Biopolymer

Index

A  B  C  D  E  F  G  H  I  L  M  N  O  P  Q  R  S  T  V  W 

A

-carbon (see C atom)

-carbon trace 31

-helices 7

amino acids 5

anomeric form (see monosaccharides)

Arnott and Hukins 1972 19

Arnott and Selsing 1974 19

Arnott et al. 1972 19

Assembly pulldown

Associate command 20

Atom pulldown 1

backbone 3, 5

building 31

tutorial 4, 32

combining virtual torsion constraint with bond angle to predict the backbone conformation from an -carbon trace 38

construction 31

from fragments of known protein structures 33

directed conformational 33

incremental construction 33

torsions 5

backbone (see also -carbon trace)

Bassolino-Klimas and Bruccoleri 1992 33

Biopolymer module 1, 3

Boberg et al., 1992 41

bond angle constraint 32

and peptide plane angles 35

comparison with other methods

by analogy with similar structures 33

the directed conformational search method 33

the incremental approach 33

the method of Rey and Skolnick 33

illustration 34

in the Protein/Backbone command 34

mathematical formulation of 36

Brookhaven Protein Databank (PDB) 31

protein information format 52

searching 11

-sheet 7

-strands 7

Builder module 1

C atoms 5, 33, 35

coordinates for given proteins 31

inter-C distances 46

Carbo pulldown (see also carbohydrates) 1, 25, 26

Alpha_Beta command 30

Append command 27

Join command 27

L_D command 30

Replace command 30

carbohydrates 25

building 26

Append and Join commands 27

bonding 28

dehydration reaction 27

dihedral angles 29

from monosaccharides 27

linkage types 29

oligosaccharides 25

polysaccharides 25

fragment library 27

modifying

an existing carbohydrate 29

Replace command 30

Pilot tutorial 26

C atom 32, 33

chirality

of replacing residue 8

clusters (see domains)

Correa 1990 33

database

protein structural information 52

query

browsing database search results 55

four types of information used to define a structure database query 53

inter-template constraints 59

intra-template constraints 58

proteins to search 53

residue and secondary structure types 56

restricting torsions on main chain and side chain 57

search constraints 53

parameters 53

templates 53

search 52, 61

program 51

structural 51

tutorial 51

dehydration reaction 27

deoxyribonucleic acid (DNA) 13

domain analysis

query structures 46

tutorials 45

domains 45

browsing results 48

clustering algorithm 46

clusters

creation of 48

loading 48

cutoff for the increase of the average interdomain distance 47, 48

definition 46, 48

inter-C distances 46

loop regions 47

offspring distance cutoff 47, 48

union, intersection and difference operations 48

exclusion range of residues 60

files

$BIOSYM/data/biopolymer/database.dat 51, 52, 54

$BIOSYM/data/biopolymer/wildcard.dat 57

$BIOSYM/gifts/biopolymer/structure.db 51

Forcefield pulldown 1

Fragment pulldown 1

glycolipids 25

glycoproteins 25

Holm and Sander 1991 33

Hoogsten

base pairing 15

IUPAC-IUB 1970 36

Levitt 1992 33

Luo et al. 1992 34, 36, 39, 40

Modify pulldown 1

Unmerge command 20

monosaccharides

altering anomeric configuration 30

anomeric form 30

custom 26

predefined library 25

replacing one with another 30

tutorial 26

Nishikawa et al. 1974 36, 38

nucleic acids 13

"standard" form 19

bases 13

building 13

building and manipulating 18

helical structures 14, 16, 17

ligation 23

sense and antisense strands 16

structure 14

Nucleic_Acid pulldown 1, 13

Ligate command 23

Prime command 23

Nucleotide pulldown 1, 13

Append command 19, 23

Delete command 20

Measure command 19, 22

Replace command 21

oligosaccharides 25

tutorial 26

Payne 1993 34, 36, 40, 43

PDB (see Brookhaven Protein Databank)

peptide bond 5

Pilot tutorials 2, 4, 25, 26, 31, 32, 45, 51

polymers 5

linear 13

polysaccharides 25

constructing 27

primary structure 5

protein backbones

algorithm used by the Protein/Backbone command 40

bond angle constraint (see also bond angle constraint)

construction

bond angle constraint method 32

dynamic programming algorithm 40

Pilot tutorial 32

protein backbone algorithm

accuracy of 43

atom coordinates calculated 41

break threshold parameter 40

cis threshold 40

described 40

dynamic programming algorithm 41

Ramachandran cost 41

virtual torsion constraint (see also virtual torsion constraint)

Protein pulldown 1, 3, 31, 32, 45

Backbone command 1, 10, 31, 34, 40

implementation 43

Cap command 9

DispLoop command 11

Domain_Analysis command 1, 45, 46, 47

Dom_Diff parameter 49

Dom_Frac parameter 49

Domain_Action parameter 49

Domain_Clusters parameter 50

Domain_Subsets parameter 50

Max_Dom_Num parameter 49

Protein_ID parameter 49

Run_Name parameter 50

typical task 47

List command 9

Rename command 9

SearchLoop command 11

tutorial 4

Secondary command 9

SpliceLoop command 12

Turn command 10

proteins 3, 5

building 3

domains 46

Pseudo_Atom pulldown 1

Purisima and Scheraga 1984 34, 36, 39, 40

quaternary structure 7

query structures

domain analysis 46

Ramachandran plot 5

Reid and Thornton 1989 33

residue and secondary structure types 56

Residue pulldown 1, 3

Append command 8

Auto_Rotamer command 10

Delete command 8

Manual_Rotamer command 10

Rename command 20

Repeat command 8

Replace command 8

Rey and Skolnick 1993 33

ribonucleic acid (RNA) 13

RNA (see also ribonucleic acid)

Saenger 1984 14

searching

the structure database 52

secondary structure 5

characteristic properties of 7

side chain 3

tutorial 4

solvent simulations

tutorial 4

Str_DB pulldown 1

Create_DB command 63

Delete_Query command 63

InterTmplt_Cnstrnt command 59

Intertmplt_Cnstrnt command 63

Intratmplt_Cnstrnt command 63

List_Query command 63

Read_Search_Results command 63

Run_Search command 63

tertiary structure 7

tutorials

backbone building 4

customizing monosaccharides 26

oligosaccharides/polysaccharides 26

SearchLoop command 4

side chain conformations with rotamers 4

solvent simulations 4

virtual torsion constraint 38

combining with bond angle to predict the backbone conformation from an -carbon trace 38

Wako and Scheraga 1982 36

Watson 1976 15, 18

Watson-Crick

base pairing 14