Greetings,
I am interested in performing docking calculations for a 1:1 proteinA:proteinB
complex based on the a) pre-determined DelChi tensor (via Paramagpy) for the
lanthanide-tagged protein (protein A), b) measured PCS on the partner (protein
B), and CSPs on both sides of the interface. In this case, I am using a model
system where I already know the complex structure, so I am starting from
components where any adjustment upon binding will be minimal (i.e. it should be
fine to do rigid body docking). In scouring what might already be available
for this calculation, I found the script pasted below, which was included as
part of the supplementary material for this paper: Saio, et al, J Biomol NMR
(2010) 46:271–280.
Essentially, the procedure is to keep the lanthanide and the component ( from
which the DelChi tensor was determined, protein A) fixed, and then dock protein
B onto this based on the measured PCS and CSPs. In this case, it should work
since I already know the complex structure and since I can see that the DelChi
tensor is nicely predicting the PCS measured for protein B.
My question is, since the procedure below was reported some time ago, might
there be anything newer with better performance that I might have missed?
Many thanks,
Andy
parameter
@TOPPAR:parallhdg.pro
end
structure
@D.psf
@K.psf
@tb.psf
@axis_new_500.psf
@axis_new_600.psf
end
delete select
((resi 100 and name ot2) or (resi 300 and name ot2))
end
delete select
((resi 64 and name he2) or (resi 264 and name he2) or (resi 1) or (resi
201))
end
evaluate ($knoe = 0.01) !0.01)
evaluate ($kandb = 0.001)
evaluate ($kimdb = 0.001)
evaluate ($kvirt1doverall=0.0)
evaluate ($kvirt1d=0.001)
evaluate ($kvirt2d=0.001)
evaluate ($kvirt3d=0.001)
evaluate ($k_ncs = 200.01)
! Read experimental restraints
noe
nres=30000
class tensor
@tensors.tbl
class others
@metalcenter.tbl
class all
@NK-nonL3D_CSdel.tbl
end
noe
ceiling=10
averaging * cent
potential * soft
scale tensor 500.
scale others 50.
sqoffset * 0.0
sqconstant * 1.0
sqexponent * 2
soexponent * 1
asymptote * 0.1
rswitch * 0.5
!-for Chem Shift restraints-!
averaging all r-6
scale all $knoe
end
flags exclude * include bonds angle impr vdw noe xpcs xrdc xccr xang end
vector do (fbeta=10) (all)
vector do (mass=100) (all)
xpcs
nres=2000
class thulium
force 0.8
coeff -7320 -4641
@TmPdel2.tbl
class terbium
force 0.8
coeff 12015 6074
@TbPdel2.tbl
end
evaluate ($rcon = 0.003)
parameter
nbonds
repel=1.0
rexp=2
irexp=2
rcon=$rcon
nbxmod=3
wmin=0.01
cutnb=4.5 ctonnb=2.99 ctofnb=3.
tolerance=0.5
end
end
set abort off end
constraints inter (resid 2:100) (resid 202:300) end
! read tensor pdb
coordinates @axis_xyzo_3_500.pdb
coordinates @axis_xyzo_3_600.pdb
evaluate ($end_count=10)
evaluate ($count = 0)
while ($count < $end_count ) loop main
evaluate ($count=$count+1)
evaluate ($nodenum=$count+0)
evaluate ($med="med_str/med_"+encode($nodenum)+".pdb")
coordinates @@$med
!!=== minimization ===!!
evaluate ($cool_steps = 3000)
evaluate ($init_t = 3000.01)
evaluate ($ini_rad = 1.0) evaluate ($fin_rad = 0.78)
evaluate ($ini_con= 0.004) evaluate ($fin_con= 1.0)
evaluate ($ini_ang = 1.0) evaluate ($fin_ang = 1.0)
evaluate ($ini_imp = 1.0) evaluate ($fin_imp = 1.0)
evaluate ($ini_noe = 0.01)
evaluate ($fin_noe = 0.01)
evaluate ($knoe = $ini_noe) ! slope of NOE potential
flags exclude * include bonds angle impr vdw noe xpcs xrdc xccr xang end
parameters
nbonds
atom
nbxmod 3
wmin = 0.01
cutnb = 4.5
tolerance 0.5
repel= 1.0
rexp = 2
irex = 2
rcon = 4
end
end
dynamics internal
reset
itype=powell
stepsize = 0.1
nstep=1000
depred=1
fix = (resi 2:100)
fix = (resi 400)
group = (resi 202:300)
group = (resi 500)
group = (resi 600)
etol = 0.0000001
gtol = 0.0000001
nprint= 1
end
evaluate ($final_t = 100) { K }
evaluate ($tempstep = 200) { K }
evaluate ($ncycle = ($init_t-$final_t)/$tempstep)
evaluate ($nstep = int($cool_steps*1.6/$ncycle))
evaluate ($bath = $init_t)
evaluate ($k_vdw = $ini_con)
evaluate ($k_vdwfact = ($fin_con/$ini_con)^(1/$ncycle))
evaluate ($radius= $ini_rad)
evaluate ($radfact = ($fin_rad/$ini_rad)^(1/$ncycle))
evaluate ($k_ang = $ini_ang)
evaluate ($ang_fac = ($fin_ang/$ini_ang)^(1/$ncycle))
evaluate ($k_imp = $ini_imp)
evaluate ($imp_fac = ($fin_imp/$ini_imp)^(1/$ncycle))
evaluate ($noe_fac = ($fin_noe/$ini_noe)^(1/$ncycle))
evaluate ($knoe = $ini_noe)
flags exclude * include bonds angle impr vdw noe xpcs xrdc xccr xang end
evaluate ($i_cool = 0)
while ($i_cool < $ncycle) loop cool
evaluate ($i_cool=$i_cool+1)
evaluate ($bath = $bath - $tempstep)
evaluate ($k_vdw=min($fin_con,$k_vdw*$k_vdwfact))
evaluate ($radius=max($fin_rad,$radius*$radfact))
evaluate ($k_ang = $k_ang*$ang_fac)
evaluate ($k_imp = $k_imp*$imp_fac)
evaluate ($knoe = $knoe*$noe_fac)
parameter
nbonds
cutnb=4.5 rcon=$k_vdw nbxmod=3 repel=$radius
end end
noe scale all $knoe end
dynamics internal
itype=powell
nstep=1000
depred=1
end
end loop cool
dynamics internal
itype=powell
nstep=1000
depred=1
end
flags exclude * include bonds angle impr vdw noe xpcs xrdc xccr xang end
dynamics internal
itype=powell
nstep=1000
depred=1
end
flags exclude * include bonds angle impr vdw noe xpcs xrdc xccr xang end
noe scale all 1.0 end
parameter nbonds rcon 3 repel 0.78 end end
dynamics internal
itype=powell
nstep=1000
depred=1
end
flags exclude * include bonds angle impr vdw noe xpcs xrdc xccr xang end
noe scale all 1.0 end
dynamics internal
itype=powell
nstep=1000
depred=1
end
flags exclude * include bonds angle impr vdw noe xpcs xrdc xccr xang end
noe scale all 1.0 end
parameter nbonds rcon 3 repel 0.78 end end
dynamics internal
itype=powell
nstep=1000
depred=1
end
!!=== Write out the final structure ===!!
print threshold=0.5 noe
evaluate ($rms_noe=$result)
evaluate ($violations_noe=$violations)
xpcs print threshold 0.15 all end
evaluate ($rms_xpcs=$result)
evaluate ($violations_xpcs=$violations)
print thres=0.05 bonds
evaluate ($rms_bonds=$result)
print thres=5. angles
evaluate ($rms_angles=$result)
print thres=5. impropers
evaluate ($rms_impropers=$result)
remarks ============================================================
remarks overall,bonds,angles,improper,vdw,noe
remarks totalE : $ener, $bond, $angl, $impr, $vdw, $noe
remarks
remarks xpcs,xrdc,xccr,xang
remarks energies: $xpcs, $xrdc, $xccr, $xang
remarks ============================================================
remarks bonds,angles,impropers,noe
remarks rms-d: $rms_bonds,$rms_angles,$rms_impropers,$rms_noe
remarks
remarks xpcs,xrdc,xccr,xang
remarks rms-d: $rms_xpcs,$rms_xrdc,$rms_xccr,$rms_xang
remarks ============================================================
remarks noe
remarks violations.: $violations_noe
remarks
remarks
remarks xpcs,xrdc,xccr
remarks violations.: $violations_xpcs,$violations_xrdc,$violations_xccr
remarks xang
remarks violations.: $violations_xang
remarks ============================================================
evaluate ($filename = "FINAL/comp_" + encode($nodenum) + ".pdb")
write coordinates output=$filename end
end loop main
stop
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