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Computational Methods for Protein Structure Prediction & Modeling V1 - Xu Xu and Liang

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390

Index

contact map prediction 255, 262

contact order (CO)

258–259, 269

contact potentials

74, 109, 256

contact substitution matrix

271

contact, residues 73

 

contiguous, domain

129, 134

convex hull 95, 185, 191–192

cooperative, cooperativity

110, 231

correlated mutation

262–263, 265–268,

271–272

 

 

Coulombic interactions 45, 47 convex spherical surface 184

Critical Assessment of Structure Prediction (CASP)

12, 14–16, 25, 238–239, 268–269, 337, 347 cross-linking 288–289, 329

crossstructure 293, 295–296

cryo-EM 27–28, 181–182, 285, 292, 359, 363–365, 370–371, 374, 377, 382

curved lineg segments 184 CVFF 58

Dali 22, 151, 154–156, 161, 164–165, 167,

169, 171

deconvolution method

366–367, 370–371, 373

Decoys ‘R’Us

 

101

 

 

 

DEE (Dead End Elimination)

13

Delaunay complex

186–187

Delaunay edge

89, 185–186, 192

Delaunay tetrahedrization

112, 185–187,

191–193, 196, 202

 

 

 

Delaunay triangulation

88, 110, 185, 190,

192–193

 

 

 

 

 

 

density maps

27–28, 225, 359

DFIRE

87, 111–112

 

 

 

dihedral angle

 

47, 52, 55, 73–74, 329, 377–378

discontinuous molecular dynamics 303

discrete flow

190–191

 

 

discrete molecular dynamics

303

DisEMBL 226, 238

 

 

 

DISOPRED

226, 239

 

 

 

disordered region detection

224, 243

DISPRO

226, 239

 

 

 

distance matrix

149, 153, 175, 256–257

distance matrix error (DME)

150, 256

docking 12–13, 15, 24–26

 

domain assignment

22–23

 

domain, structural

129–130

 

domain-domain interactions

 

22, 24

DomainParser 22, 133, 137, 139, 141–142

double dynamic programming

8, 152–153

Drude oscillator

59

 

 

 

drug design

59, 323

 

 

 

dynamic programming 7–8, 152–153, 155–156,

159, 197, 219, 236, 324, 335

edge-flip

192

 

 

 

 

effective energy

71, 110, 336–337

effective resolution

373, 384

elastic scoring measure

154

electro density map

181, 225, 365

electron cryomicroscopy

27, 359

electron microscopy

27, 181, 271, 285, 291, 323

electron spin resonance

286

electronegativity equilization methods 52

electronic polarizability

52, 59

electrostatic interactions

2, 26, 46, 49, 53, 82,

334

 

 

 

 

 

electrostatic potential

82

 

elementary surface pieces

184

elongation kinetics

290

 

EM density map

27–28, 31, 364, 374

empirical force field optimization 51

empirical Force Fields

45

 

empirical potential function

360, 373–374

ENCAD 50, 58, 344–345

energy minimization

2–5, 11, 339, 341, 344

ensemble

30, 49, 97, 101, 106, 111, 171–173,

239, 271

ensemble averaging 360, 374 ensemble classifier 171–173 environmental features 7

EPR 291, 295 ESP 52–53

Euclidean distance 77, 114, 175, 185, 214

evolutionary relationship

151, 187, 166–167,

196, 319

 

 

 

 

Ewald method

49

 

 

extended atom force field

58

 

F3C

49–50

 

 

 

family 4, 12, 21, 166, 168

 

feature vector

162–163, 175

FFAS

8

 

 

 

 

FFT (Fast Fourier Transform)

25–26

fold 2, 5–9, 11, 23

 

 

fold recognition

6, 23, 29

 

FoldIndex

226, 238

 

 

force field

2, 45

 

 

forward/backward algorithm

268

Fourier transform infrared spectroscopy 286 fragment 3, 8, 11, 24, 129, 133–135 framework 5, 71–72, 158, 328, 336, 344 FSSP 161, 167, 176

function annotation 323

Index

391

function prediction

181, 195–197

functional interpretation

359

 

fused ball model

182

 

 

 

gaps 97, 148, 150, 155, 219, 227, 229, 235,

321, 323, 325–327, 344–345

 

generalized-Born 50, 332, 336

 

genetic algorithm

11, 25–26, 267, 335, 344

genomes 16, 19, 29, 31, 166, 226

GenTHREADER

8

 

 

 

geometric hashing

26, 149, 152, 155–156, 158,

160, 196

 

 

 

 

 

geometric nature of discrimination

95

geometric potential function

88, 101, 105, 112,

200

 

 

 

 

 

geometry-based procedure

46, 181

global free-energy minimum

9, 320

global optimality

326

 

 

 

GLOBPLOT

226, 239

 

 

Go models

299

 

 

 

 

GROMOS 2, 46, 50, 58

 

 

hard-sphere model

182

 

 

Helixhunter 28, 359, 363, 373

 

Hidden Markov models (HMM)

8, 19, 210, 213,

216, 223, 234, 262, 325

 

 

HMMSTR

268

 

 

 

 

homologous modeling

3–4

 

 

homologous topology 167

homology detection 6, 8–9, 29, 213, 229,

324–325

homology modeling 3–6, 9, 12–13, 18, 22–23,

25, 28, 31, 230–231, 319–322

homotopy equivalent

184

 

HP model

10, 84, 109, 298–299

hydrogen bonds

2, 47, 208, 266, 285, 296, 326,

334, 342, 344

 

 

 

 

hydrogen-deuterium exchange

287

hydrophobic core

23, 126, 130–131, 221, 303

idealized ball model

182

 

Implicit solvation models

50

Improper angle

46–47, 52

 

inclusion bodies

281, 300

 

inclusion-exclusion formula

188, 190

index structure 161–163, 174–175

insertion 4–5, 192, 227, 231, 289–290,

321–323, 325–326, 330, 337–342

InsightII

4, 327

 

 

 

interatomic interactions

1–7

 

inter-domain, contact

127

 

interface, domain 130, 138–139, 141 intermediate resolution 27, 292, 301, 359–360 inter-residue contact 274

inverse spherical surface 184

iterative dynamic programming 153, 156, 159

Jpred 235–236

kernel voxel 360 kinetic partitioning 281

k-nearest neighbour (kNN) 210, 214, 232–233 knowledge-based effective potential function 72

knowledge-based potential

71–73, 75–76,

85–86, 93–94, 101–103, 108–115

K-segment clustering

366, 368

Langevin Dipoles Model

51

lattice models

10, 230, 297–299, 301

Lee-Richards surface

183

Lennard-Jones (LJ)

 

46–47, 134, 302

Levinthal’s Paradox

 

2, 280

ligand binding

231, 291, 323, 345

likelihood matrix

264

 

limited proteolysis

287–288, 291, 297

local conservation

197

 

local contacts

257–259, 264–265

local peak filter

366, 368

local structure motifs

268

locally Delaunay 192–193

locally enhanced sampling

49

loop connectivity

359, 373

loop prediction

331–334, 338

loops 5, 12, 19, 134–135, 230, 259, 322–323, 327, 330–332, 336, 345, 373–374, 377

machine learning 19–20, 100, 171, 210–211,

213, 215, 217, 222, 232, 239, 255, 257, 272–273

maximum disk inclusion number 360

MD (Molecular Dynamics simulation) 11, 13, 56,

59, 302, 336

MD simulation 9, 11, 20–21, 48–52, 54–56, 291–296, 301, 303, 336

median of energy value 380 membrane proteome 21–22 meta servers 8, 16, 343–344

methods, for domain partitioning 125, 129 minimum local thickness 360

misfolded models 337

Miyazawa-Jernigan contact statistical potential 71 MM3 66

MMFF 48, 58

392

Index

ModBase 29

 

 

 

 

model assessment

336–337

 

model building

289, 322, 325, 327–329, 333,

337–339, 343

 

 

 

model quality

13, 335–336, 344

modeling target

3, 347–348

 

Modeller 5, 13, 24, 28–29, 327, 329, 344–345

molcular surface (MS)

184, 287, 329

molecular dynamics

2, 9, 20, 48, 303

molecular dynamics simulations

9, 11, 20–21,

48–52, 54–56, 291–296, 301, 303, 336

molecular mechanics

2, 45, 332

Monte Carlo simulation (MC)

223–224

Morphological analysis

360, 366

Morse function

47

 

 

Motif 11, 20, 147, 149–150, 157–159, 166,

173, 175–176, 196–197, 221–222, 305, 320

Multi-dimensional hyperplane

95, 100

multi-domain, chains

142

 

 

multiple sequence alignment

23, 207, 210, 212,

228, 230, 262

 

 

 

 

multiple structure alignment

147, 149, 157,

159–161, 175–176, 325, 327

 

multiple-domain proteins

22

 

 

native conformation

1–2, 72, 94, 101, 106, 108,

200, 331–334, 336, 341

 

 

Native topology

359–360, 373–375, 377,

379–384

 

 

 

 

 

 

neural network (NN)

19–20, 168, 171,

215–216, 222

 

 

 

 

nonadditivity effect

110

 

 

 

non-contiguous, domain

129, 132, 134–135

Non-local contacts

264, 266, 269–270, 272

non-order-preserving 150

 

 

Non-sequential structure alignment

150

nucleated growth polymerization

289

nucleation 270, 282, 290, 303

 

nucleation site

270

 

 

 

 

OPLS 45, 50, 53–55

 

 

 

OPLS/AA

45, 54–56

 

 

 

OPLS/UA

58

 

 

 

 

 

optimal local alignment

324

 

 

optimized linear potential function

97–98, 115

optimized nonlinear potential function 98, 100,

106

order preserving 150 orthogonal bundle 377

packing 13, 90–91, 101, 104, 112, 130 packing geometry 377

pair-wise search

325

 

 

 

 

parallel tempering

49, 181

 

PARAM19

181

 

 

 

 

 

parameter optimization

51, 56

parametrization

65

 

 

 

 

partial atomic charges

 

47, 52–55, 58

particle Mesh Ewald

49

 

 

partition function

74–75, 106–108, 110–111

partitioning 125–129, 133, 137–138, 142

pathway models

268

 

 

 

 

PDB 28, 56, 142

 

 

 

 

PDISORDER

226, 239

 

 

PDP 22, 134, 139, 141

 

 

phase diagram

300, 303

 

 

PHD 212, 230, 232–233, 235–236

phi, psi angles

52

 

 

 

 

 

photo-affinity labeling

 

289

 

physical potential function

114

physical/non-physical contacts

299

physical-chemical energy

341

physics-based effective potential function 72

pockets

190–191, 194–195

Poisson-Boltzmann 50, 332

 

polyalanine

302–303

 

 

 

polyglutamine 282, 289–290, 295

PONDR

226, 238

 

 

 

 

position specific score matrix

325

potential energy functions

45, 48

potential function

9, 71–76, 85–86, 88, 93–95,

97–99

 

 

 

 

 

 

 

 

power distance

185

 

 

 

 

PRALINE

229

 

 

 

 

 

profile analysis

324, 346

 

 

profile-based 6, 8

 

 

 

 

 

profile-profile alignment

6, 8–9

PROFsec 229, 233, 235–236

protein classification

165, 168, 174

protein complexes

3, 15, 25

 

protein design

71–72, 94, 99, 105–106

protein family

4

 

 

 

 

 

protein fold

7, 11, 105

 

 

Protein folding

9–10, 50, 59, 71–72, 84, 94, 99,

101

 

 

 

 

 

 

 

 

protein folding simulation

9

 

Protein force fields

54–58

 

protein function

195–200

 

protein interaction pathways

323

protein structure alignment

147, 174

protein surface evolution

197

protein threading

7, 102, 148, 291, 293–294

protein-protein docking

13, 15, 26, 72, 103,

200

 

 

 

 

 

 

 

 

Index

393

protofilament 280, 283–286, 292, 294,

296–298, 302, 305

Pseudo-atomic model 359

PSI (Protein Structure Index)

161–162, 165

PSI-blast 8, 168–171, 212

 

 

 

PSIPred

212, 233

 

 

 

 

PSSM (Position Specific Scoring Matrix)

7–8,

212, 233–235, 325

 

 

 

PUU 23, 139, 141–142

 

 

 

QM 45, 48, 51–56

 

 

 

 

quantum mechanical

45, 71

 

 

 

quasi-chemical approximation

80

 

 

RADAR

227, 240–241

 

 

 

reduced models

 

10

 

 

 

 

re-entrant surface

184, 187

 

 

 

reference frame

 

155–156, 158, 257

 

reference state

72, 75–76, 80

 

 

refolding

1, 281–282

 

 

 

remote homolog

 

212, 319

 

 

 

remote homology recognition

6

 

 

REP 241

 

 

 

 

 

 

repeats detection

 

226–227, 232, 241, 243

replica-exchange

 

49

 

 

 

REPRO

 

227, 240

 

 

 

 

Resolution dependency 363

 

 

 

RESP

53–55, 58

 

 

 

 

reverse Boltzmann Principle

7

 

 

rigid-body assembly

321

 

 

 

Root mean square deviation (RMSD)

257

Root Mean Square Distance

150, 175, 195, 197,

327,

343

 

 

 

 

 

 

ROSETTA 9, 11, 12, 15, 29, 103, 107, 336

Rule-based filtering

269

 

 

 

salt bridges 221, 266, 326

 

 

 

SAM 8, 168, 234–235, 325

 

 

scanning proline mutagenesis

284

 

 

SCOP 22, 23, 126, 137,139, 158, 164,

 

166–169

 

 

 

 

 

 

scoring matrix

8, 151, 153, 197, 212, 335, 337

SCR (structurally conserved region)

5

 

secondary structure prediction

18–19, 207–220,

222,

224

 

 

 

 

 

 

segment assembling

11

 

 

 

Segment clustering

366

 

 

 

segment matching

327–329

 

 

 

Self-organizing map algorithm (SOM)

267

semi-empirical effective potential function

72

Sensitivity 6, 8–9, 19–20, 24, 176, 198, 211,

237,

243

 

 

 

 

 

 

sequence alignment 4–8, 23 sequence analysis 196

Sequence conservation 23–24, 262, 265, 267,

296

Sequence dependency of partition function 110

Sequence profile

6, 8, 12, 262, 265–268, 325,

346

 

 

 

 

sequence similarity

6, 166, 197, 221, 227, 229,

294, 320

 

 

 

 

sequence-structure alignment 8,24, 29, 295

Sheetminer

360–365

 

Sheettracer 359, 366–373, 383

side-chain prediction

13, 333–334

side-chains 73, 230

 

simplices 90, 186–189, 191, 195

simplicial complex

186–187, 189

sink 137, 190–191

 

size, domain

24, 133–134, 138

size, interface

103

 

 

Skeleton of Secondary Structure

373

solid state NMR

284, 286, 291, 293, 295, 304

solvent accessibility

7, 50, 74, 90, 239, 266,

286, 325, 334

 

 

 

solvent accessible surface (SA)

73, 183–184,

188, 195, 200, 332, 342

 

solvent ball

183–184, 191

 

space filling model

182

 

spatial restraints

5, 13, 329

 

SPC 49–50, 52, 55

SPC/E 49–50

specificity 13–14, 19, 198, 224, 322, 362–363, 367, 369–370, 372

sphere intersection graph (SIG) 261–262

SSAP 152–153, 167 SSPro 229, 233–234, 236 star alignment 159 statistical energy 92, 111

statistical potential 7, 23, 71, 74, 76, 85, 88, 90,

94, 105–109, 113, 115

statistical potential function 74, 76, 85,

107–108, 113

structure determination 30, 359, 384 structural differences 13–14, 284, 303

structural genomics 9, 16–17, 29–30, 125–126,

200, 319, 321–323

structural motif 147, 149, 157–158, 175, 221,

272

structure alignment 8, 24, 29, 147, 149–150,

152, 157, 159–161, 167, 174 structure prediction software 232 structure refinement 110, 114, 373 structure template 7, 24

394

 

 

 

 

 

 

 

 

 

 

 

 

 

Index

structure-sequence conservation

23, 262, 265,

tracing secondary structure

296

 

 

 

 

 

 

 

TRILOGY

158

 

 

 

substitution matrices

324

 

 

 

triplet

110, 162–163

 

substrate specificities

323

 

 

 

TRUST

227, 243

 

superfamily 164, 166, 168–173, 239

 

 

 

 

 

 

 

super-secondary structure prediction

236, 243

unfolding-induced aggregation 280–281

support vector machines (SVMs)

20, 210, 217,

union of balls

182–183, 188, 202

222–223, 235

 

 

 

 

 

united atom

54, 58, 182, 301–302

supramolecular complex

27

 

 

united atom force field

58

SVR (structurally conserved region)

4–5

up-down bundle

377

 

SWISS-MODEL 5, 344–345

 

 

Urey-Bradley

46–47, 51–52

SymSSP 236

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

van der Waals radii

133, 182, 342

Template 3–9, 12–13, 22, 24, 27–28, 196, 198,

variable regions

4, 209, 321–322, 326–327,

230, 255–256, 268, 272, 294–295, 320–340,

330, 336, 344

 

 

 

343–346

 

 

 

 

 

 

Vast 23, 156, 161, 164–165, 169–171

template consensus sequences 324

 

vibrational spectra

48, 52, 55

tertiary structure prediction

9, 207, 230

voids 87, 190–191, 193–197

TESS

158

 

 

 

 

 

 

volume exclusion

 

109

 

thermodynamic analysis

290

 

 

Voronoi cell

133, 184–187

thermodynamic control of folding

280

Voronoi diagram

 

88, 184–186, 191,

thermodynamic hypothesis

71, 94, 115

193–194

 

 

 

 

threading 6–9, 12, 22, 24, 27–29, 102, 106,

Voronoi edge

89, 186–187

148, 222, 224, 256, 291, 293–296, 384

Voronoi plane

186, 188

Tinker

60

 

 

 

 

 

 

 

 

 

 

 

 

 

TIP3P 49, 52, 55

 

 

 

 

 

WD-repeats

273

 

 

TIP4P 49–50, 52, 55

 

 

 

 

 

 

 

 

 

 

 

topological structure

186, 190, 200–201

X-ray crystallography

17, 181, 319, 323, 359

topology 18, 21, 167, 186, 201, 210, 231, 260,

X-ray diffraction

 

20, 22, 181–182, 279, 284,

359–360, 373–375, 377–383

 

 

292,

365

 

 

 

 

topology model

18, 20–21

 

 

 

X-ray fiber diffraction

289

TOPS diagram

260

 

 

 

 

 

 

 

 

 

 

 

 

torsion angle 5, 46–47, 333–334, 337, 341

YASPIN

216, 234

 

(continued from page ii)

Physics of the Human Body: A Physical View of Physiology Herman, I.P., 2006

Intermediate Physics for Medicine and Biology Hobbie, R.K., Roth, B., 2006

Computational Methods for Protein Structure Prediction and Modeling (2 volume set) Xu, Y., Xu, D., Liang, J. (Eds.) 2006

Artificial Sight: Basic Research, Biomedical Engineering, and Clinical Advances, Humayun, Weiland, Greenbaum., 2006

Physics and Energy Landscapes of Proteins Fraunfelder, H., Austin, R., Chan. S., 2006

Biological Membrane Ion Channels Chung, S.H., Anderson, O.S., Krishnamurthy, V.V., 2006

Cell Motility, Lenz, P., 2007

Applications of Physics in Radiation Oncology, Goitein, M., 2007

Statistical Physics of Macromolecules, Khokhlov, A., Grosberg, A.Y., Pande, V.S. 2007

Biological Physics, Benedek, G., Villars, F., 2007

Protein Structure Protein Modeling, Kurochikina, N., 2007

Three-Dimensional Shape Perception, Zaidi, Q., 2007

Structural Approaches to Sequence Evolution, Bastolla, U.

Radiobiologically Optimized Radiation Therapy, Brahme, A.

Biological Optical Microscopy, Cheng, P.

Microscopic Imaging, Gu, M.

Deciphering Complex Signatures: Applications in Life Sciences, Morfill, G.

Biomedical Opto-Acoustics, Oraevsky, A.A.

Mathematical Methods in Biology: Mathematics for Ecology and Environmental Sciences,

Takeuchi, Y.

Mathematical Methods in Biology: Mathematics for Life Science and Medicine, Takeuchi, Y.

In Vivo Optical Biopsy of the Human Retina, Drexler, W., Fujimoto, J.

Tissue Engineering: Scaffold Material, Design and Fabrication Principles, Hutmacher, D.W.

Ion Beam Therapy, Kraft, G.H.

Biomaterials Engineering: Implants, Materials and Tissues, Helsen, J.A.

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