Prime User Manual - ISP

K
killing jobs ........................................................ 15
L
leaving group
ligand .......................................................... 78
receptor....................................................... 79
libraries
backbone dihedral....................................... 40
side-chain rotamer ...................................... 40
ligands................................................. 36, 37, 135
covalently bound......................................... 51
ligands, covalently bound ........................... 52, 77
lipophilic term................................................... 69
locking gaps ................................................ 14, 33
log file ............................................................... 38
loop refinement ................................................. 51
cooperative.................................................. 60
invalid features check ................................. 60
options ........................................................ 64
order of ....................................................... 60
settings........................................................ 59
time required............................................... 59
loops................................................................ 136
M
Maestro, starting ................................................. 3
Manual Threading............................................. 33
maximum length ............................................... 25
maximum sequence length................................ 18
menu bar (Prime) ............................................ 8, 9
menus
Display (Prime) .................................... 10, 13
Edit (Prime) ................................................ 13
File (Prime)............................................. 6, 14
merging projects.................................................. 5
metals, bonds to ................................................ 52
minimization ............................................... 36, 62
missing residues.............................................. 125
Monitor panel................................................ 8, 38
monitoring jobs ................................................. 15
mouse functions ............................................ 8, 22
multimers, building ........................................... 88
multiple chains
building as multimer................................... 88
with same sequence .................................... 18
Index
with SKA.................................................. 102
multiple sequences............................................ 18
multiple templates............................................. 36
exporting................................................... 115
N
NAME_pfam sequence ..................................... 21
names
chains.......................................................... 23
extracting sequence..................................... 18
non-unique.................................................. 18
sequences.............................................. 18, 23
native Schrödinger format................................. 30
New command .................................................... 6
non-conserved residues..................................... 36
None color scheme............................................ 10
N-terminal gaps........................................... 13, 33
O
Open command ................................................... 6
OPLS_2005 force field ................... 40, 52, 58, 62
optimizing side chains....................................... 37
options
job........................................................... 9, 14
in panel layout .............................................. 8
P
panel layout......................................................... 7
panels
Job Options................................................. 14
Monitor......................................................... 8
path
Comparative Modeling ................. 1, 9, 17, 25
Threading.................................................... 17
PDB........................................................... 47, 121
ATOM records .......................................... 125
chain ID ...................................................... 23
header ......................................................... 18
ID code ....................................................... 23
SEQRES ................................................... 125
updating database ..................................... 120
PDB atom names, correcting for receptor-ligand
complex.......................................................... 54
Pfam .................................................... 21, 28, 121
PIR .................................................................... 18
plus sign (+), in Pfam sequence ........................ 21
Prime 2.5 User Manual 139