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7 votes
Accepted

Generate ligands candidates based on protein shape

TL;DR: docking is much slower than any ML approach, but the ML approach can be constrained by pharmacophores dictated by the active site. Side note: Scale The scale for ligand space exploration is ...
Matteo Ferla's user avatar
  • 4,244
5 votes
Accepted

How could I match atom orders between a .mol2 and a .pdb?

Atom reordering is a common problem in compchemistry. Rdkit (a python package) can do this, but it is limited by the formats it can read and mol2 files are a bit hit or miss. It works really well ...
Matteo Ferla's user avatar
  • 4,244
4 votes
Accepted

Extract autodocked protein-ligand connections programatically

With pymol as a python module (conda install -c schrodinger pymol, not the GUI one), it is very easy. ...
Matteo Ferla's user avatar
  • 4,244
4 votes
Accepted

Asking for Docking programme

It's case specific Docking small compounds well is problematic and you need to consider whether: if a single conformer is okay if rigid sidechains are okay if implicit water is okay if a non-...
Matteo Ferla's user avatar
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4 votes

Why is it necessary to add hydrogen and delete water before protein-ligand docking?

Hydrogens Most crystallographic structures are X-ray and the hydrogens are absent. In the case of neutron diffraction models, there may be many missing high b-factor ones (example in PDB:5MOP). As a ...
Matteo Ferla's user avatar
  • 4,244
4 votes

Why is it necessary to add hydrogen and delete water before protein-ligand docking?

My answer is mainly based on molecular dynamics,but in this context it shouldn't make much of a difference. The main reason has to do with the force-field-...
fra's user avatar
  • 567
4 votes

How to show electrostatic interactions in Pymol on the wanted residue

Depends whether you work with named selections which is preferable and helpful if you want to use this Pymol session for future images. In this case, use the distance command for your two selections, ...
bunher's user avatar
  • 71
4 votes

What is the correct method of identifying the interacting residues for specific molecular docking?

Not an answer either. But a series of caveats. First, HEM parameterisation. For molecular thermodynamics tools you will need to generate a topology file for this ...
Matteo Ferla's user avatar
  • 4,244
3 votes
Accepted

How to choose docking score cutoff?

It is utterly arbitrary and depends on your resources. We can all agree your cutoff would be a lot lower during the ordering step than at followup in silico analyses, but even then if you were ...
Matteo Ferla's user avatar
  • 4,244
3 votes
Accepted

Do I need to remove water molecules before protein-ligand docking?

Yes, if you are using implicit solvent you ought to remove all of them. Exception. Unless the crystallographic waters are trapped essential structural components of your active site and your ligand is ...
Matteo Ferla's user avatar
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3 votes
Accepted

How can I dock a protein to a nucleic acid?

I'm not sure what you meant but you can take a look at NPDock (disclaimer we wrote that tool). If you have a structure of your protein of interest, you can dock it to the structure of your DNA/RNA of ...
Marcin Magnus's user avatar
3 votes

What is the correct method of identifying the interacting residues for specific molecular docking?

not an answer, just more inputs, but https://proteins.plus/5tl8#poseview gives me this: references: ProteinsPlus: interactive analysis of protein–ligand binding interfaces Molecular complexes at a ...
pippo1980's user avatar
  • 1,108
3 votes
Accepted

What is the correct method of identifying the interacting residues for specific molecular docking?

I think I've found the answer to my own question. So, I tried using this PRANK web server for predicting the binding site of my protein. The results is suprisingly very similar to the one from the ...
Dembappe's user avatar
2 votes

What value of reference RMSD after docking simulation from any starting coordinate would be considered outrageous to have?

Let's get some definitions out of the way: RMSD, root mean square deviation, is a metric of distance of molecule A and molecule B. Think of it as average euclidean distance. It us casually called ...
Matteo Ferla's user avatar
  • 4,244
2 votes

Post docking evaluation

You can run a Molecular Dynamics simulation to see if the pose is stable and whether the protein changes/adapts it’s conformation. You can calculate the ligand efficiency, the docking score divided ...
Soerendip's user avatar
  • 1,295
2 votes

Protein ligand docking: how to convert <protein>.pdb to <protein>.maps.fld?

There are a few steps in between pdb and .maps.fld. Here is the list of several scripts that can do tasks for you that you ...
Matteo Ferla's user avatar
  • 4,244
2 votes
Accepted

What is the perferred method of optimization or energy minimization of small molecules downloaded from PubChem?

The difference between different force-fields is not going to be major, it is the side steps which are. When If you are starting from a SMILES string, optimisation is a must obviously. If you are ...
Matteo Ferla's user avatar
  • 4,244
2 votes

Asking for Docking programme

Autodock-Vina is a free molecular docking solution. You need to generate different input conformations for each ligand though, e.g. with RDKit. Here is a link to ...
Soerendip's user avatar
  • 1,295
2 votes
Accepted

predict the IC50 after using Schrodinger suite Glide tool for docking

I don't think it is possible just from the docking scores. Docking scores are designed to give you an estimate of the binding affinity (entalphy), but they do not take entropic contributions into ...
Soerendip's user avatar
  • 1,295
2 votes
Accepted

Do I need to fill in missing side chains and loops before protein-ligand docking for VLS?

In general Most if not all docking applications will tolerate a jump. Furthermore, you really don't want to dock anything to the flexible regions even if you are using a program that does properly ...
Matteo Ferla's user avatar
  • 4,244
2 votes

Generating 3D coordinates error

An ent file is a pdb file. Just change the extension. PDBe for example provides their PDB files as such.
Matteo Ferla's user avatar
  • 4,244
2 votes

Why Do I Get Different Results Each Time From AutoDock Vina?

Vina uses a non-deterministic docking algorithm. See the manual. The docking algorithm is non-deterministic. Even though with this receptor-ligand pair, the minimum of the scoring function ...
Throckmorton's user avatar
2 votes

How to tell if our ligand-protein docking is good from AutoDock Vina's result

It is best to contextualise the numbers. -1 kcal/mol is about the potential energy gained from a hydrogen bond —technically described in the r^6 part of the Lenard–Jones term, it is also the average ...
Matteo Ferla's user avatar
  • 4,244
2 votes

Programmatically adding hydrogen and remove water to multiple PDB files

I believe PDB2PQR CLI will do the work wonderfully. Don't let the name trick you: PQR files are organized like PDB ones. Under the hood it runs propka, which is state-of-the-art for predicting a ...
O.Laprevote's user avatar
1 vote

Do you know any virtual screening libraries with small, soluble compounds?

ZINC20 is a free database of commercially-available compounds for virtual screening. It contains 1.3M compounds with molecular weight less than 200. https://zinc20.docking.org/ Cartblanche22 is an ...
SuleymanSelim's user avatar
1 vote

Do you know any virtual screening libraries with small, soluble compounds?

Lipinski and logP Most datasets will be filtered by the Lipinski rule, plus in the some cases, such as Enamine Real whether they can be bought. One criterion in the Lipinski rule filter is the logP, ...
Matteo Ferla's user avatar
  • 4,244
1 vote

Building small molecules de novo

Most universities have a ChemDraw site lincence, so you may want to check that for drawing a non–3D-embedded molecule. Alternatively there are many other programs. PyMOL is not really a good choice. ...
Matteo Ferla's user avatar
  • 4,244
1 vote

Error pasing the following line in pdb

A PDB file has strict spacing rules as documented here. The coordinates should be: ...
Matteo Ferla's user avatar
  • 4,244
1 vote

.SDF file to .PDB file

Bizarrely, Obabel seems to have written a PDB that was incorrectly spaced for the OP as seen in Error pasing the following line in pdb If you can use python, rdkit ...
Matteo Ferla's user avatar
  • 4,244
1 vote

.SDF file to .PDB file

Use OpenBabel. Something like babel -isdf file_in.sdf -opdb file_out.pdb.
jgreener's user avatar
  • 941

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