Prime User Manual - ISP

140
Index
polar residues .................................................... 33
position-specific substitutional matrix (PSSM) 33
Positives column ............................................... 23
Preferences........................................................ 12
command .................................................... 11
Prime Guide .................................................. 8, 13
Prime menu bar............................................... 8, 9
Prime runs ........................................................... 5
Prime Sequence Viewer ...................................... 8
Prime toolbar................................................. 8, 13
Prime workflow................................................... 9
Prime-Refinement ......................................... 1, 51
Prime–Structure Prediction....................... 1, 7, 17
processors, maximum number .......................... 65
product installation.......................................... 131
programs, third-party ...................................... 121
Project Table ............................................. 16, 136
projects............................................................ 136
proximity........................................................... 11
Proximity color scheme .................................... 11
proximity cutoff .......................................... 11, 12
PSIPRED ........................................................ 121
Q
query sequence................................................ 136
query, maximum length .............................. 18, 25
R
random seed, for side-chain prediction............. 64
Ranking Score................................................. 136
read sequence.................................................... 18
records
ATOM....................................................... 125
SEQRES ................................................... 125
Refine Structure ................................................ 16
Refinement .......................................................... 1
refinement ....................................................... 136
cooperative.................................................. 60
protocols ..................................................... 51
Refinement panel .............................................. 51
regions
aligned ........................................................ 36
of multiple templates .................................. 36
of templates, setting.................................... 36
Rename command............................................... 6
Res1................................................................... 59
Prime 2.5 User Manual
Res2................................................................... 59
Residue Matching color scheme ....................... 11
residue names, correcting for receptor-ligand
complex.......................................................... 54
Residue Property color scheme......................... 11
Residue Type color scheme .............................. 11
residues
charged........................................................ 33
conserved.............................................. 36, 47
hydrophobic................................................ 33
incomplete .................................................. 61
missing...................................................... 125
non-conserved............................................. 36
nonstandard................................................. 52
polar............................................................ 33
standard, list of ........................................... 51
variable ....................................................... 47
rotamers............................................................. 37
ruler..................................................................... 8
Run SSP ................................................ 31, 44, 46
runs.......................................................... 5, 6, 136
S
sampling accuracy, loop refinement.................. 64
Save As ......................................................... 6, 25
saving Prime runs................................................ 6
Schrödinger contact information..................... 132
schrodinger.hosts file............................ 14
SCOP domains.................................................. 47
score
alignment .................................................... 34
BLAST bit .................................................. 23
Z.................................................................. 46
scratch projects.................................................... 5
Search program
in Find Homologs....................................... 20
in Fold Recognition .................................... 47
secondary structure assignment .................. 14, 33
Secondary Structure color scheme.................... 11
secondary structure prediction programs........ 121
See also SSPs
Select toolbar command.................................... 13
seqconvert utility.......................... 30, 43, 116
SEQRES records............................................. 125
sequence identity............................................... 23
sequence positives............................................. 23
Sequence Viewer (Prime).............................. 8, 21