Unable to set number of molecules as 1 on haddock 2.4 web server to run single-molecule mode

HADDOCK
21

Thank you so much for your help. I am really appreciated for your time and help.
I have some questions on setting parameters to run cyclic peptide to protein docking on haddock2.4 web server. I am not sure if I match my parameter setting in the web server to the cyclic peptide docking paper. I am wondering if you could please help me with this.

Question 1.
For “Molecule 1 Input” tab
choose “What kind of molecule are you docking?” as “Protein or Protein-Ligand”
For “Molecule 2 Input” tab
choose “What kind of molecule are you docking?” as “Peptide”. Also set this molecule as cyclic by turning “Is it a cyclic peptide?” on.

Question 2.
At HADDOCKing of the p53 N-terminal peptide to MDM2 – Bonvin Lab it choose the peptide asFully flexible segments so I am wondering if I also including all residues of my peptide in the box of “Fully flexible segments” under “Molecule 2-Parameters” when I submitting jobs through the haddock2.4 web server for my case as my peptide is cyclic and in the protocol the peptide is linear.

Question 3.
Under “Molecule 2-Parameters” the option of “Automatically define passive residues around the active residues” is set on. I am wondering if I keep it as on. Or turn it off and specify numbers of all residues of my peptide in the "Passive residues (surrounding surface residues) "box.

Question 4.
By default the option of “Create DNA/RNA restraints?” is set on. In my case I do not have either DNA or RNA molecule so I am wondering if I can turn it off.

Question 5.
Under the “Sampling parameters” tab
For the “Number of structures for rigid body docking” I guess this correspond to “structures_0=5000” in run.cns from cyclic peptide paper. However, in docking protocol (HADDOCKing of the p53 N-terminal peptide to MDM2 – Bonvin Lab) it is set to 10000. But I guess setting it to 5000 is enough but I am not sure so I want to check with developer.

Question 6.
Under the “Sampling parameters” tab
I guess that “Number of structures for semi-flexible refinement” correspond to " structures_1=400" in run.cns from cylcic peptide paper.
I guess that “Number of structures for the final refinement” corresponds to “waterrefine=400” in run.cns from cylcic peptide paper.
I guess that “Number of structures to analyze” corresponds to “anastruc_1=400” in run.cns from cylcic peptide paper.

Question 7.
For the Hydrogen bond restraints in run.cns from cylcic peptide paper “hbonds_on=true”.
However, for the web server under “Dihedral and hydrogen bonds restraints” it ask to upload Hydrogen bond restraints TBL file. So I am wondering how I match setting of “hbonds_on=true” in run.cns from cylcic peptide paper to parameter settings in haddock2.4 web server.

Question 8.
Under the " Advanced sampling parameters " the option of “Perform cross-docking” is set on by default I am wondering if I adapt this in my case.

Question 9.
Under the " Advanced sampling parameters " and under “it1 parameters” sub-tab,
I guess that "Number of MD steps for rigid body high temperature TAD " corresponds to “initiosteps=2000” in run.cns from cylcic peptide paper.
I guess that "Number of MD steps during first rigid body cooling stage " corresponds to "cool1_steps=2000 " in run.cns from cylcic peptide paper.
I guess that "Number of MD steps during second cooling stage with flexible side-chains at interface " corresponds to “cool2_steps=4000” in run.cns from cylcic peptide paper.
I guess that "Number of MD steps during third cooling stage with fully flexible interface " corresponds to "cool3_steps=4000 " in run.cns from cylcic peptide paper.

Thank you very much
Best regards

22

Question 1.
For “Molecule 1 Input” tab
choose “What kind of molecule are you docking?” as “Protein or Protein-Ligand”

Protein-Ligand would be in case your protein contains already a ligand or co-factor in it

For “Molecule 2 Input” tab
choose “What kind of molecule are you docking?” as “Peptide”. Also set this molecule as cyclic by turning “Is it a cyclic peptide?” on.

Correct

Question 2.
At HADDOCKing of the p53 N-terminal peptide to MDM2 – Bonvin Lab it choose the peptide asFully flexible segments so I am wondering if I also including all residues of my peptide in the box of “Fully flexible segments” under “Molecule 2-Parameters” when I submitting jobs through the haddock2.4 web server for my case as my peptide is cyclic and in the protocol the peptide is linear.

In our paper we did not define the peptide as fully flexible. Just using the automatic semi-flexible option

Question 3.
Under “Molecule 2-Parameters” the option of “Automatically define passive residues around the active residues” is set on. I am wondering if I keep it as on. Or turn it off and specify numbers of all residues of my peptide in the "Passive residues (surrounding surface residues) "box.

Bette to leave it on (and simpler)

Question 4.
By default the option of “Create DNA/RNA restraints?” is set on. In my case I do not have either DNA or RNA molecule so I am wondering if I can turn it off.

Does not matter, but you can turn it off.

Question 5.
Under the “Sampling parameters” tab
For the “Number of structures for rigid body docking” I guess this correspond to “structures_0=5000” in run.cns from cyclic peptide paper. However, in docking protocol (HADDOCKing of the p53 N-terminal peptide to MDM2 – Bonvin Lab) it is set to 10000. But I guess setting it to 5000 is enough but I am not sure so I want to check with developer.

The sampling in our cyclic peptide paper was 5000/400/400 (see Table S6 from the supplementary material)

Question 6.
Under the “Sampling parameters” tab
I guess that “Number of structures for semi-flexible refinement” correspond to " structures_1=400" in run.cns from cylcic peptide paper.
I guess that “Number of structures for the final refinement” corresponds to “waterrefine=400” in run.cns from cylcic peptide paper.
I guess that “Number of structures to analyze” corresponds to “anastruc_1=400” in run.cns from cylcic peptide paper.

Yes

Question 7.
For the Hydrogen bond restraints in run.cns from cylcic peptide paper “hbonds_on=true”.
However, for the web server under “Dihedral and hydrogen bonds restraints” it ask to upload Hydrogen bond restraints TBL file. So I am wondering how I match setting of “hbonds_on=true” in run.cns from cylcic peptide paper to parameter settings in haddock2.4 web server.

Do you have hydrogen bond restraints? If not let it off.
In the paper, as we run a local version, we used those to maintain the protein structure in case it had chain breaks.
The server will automatically detect that.

Question 8.
Under the " Advanced sampling parameters " the option of “Perform cross-docking” is set on by default I am wondering if I adapt this in my case.

Keep defaults :slight_smile:

Question 9.
Under the " Advanced sampling parameters " and under “it1 parameters” sub-tab,
I guess that "Number of MD steps for rigid body high temperature TAD " corresponds to “initiosteps=2000” in run.cns from cylcic peptide paper.
I guess that "Number of MD steps during first rigid body cooling stage " corresponds to "cool1_steps=2000 " in run.cns from cylcic peptide paper.
I guess that "Number of MD steps during second cooling stage with flexible side-chains at interface " corresponds to “cool2_steps=4000” in run.cns from cylcic peptide paper.
I guess that "Number of MD steps during third cooling stage with fully flexible interface " corresponds to "cool3_steps=4000 " in run.cns from cylcic peptide paper.

Indeed

23

Hi,
Thank you so much for your help. I am really appreciated for it.

For question1.
For “Molecule 1 Input” tab
choose “What kind of molecule are you docking?” as “Protein or Protein-Ligand”
I am docking cyclic peptide to a protein solely. So I am wondering if I can still choose “Protein or Protein-Ligand”. As I see options for peptide but not options for protein alone.
My protein does not contain a ligand or co-factor in it and it only consist of one chain.
Thank you very much,
Best regards

24

The OR is the option means it covers both options :slight_smile:

25

Hi,

Thank you very much for your help all the time.
I got some results from haddock web server. I have a question and need your help. I am wondering if you could please help me and I would be much appreciated.
I did an ensemble of cyclic peptides with 50 conformers docking to a protein. In the ensemble each cluster is name from 1 to 50. In the results, it reports the best 10 results and each ranking assigned to a cluster number. My question is how the cluster number in the results matches the cluster number in the input of ensemble of cyclic peptide. So if the best ranking cluster is cluster 1 whether this is cluster 1 in the input pdb file of 50 cyclic peptides. Or it the the first conformation in the input pdb file of 50 cyclic peptides.
Thank you very much
Best regards
jin

26

Hi Jin,

In the clustering step of HACCOCK, we cluster based on either RMSD or Fraction of Common Contacts (FCC).
In both cases, we attribute the cluster ID based on the size of the cluster (clusters with higher number of members will have lower value).
Then we rank clusters based on their average HADDOCK score.

Also note that there is no relation between your input ensemble and output clusters in terms of numbering.
Therefore the best ranking cluster is probably not the first input in your pdb file ensemble.

Cheers