718 Index
complexity, 329–330
domain decomposition, 324–326, 326f
multipole expansion, 325, 327, 328b
spherical coordinates, 330–332
variants, 333
Multivariate Minimization, 345–385
muramidase, 115
myoglobin, 46, 78, 94, 96f, 106, 109f, 115
myohemerythrin, 108f, 114
myosin, 126
nanotechnology, 240
Nathans, Daniel, 7t, 22
Newton equations, 369
Newton’s method, 363–369
classic example, 366–367
historical perspective, 364
multivariate version, 368–377
one-dimensional version, 364–367
Newton, Sir Isaac, 429
Newtonian physics, 426–437
limitations, 432–435
Nirenberg, Marshall, 7t
Nonbonded Computations, 299–344
nonbonded computations
CPU time, 302f, 303t
normal modes, 267–272, 438, 444
NP-complete, 349, 538
nuclear magnetic resonance (NMR)
high resolution, 21
NOEs, 21
residual dipolar coupling, 22
technique details,
20–22
Nuclear Overhauser Effects (NOEs), 21
nucleic acid
atom labeling, 141–142
backbone torsion analysis, 147f
building blocks, 137f, 135–142
nitrogenous bases, 135
nucleoside, 137, 140
nucleotide, 137, 140
bulge, 210, 216, 218f
dihedral angle, 585h
flexibility, 142–155
backbone torsions, 145, 147f
base-pair, 153f, 155f, 151–155,
165–169
glycosyl rotation, 149f, 148–150
helical parameters, 150–155
sugar, 143–145, 146f, 149f
hairpin, 218f
loop, 210, 218f
polynucleotide chain, 139f, 137–142
pseudorotation, 143f, 144f, 145f,
143–145
stacking, 140, 157, 166–168, 168b, 206,
213b, 216, 224
sugar pucker analysis, 146f
torsion-angle labeling, 142t, 142
Nucleic Acid Database (NDB), 133, 135,
165, 206, 572h, 582h, 584h, 589,
590h
backbone torsion analysis, 147f
sugar pucker analysis, 146f
Nucleic Acids Structure, 129–
237
nucleosome, 4n, 189f, 186–193, 239
H3 K79 dimethylated nucleosome, 190f
poly(dA•dT) nucleosome, 190f
tetranucleosome, 190f
nutraceuticals, 71b, 91
nutrigenomics, 39b, 72–73, 530b
nutritional genomics, see nutrigenomics
OPLS, 262
optimization, see minimization
Overton, Michael, xv
p53 tumor suppressor protein
DNA binding, 181t
p53 gene
mutations, 24b
p53 tumor suppressor gene, 27
P-DNA, 215b
Paracelsus challenge, 47f, 50b
partition function, 412
Pauling, Linus, 7t, 15, 215, 530b
pectin lyase A, 112f, 117
peptide, 82f
aspartame, 84f, 85
Met-enkephalin, 577h, 612h
peptide nucleic acid (PNA), 212f, 212,
213b
periodic boundary conditions, 311–314
cube, 311
elongated dodecahedron, 313f
face-centered cube, see rhombic
dodecahedron