field
AMBER, xvii, 262, 388, 594h
parameter examples, 286–297
approximations, xiv, 594h
polarizability, 263
assessment, 594h
CFF, 262
CHARMM, xvii, 255, 257f, 262, 388,
594h
cutoff functions examples, 306f, 307,
310
Monte Carlo, 416
nonbonded CPU examples, 302f,
303t
parameter examples, 286–297
criticisms, 248, 594h
CVFF, 262, 287
debate, xvii
early successes, 248
ECEPP, xvii, 262, 594h
first-generation, 10–11
GROMOS, 262
limitations, 262–264
MMFF, 262
714 Index
nonbonded vs. bonded computations,
599h
OPLS, 262
potential
bond angle, 276–280
bond length, 272–276, 600h
bond length, harmonic, 272–274
bond length, Morse, 274–276
Buckingham, 288
Coulomb, 293b, 291–295, 599h
hydrogen bond, 263
Lennard, 599h
torsional, 280–288, 600h
van der Waals, 288–291
second-generation, 267
third-generation, 264, 267
transferability, 284
Force Fields, 265–297
force fields
CHARMM
atom types, 256t
Franklin, Rosalind, 7t, 17, 17n
Frauenfelder, Ulrich Hans, 443q
Fuller, F. Brock, 195
function
curvature, 353, 355, 365, 369, 370, 379
derivatives, 352
least-square, 350
non-differentiable, 350
nonlinear, 350
separable, 350
galactose oxidase, 112f, 117
Galilei, Galileo, 429
Gauss double integral, 197
Gauss’ law, 338
Gaussian distribution, 392
Gaussian random variates, 403–405
Box/Muller/Marsaglia method,
405
Odeh/Evans method, 404–405
gene chips, 39b
gene therapy, 67–68, 68b
genetic code, 131, 132t
genetic engineering, 69–72
genome
content, 182–184, 185t
non-coding, 28
sequencing, 25–39
Arabidopsis thaliana, 27–28
Bacillus subtilis, 25
Haemophilus influenzae,7t,25, 33
M. tuberculosis, 25, 92
fruitfly (Drosophila), 8t, 26–27, 33b
human, 30–39
implications, 35–37
mouse, 28–29
pufferfish (Fugu), 29
rice, 29
roundworm, 7t, 25–26
strategies, 33b
yeast (Saccharomyces cerevisiae), 7t,
25
genomics
comparative, 26, 29, 35, 42
functional, 42, 119
structural, 42, 119
geometry optimization, see
minimization
Gerstmann-Straussler-Scheinker disease
(GSS), see mad cow disease
glycine amidinotransferase, 121f
glycosyl rotation, 148–150
Gosling, Raymond, 17
gradient vector, 352, 435–436
GRASP, 342
Griffith, Fred, 17
Griffith, J.S., 54
GroEL/GroES, 51f, 52b
GROMOS, 262
guanine nucleotide-binding protein, 109f,
115
hairpin, 218f
harmonic oscillator, 619h
Hartree-Fock, 242–244, 324
Hauptman, Herbert, 19
heat equation, 616h
Heisenberg, Werner, 3
helical parameters, 150–155
helix-loop-helix-motif
EF-hand family, 94
hemoglobin, 46, 78, 94, 106, 119
hemophilia, 67
Heraclitus of Ephesus, 41q
Hershey, Alfred, 7t, 17
Hessian matrix, 353
positive-definite, 353
hexagonal prism, see periodic boundary
conditions
Index 715
Hexameric HIV-1 CA, 122f
histone, 187f, 185–188
Hitchings, George, 58
HIV integrase, 523
HIV protease, 59f, 59, 521, 523
HIV reverse transcriptase, 59f, 59
Hoffman, Roald, xiii
Hofstadter, Douglas R., 301q
Holley, Robert, 7t
Homework Assignments, 571–621
homework assignments
in syllabus, 557–558
homology, 589h
analysis tools
BLAST, 590h
Honig, Barry, 343
Hooke’s law, 273
Horvitz, Robert, 26
Hugo, Victor, 238q
Human Genome Project, 7t, 30–39
sequencing strategies, 33b
human growth hormone, 114
human lysozyme, 106
Huxley, Thomas Henry, 105q
hybrid Monte Carlo, 420–422
HydB/Nqo4-like, 122f
hydrogen bond, 80b
acceptor, 80b
donor, 80b
Hoogsteen, 207, 209f
in DNA, 130, 135, 140, 206–210
reverse Hoogsteen, 208
reverse Watson-Crick, 207
strength, 80b
water, 81f
Watson-Crick, 136–137, 138f, 206–207
hydrophilic, 51n
hydrophobic, 51n
immunoglobulins, 96f
implicit integration, 496–503
computational time, 498–499
damping, 498
Euler, 498f, 497–
499, 619h
midpoint, 499–500, 500b, 500f
resonance, 499–502
symplectic, 502b
in silico biology, 239
inclination, 153f, 152–153
Ingenhausz, Jan, 489
Ingram, Vernon, 530b
Insight package, xvii, 574h, 577h
in syllabus, 557
integer programming, 349
interdisciplinary collaborations, 2, 240
ion channel proteins, 239
isothermal compressibility, 457, 458b
Janus, 50b
Joachim, Frank, 711
Jorgensen, William, 11
Kagay, Michael R., 386q
Karle, Jerome, 19
Karlin, Samuel, 266q
Karplus, Martin, xvii,7t,11, 262
Lord Kelvin, 387
Kendrew, John, 7t, 15, 16, 19
Kepler, Johannes, 429
Khorana, Gobind, 7t
Kirkwood-Riseman approximation, 494b,
494
Klug, Aaron, 189
knots, 103
Kohn, Walter, 238
Kollman, Peter, xvii, 11, 262
Kornberg, Roger, 186
L’Ecuyer, Pierre
combined generators, 399
expert advice, 402
long-period generators, 399
reviews, 389
website, 402
Langevin dynamics, 335–337, 479–484
diffusion constant, 337
diffusive limit,
337–338
discretization, 482, 484f
effect of γ, 336, 481f, 480–481,
486–488f
equilibration, 439
exercise, 619h
LN integrator, 484f, 485b, 486f,
482–486, 487, 488f
mollified method, 479
parameterization of γ, 336–337,
480–481
relation to thermostat coupling, 456
716 Index
resonance, 477f
versus Newtonian, 483f
Langevin piston, 458
de Laplace, Pierre Simon, 431, 432b,
432q, 464q
Laplace’s equation, 320b
Laplacian operator, 319, 320b, 617h
leapfrog integrator, see Verlet integrator
Lehmer, D. H., 392
Leibowitz Schmidt, Shira, xiii
lentivirus, 68b
Levinthal, Cyrus, 252b
Levitt, Michael, 245f
Lifson, Shneior, 7t, 10, 248
linear programming, 350
linking number, 196f, 195–196
Liouville operator, 475
Los Alamos pioneers, 387
Luria, Salvador, 17
Lyapunov exponent, 440n
Lyapunov instability, 440
lysozyme, 96f, 121f
MacLeod, Colin, 17
mad cow disease, 53–54, 55b
Maddox, John, 240
Maddox, Sir John Royden, 426q
maltate dehydrogenase, 118, 120f
Markov chain, 414
Marsaglia, G., 395
materials
designed, 74
matrix
dense, 353
indefinite, 353
negative-definite, 353
positive semi-definite, 353
positive-definite, 353
sparse, 353
symmetric, 350
McCammon, Andrew, 343
McCarty, Maclyn, 17
Mendel, Gregor, 7t
metabolome, 43
Metropolis algorithm, 411–416
Mezei, Mihaly, 314
MgtE membrane domain-like, 123f
microarrays, 39b, 526, 530b
minimization, 428t
algorithm
conjugate gradient, 244, 372–374
convergence criteria, 362–
363
descent algorithm, 359–363
descent direction, 359–360
interior methods, 349
line search, 359–363
Newton’s method, 363–369, 618h
quasi-Newton, 370–372
truncated Newton, 374–376
trust-region methods, 361–362
DNA/adduct, 430f
exercise — advanced, 616h
exercise — biphenyl structure, 606h
exercise — pentapeptide global
minimum, 612h
for large-scale functions, 369–383
recommendations, 380–383
software, 378t, 378–380
with restraints, 608h
minimum
global, 616h
local and global, 351–352
MMFF, 262
molecular biology
momentum, 130–132
Molecular Dynamics, 425–519
molecular dynamics
accuracy, 447
as refinement tool, 436
as sampling tool, 436
background reading, 427–428
butane simulation, 442f, 444f
chaos, 441f, 440–441
computational complexity, 443–444,
446–448
constrained, 447–448, 453–455
convergence of properties, 441
–442,
442f, 444f
degrees of freedom, 438
Desmond, 11
ensembles, 439, 455–461
equilibration, 439, 439f
exercise — advanced, 619h
explicit-Euler, 619h
historical perspective, 12–14, 15, 16f
implicit integrators, 496–503
computational time, 498–499
damping, 498