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How to use MODELLER to build DIMER homology model with ligand?

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How to use MODELLER to build DIMER homology model with ligand?

Procedure:

    Get Fasta sequence from UNIPROT database.

    Predict sequence alignment from HHPRED

    Prepare INPUT files for MODELLER

###############
from modeller import *
from modeller.automodel import *
#from modeller import soap_protein_od
env = environ()
env.io.hetatm = True
a = automodel(env, alnfile='TvLDH-1bdm.ali',
              knowns='1bdm',
              sequence='TvLDH',
              assess_methods=(assess.DOPE,
                              #soap_protein_od.Scorer(),
                              assess.GA341))
a.md_level = refine.very_slow
a.starting_model = 1
a.ending_model = 1   #Number of output models
a.final_malign3d = True
a.make()
################

>P1;1bdm
structureX:1bdm.pdb: 0: A: 333: B:undefined:undefined:-1.00:-1.00
MKAPVRVAVTGAAGQIGYSLLFRIAAGEMLGKDQPVILQLLEIPQAMKALEGVVMELEDCAFPLL
AGLEATDDPDVAFKDADYALLVGAAPR---------LQVNGKIFTEQGRALAEVAKKDVKVLVVG
NPANTNALIAYKNAPGLNPRNFTAMTRLDHNRAKAQLAKKTGTGVDRIRRMTVWGNHSSIMFPDL
FHAEV----DGRPALELVDMEWYEKVFIPTVAQRGAAIIQARGASSAASAANAAIEHIRDWALGT
PEGDWVSMAVP--SQGEYGIPEGIVYSFPVTA-KDGAYRVVEGLEINEFARKRMEITAQELLDEM
EQVKALGLI----./
MKAPVRVAVTGAAGQIGYSLLFRIAAGEMLGKDQPVILQLLEIPQAMKALEGVVMELEDCAFPLL
AGLEATDDPDVAFKDADYALLVGAAPRKAGMERRDLLQVNGKIFTEQGRALAEVAKKDVKVLVVG
NPANTNALIAYKNAPGLNPRNFTAMTRLDHNRAKAQLAKKTGTGVDRIRRMTVWGNHSSIMFPDL
FHAEV----DGRPALELVDMEWYEKVFIPTVAQRGAAIIQARGASSAASAANAAIEHIRDWALGT
PEGDWVSMAVP--SQGEYGIPEGIVYSFPVTA-KDGAYRVVEGLEINEFARKRMEITAQELLDEM
EQVKALGLI----.*
>P1;TvLDH
sequence:TvLDH:::::::0.00:0.00
MSEAAHVLITGAAGQIGYILSHWIASGELYG-DRQVYLHLLDIPPAMNRLTALTMELEDCAFPHL
AGFVATTDPKAAFKDIDCAFLVASMPLKPGQVRADLISSNSVIFKNTGEYLSKWAKPSVKVLVIG
NPDNTNCEIAMLHAKNLKPENFSSLSMLDQNRAYYEVASKLGVDVKDVHDIIVWGNHGESMVADL
TQATFTKEGKTQKVVDVLDHDYVFDTFFKKIGHRAWDILEHRGFTSAASPTKAAIQHMKAWLFGT
APGEVLSMGIPVPEGNPYGIKPGVVFSFPCNVDKEGKIHVVEGFKVNDWLREKLDFTEKDLFHEK
EI--ALNHLAQGG./
MSEAAHVLITGAAGQIGYILSHWIASGELYG-DRQVYLHLLDIPPAMNRLTALTMELEDCAFPHL
AGFVATTDPKAAFKDIDCAFLVASMPLKPGQVRADLISSNSVIFKNTGEYLSKWAKPSVKVLVIG
NPDNTNCEIAMLHAKNLKPENFSSLSMLDQNRAYYEVASKLGVDVKDVHDIIVWGNHGESMVADL
TQATFTKEGKTQKVVDVLDHDYVFDTFFKKIGHRAWDILEHRGFTSAASPTKAAIQHMKAWLFGT
APGEVLSMGIPVPEGNPYGIKPGVVFSFPCNVDKEGKIHVVEGFKVNDWLREKLDFTEKDLFHEK
EI--ALNHLAQGG.*

    In the alignment file dot ( . ) represents the ligand and slash ( / ) represents the chain break.

    Precautions to be taken:

Make sure ligand is at the end of each chain before TER in the template PDB (here 1bdm.pdb) and delete all other molecules (for example: Water)

    Execute modeller in the linux terminal

        follow the command

mod9.17 model-dimer.py

( OR  for higher version of modeller

mod9.18 model-dimer.py )

That's all. You are ready to analyze models. 🙂
 

For Homology model validation follow the links below:

Homology model validation

Evaluation and Validation of Protein Structures (Single or Multiple)

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