# YASARA MACRO

# TOPIC: 5. Structure prediction

# TITLE: Docking a ligand to a receptor ensemble with flexible side-chains
# REQUIRES: Structure
# AUTHOR: Elmar Krieger
# LICENSE: GPL
# DESCRIPTION: This macro runs VINA or AutoDock to predict the structure of a
ligand-receptor complex. Receptor flexibility is considered by creating a receptor
ensemble with alternative high-scoring solutions of the side-chain rotamer network.
An analysis log file is written at the end. The macro can also continue a docking
run that got interrupted, especially if the scene has not been moved or rotated
manually during the docking.

# Parameter section - adjust as needed, but NOTE that some changes only take effect
# if you start an entirely new docking job, not if you continue an existing one.
# =================================================================================

# You can either set the target structure by clicking on Options > Macro > Set
target,
# by providing it as command line argument (see docs at Essentials > The command
line),
# or by uncommenting the line below and specifying it directly.
#MacroTarget='/home/myname/projects/docking/1sdf'

# Docking method, either AutoDockLGA or VINA

method='VINA'

# Size of the receptor ensemble with alternative side-chain rotamers.

# Not used if you provide your own ensemble.
receptors=5

# Number of docking runs per receptor ensemble member, '0' leaves the choice to
YASARA.
# (maximally 999, each run can take up to an hour).
# The total number of docking runs is receptors*receptorruns.
receptorruns=0

# Docking results usually cluster around certain hot spot conformations,

# and the lowest energy complex in each cluster is saved. Two complexes belong to
# different clusters if the ligand RMSD is larger than this minimum [A]:
rmsdmin=5.0

# Set to 0 if you don't want to merge clusters from the receptor ensemble members
# in the end (merging keeps only one cluster within the 'rmsdmin' limit set above).
merged=1

# Set to 1 to keep the ligand completely rigid (alternatively you can provide
# the ligand as a *.yob file and fix certain dihedral angles only).
rigid=0

# A selection of receptor residues whose side-chains should be kept flexible, e.g.

# flexres = 'Lys 91 Leu 100', or (if the receptor is not a monomer)
# flexres = 'Res Lys 91 Mol A or Res Leu 100 Mol B'.
# Alternatively you can provide the receptor as a *.sce or *.yob file with fixed
# atoms, which gives better control (e.g. you can keep only part of a side-chain
# or even a terminal backbone flexible, but not loops in the middle).
flexres=''

# The docking temperature. This currently affects the receptor flexibility only
temp='298K'

# Flag if a scene with all results should be saved for visualization with
dock_play.mcr.
# If you use a large receptor ensemble with large ligands and many docking runs, it
may
# exhaust the available memory to show them all together on screen. In this case
set
# scesaved to 0. The docking result player will then only show clusters but not all
results,
# which can of course still be found in the logfile.
scesaved=1

# YASARA commands follow below, no '=' is used

# --------------------------------------------

# Force field used for charge assignment (AutoDock only, not VINA) and to determine
which ligand bonds can rotate.
# Do not change to an in vacuo force field (NOVA), all other force fields should
work too (not tested).
ForceField AMBER03

# Uncomment below to set a certain random seed

# RandomSeed 1000

# Normally no change required below this point

# ============================================

chargefof = ForceField
if !receptorruns
# For an optimum speed/accuracy tradeoff, we select at least 20 runs, but more if
CPUs are available
cpus = Processors
receptorruns=cpus
while receptorruns<20
receptorruns=receptorruns+cpus

# Sanity checks
if MacroTarget==''
RaiseError "This macro requires a target. Either edit the macro file or click
Options > Macro > Set target to choose a target structure"
if receptors>999 or receptorruns>999 or receptors*receptorruns>9999
RaiseError 'Too many docking runs selected, (receptors)/(receptorruns) would take
forever'

structlist='receptor','ligand'

Clear
# Do we have a user-supplied ensemble?
ensfilename='(MacroTarget)_receptor_ensemble.sce'
scene = FileSize (ensfilename)
if !scene
# Do we already have an automatically generated receptor ensemble scene?
ensfilename='(MacroTarget)_receptor_ensemble(receptors).sce'
scene = FileSize (ensfilename)
if !scene
# Not yet. Do we have a receptor scene?
scefilename='(MacroTarget)_receptor.sce'
scene = FileSize (scefilename)
 if !scene
# No, load PDB or YOB file of receptor and ligand (only needed to determine
cell size)
for struct in structlist
(struct)=0
for type in 'yob','pdb','sdf','mol2'
filename='(MacroTarget)_(struct).(type)'
exists = FileSize (filename)
if exists and (type=='yob' or type=='pdb' or struct=='ligand')
(struct) = Load(type) (filename)
break
if not (struct)
RaiseError 'The (struct) was not found at (MacroTarget)_(struct).* Please
follow the instructions in the "Recipes" section exactly, especially when setting
the macro target'
# Orient the receptor, create a docking cell that includes the entire receptor
# and also has enough empty space around to accomodate the ligand (which has to
# be removed temporarily, since 'Cell Auto' encloses the entire soup).
ligandradius = RadiusObj (ligand)
NiceOriObj (receptor)
# Ligand was only needed to determine the required cell size, will be loaded
later
DelObj (ligand)
Cell Auto,Extension=(ligandradius*2)
else
# Load receptor scene
LoadSce (scefilename)
# Verify that the cell is present
simcell = CountObj SimCell
if !simcell
RaiseError 'If you provide a scene, it must contain a simulation cell, but
none was found in (scefilename)'
if Objects>2
# We can't continue, because the ensemble can only be created for a single
object
RaiseError 'Your scene contains (Objects) objects, while only the receptor
and the docking cell are expected.'
# Warn if the cell is too large
x,y,z = Cell
if x>96 or y>96 or z>96
ShowMessage "A cell axis is longer than 96 A, which may reduce docking
accuracy. Consider focusing on the active site."
Wait ContinueButton
HideMessage
# To create a receptor ensemble, the entire receptor must be inside the cell,
# so we remember the current cell and add it again later
x,y,z = Cell
posorilist() = PosOriObj SimCell
DelObj SimCell
# Start an energy minimization but stop immediately.
# This cleans the structure in case it was supplied without hydrogens.
ForceField (chargefof)
ShowMessage 'Checking if receptor is ready for docking...'
Experiment Minimization
Experiment On
Experiment Off
# Create a receptor ensemble with flexibility corresponding to the specified
temperature
ShowMessage 'Creating receptor ensemble with (receptors) members, each with
alternative high-scoring side-chain conformations...'
Style Ribbon,Stick
ForceField YASARA2
Temp (temp)
# Don't change side-chain rotamers of residues with dative bonds to metals
FixRes all with arrow to metal
OptimizeAll Method=SCWALL,Structures=(receptors-1)
FreeAll
DelObj SimCell
NumberObj all,1
# Add original cell again
Cell (x),(y),(z)
PosOriObj SimCell,(posorilist)
# Optimize the hydrogen bonding network of the ensemble members
RemoveObj !SimCell
for i=1 to receptors
AddObj (i)
ShowMessage 'Optimizing hydrogen bonding network of receptor ensemble member
(i)/(receptors)...'
OptHydAll
NameObj (i),Receptor(i)
RemoveObj (i)
AddObj !SimCell
SaveSce (ensfilename)
HideMessage
# Load receptor ensemble scene
LoadSce (ensfilename)
# The segment name C*** is used to tag ligand Conformations, and cannot be used for
the receptor
hit = ListAtom Segment C???
if hit
MarkAtom (hit)
segname = SegAtom (hit)
RaiseError 'Segment names starting with "C" are unfortunately reserved to
identify ligand conformations, please click "Edit > Name > Segment" to rename the
receptor segment "(segname)"'
# The molecule name 'l' is reserved for the ligand
hit = ListAtom Mol l
if hit
RaiseError 'The receptor must not contain a molecule named "l", please click Edit
> Name > Molecule and try again'
# Docking is done without periodic boundaries
Boundary Wall
Longrange None
ForceField (chargefof)
# Count receptors, in case the user provided the ensemble
receptors = CountObj !SimCell
runs=receptors*receptorruns
# Loop over the receptors in the ensemble
RemoveObj !SimCell
for i=1 to receptors
AddObj (i)
# Show progress (ShowMessage is used by the docking experiment)
LabelAll 'Receptor ensemble member (i)/(receptors)',Height=0.3,Color=Yellow,Y=3.0
# Load the ligand for this receptor ensemble member
ligand=0
for type in 'yob','pdb','sdf','mol2'
filename='(MacroTarget)_ligand.(type)'
exists = FileSize (filename)
 if exists
ligand = Load(type) (filename)
break
if not ligand
RaiseError 'The ligand was not found at (MacroTarget)_ligand.* Please follow
the instructions in the "Recipes" section exactly, especially when setting the
macro target'
# Just in case a user-defined ensemble was loaded
NameObj (i),Receptor(i)
# Number the ligands sequentially
NameObj (ligand),Ligand(i)
# Keep selected side-chains flexible
if flexres!=''
FixObj (i)
FreeAtom Res (flexres) Sidechain and Obj (i)
FixRes Cys Atom SG with bond to Atom SG or Ala Pro and Obj (i)
# Do not show secondary structure for protein ligands, this slows things down
HideSecStrObj Ligand(i)
ShowObj Ligand(i)
StickObj Ligand(i)
# Fix ligand's internal degrees of freedom if requested
if rigid
FixObj Ligand(i)
# Align ligand with the cell (to end up with the same local atom coordinates
independent
# of cell orientation, which are used to calculate the checksum for the *.adr
file)
TransferObj Ligand(i),SimCell,Local=Keep
# Perform the docking
Experiment Docking
Method (method)
ReceptorObj (i)
LigandObj Ligand(i)
Runs (receptorruns)
ClusterRMSD (rmsdmin)
# Result file number must be separated with '_', in case MacroTarget also ends
with number
# If PDB files are needed too, replace .yob with .pdb to get both
ResultFile (MacroTarget)_(i)_001.yob
# Uncomment below to set the number of energy evaluations (AutoDock
ga_num_evals):
# DockPar ga_num_evals 25000000
# Uncomment the two lines below to provide your own atom parameters (VdW radii
etc.)
# GridPar parameter_file /Path/To/Custom/AD4_parameters.dat
# DockPar parameter_file /Path/To/Custom/AD4_parameters.dat
# Uncomment below to keep temporary files in the current working directory:
# TmpFileID 1adb_tmp
Experiment On
Wait ExpEnd
UnlabelAll
RemoveObj (i) Ligand(i) RecepFlex
NameObj RecepFlex,RecFlex(i)
if scesaved
# Save a scene with all receptor and all ligand conformations
AddObj all
SaveSce (MacroTarget)
RemoveObj !SimCell
# Collect the initial results
Console off
for i=1 to receptors
AddObj (i) Ligand(i)
for j=001 to receptorruns
# To pass the docking results back to this macro, the docking experiment
# stores the binding energy as the B-factor...
run=(i-1)*receptorruns+j
resultlist(run),bindnrglist(run) = DockingResult i,j,'Obj (i)','Obj Ligand(i)
Segment C(j)'
if !(run%10)
ShowMessage 'Analyzing docking results, (100*run/runs)% completed...'
Wait 1
RemoveObj (i) Ligand(i)
# Sort the results by binding energy
ShowMessage 'Sorting docking results...'
Wait 1
SortResults 'bindnrglist','resultlist',''
# Save a log file with an initial analysis
RecordLog (MacroTarget)
print 'Ensemble docking result analysis'
print '================================'
print
print 'The ligand was docked (receptorruns) times ["Run"] with (method) against
each of the (receptors) receptors ["Rec"] in the ensemble, yielding the following
(runs) results, sorted by binding energy:'
print '[More positive energies indicate stronger binding, and negative energies
mean no binding]'
print
print 'Rec | Run |Bind.energy[kcal/mol]|Dissoc. constant [pM]| Contacting receptor
residues'
print '----+-----+---------------------+---------------------
+-----------------------------'
for i=1 to runs
print (resultlist(i))
print

# Get cell dimensions, needed to move the atoms in the cluster YOb files
cd1,cd2,cd3=Cell
# Delete previous resultlist and bindnrglist
bindnrglist()=0
resultlist()=0
# Now merge the clusters from the receptor ensemble members
clusters=0
for i=1 to receptors
for j=001 to receptorruns
filename='(MacroTarget)_(i)_(j).yob'
exists = FileSize (filename)
if exists
ShowMessage 'Merging clusters from receptor ensemble member (i) run (j),
(clusters) found so far...'
Wait 1
cluobj = LoadYOb (filename)
UnlabelAll
# Extract the number of the original run from the segment name C??? (crack it
into pieces and join chars 2,3,4)
run=SegAtom Segment C??? Obj (cluobj)
run()=crack run
run=run2+run3+run4
 # Place the object in the dock cell to aid visualization
MoveAtom Obj (cluobj),(-cd/2)
TransferObj (cluobj),SimCell,Local=Keep
result,bindnrg = DockingResult i,run,'Obj (cluobj) Segment !C???','Obj
(cluobj) Segment C???'
added=1
# Keep only the ligand to save time and memory, otherwise we can quickly
exceed one million atoms on screen
DelRes Segment !C??? Obj (cluobj)
if clusters and merged
# Get ligand RMSDs from all other clusters
rmsdlist() = RMSDAtom Element !H Segment C??? Obj (cluobj),Element !H Obj
(join cluobjlist)
for k=1 to clusters
if rmsdlist(k)<rmsdmin
# Another cluster is close, remember the one with the better binding
energy
added=0
if bindnrg>bindnrglist(k)
# Current one has better binding energy, delete old one
resultlist(k)=result
bindnrglist(k)=bindnrg
filenamelist(k)=filename
SwapObj (cluobjlist(k)),(cluobj)
DelObj (cluobj)
break
if added
# Found a new cluster
clusters=clusters+1
resultlist(clusters)=result
bindnrglist(clusters)=bindnrg
cluobjlist(clusters)=cluobj
filenamelist(clusters)=filename
ShowMessage 'Sorting cluster results...'
Wait 1
DelObj (join cluobjlist)
SortResults 'bindnrglist','resultlist','filenamelist'
# Save the unique clusters in order, mainly needed for the dock_play.mcr
for i=1 to clusters
obj = LoadYOb (filenamelist(i))
# Transfer again into the cell
MoveAtom Obj (obj),(-cd/2)
TransferObj (obj),SimCell,Local=Keep
SaveYOb (obj),(MacroTarget)_(000+i).yob
ShowMessage 'Saving sorted cluster (i)/(clusters)...'
Wait 1
DelObj (obj)
# Delete original clusters on disk
for i=1 to receptors
for j=001 to receptorruns
DelFile (MacroTarget)_(i)_(j).yob
if scesaved
# Bring original objects back, unless that would exhaust memory
AddAll

# Print cluster log

print 'After clustering the (runs) runs, the following (clusters) distinct complex
conformations were found:'
print '[They all differ by at least (rmsdmin) A heavy ligand atom RMSD, and have
been saved as YOb files with terminal number "Num"]'
print
print 'Num | Rec | Run |Bind.energy[kcal/mol]|Dissoc. constant [pM]| Contacting
receptor residues'
print '----+-----+-----+---------------------+---------------------
+-----------------------------'
for i=1 to clusters
print '(000+i) | (resultlist(i))'
Style Ribbon
print
rndseed = RandomSeed
print 'The current random seed is (rndseed).'
fof = ForceField
print 'Point charges and dihedral barriers were obtained from the (fof) force
field.'
StopLog
Console On
HideMessage
# Exit YASARA if this macro was provided as command line argument in console mode
and not included from another macro
if runWithMacro and ConsoleMode and !IndentationLevel
Exit

# EXTRACT DOCKING RESULT

# ======================
# Returns a result string and binding energy, extracted from atomic BFactor and
Property.
# 'rec' is the receptor number in the ensemble, 'run' is the docking run for this
receptor,
# 'recsel' selects the receptor, 'ligsel' selects the ligand.
def DockingResult rec,run,recsel,ligsel
# Get the binding energy from the B-factor...
bindnrg = BFactorAtom (ligsel)
# ...and the dissociation constant from the atomic property.
dissconst = PropAtom (ligsel)
if bindnrg<=0
dissconst=' None'
else
dissconst= 00000000000000.0000+dissconst
# Get receptor residues that contact the ligand
reslist() = ListRes (recsel) with distance<4.0 from (ligsel),Format='MOLNAME
RESNAME RESNUM'
if !count reslist
reslist='No residues in contact'
else
reslist=join reslist
result='(000+rec) | (000+run) | (000000.0000+bindnrg) | (dissconst) |
(reslist)'
return result,bindnrg

# SORT LISTS BY VALUES, HIGHEST FIRST

# ===================================
# Lists are passed by reference, see Yanaconda doc section 'Calls to user-defined
functions..'
def SortResults vallist,key1list,key2list
caller (vallist),(key1list),(key2list)

elements=count (vallist)
# Create a list of indices to sort
for i=1 to elements
indexlist(i)=i
# Sort the list of indices
passes=0
do
sorted=1
for i=1 to elements-1
if (vallist)(i)<(vallist)(i+1)
swap=(vallist)(i)
(vallist)(i)=(vallist)(i+1)
(vallist)(i+1)=swap
swap=indexlist(i)
indexlist(i)=indexlist(i+1)
indexlist(i+1)=swap
sorted=0
if elements>250 and not passes%10
ShowMessage 'Sorting results, pass (passes)/(elements)..'
Wait 1
passes=passes+1
while not sorted
# Rebuild the sorted keylists
for i=1 to 2
if key(i)list!=''
for j=1 to elements
keylist(j)=(key(i)list)(indexlist(j))
(key(i)list)()=keylist
HideMessage