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 ...
- 4,274
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 ...
- 4,274
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.
...
- 4,274
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-...
- 4,274
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 ...
- 4,274
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-...
- 577
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, ...
- 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 ...
- 4,274
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 ...
- 4,274
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 ...
- 4,274
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 ...
- 676
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 ...
- 1,299
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 ...
- 61
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 ...
- 4,274
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 ...
- 1,305
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 ...
- 4,274
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 ...
- 4,274
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 ...
- 1,305
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 ...
- 1,305
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 ...
- 4,274
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.
- 4,274
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 ...
- 810
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 ...
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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 ...
- 493
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 ...
- 118
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, ...
- 4,274
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. ...
- 4,274
1
vote
Error pasing the following line in pdb
A PDB file has strict spacing rules as documented here.
The coordinates should be:
...
- 4,274
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 ...
- 4,274
1
vote
.SDF file to .PDB file
Use OpenBabel.
Something like babel -isdf file_in.sdf -opdb file_out.pdb.
- 951
Only top scored, non community-wiki answers of a minimum length are eligible