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7 votes
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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 ...
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5 votes
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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 ...
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4 votes
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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. ...
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4 votes
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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-...
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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, ...
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  • 71
3 votes
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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 ...
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3 votes
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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 ...
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3 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 ...
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3 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-...
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  • 507
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 ...
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  • 1,181
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 ...
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  • 1,181
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 ...
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2 votes
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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 ...
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  • 1,181
2 votes
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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 ...
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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.
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2 votes
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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 ...
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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 ...
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2 votes
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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 ...
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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 ...
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1 vote

How to extract docked ligands from .maegz docking results file sorted by glide gscores in Schrodinger Maestro?

It sounds like you are saying your file is already sorted? Is this correct? RDKit Mae supplier is an iterator as is the gzip reader, so does not load all in memory, so that is the best option given ...
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1 vote
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rmsd between re-docked complex and co-crystallized complex

Welcome. The Protein-Ligand-complex is the complete protein with Ligand! If you only want to compare the two ligands, you can delete the rest of the proteins, or specify the input so only the ligand ...
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  • 136
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. ...
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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 ...
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1 vote

.SDF file to .PDB file

Use OpenBabel. Something like babel -isdf file_in.sdf -opdb file_out.pdb.
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  • 901
1 vote

Error pasing the following line in pdb

A PDB file has strict spacing rules as documented here. The coordinates should be: ...
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1 vote
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Visualizing protein-ligand interactions with LIGPLOT or any other suitable software?

You can visualize with Discovery Studio Visualizer and Schrodinger. Arpeggio and PLIP can generate output files of the different interactions.
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  • 181
1 vote

What score value is considered acceptable when using Vina Autodock tool for molecular docking simulations?

The answer is "Depends". But the best thing is always to look at what you ended up with and do some triaging before buying/synthesising anything. By triaging I mean filtering by its ...
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1 vote

Are crystal structure of Ligands used in volunteer computational docking like FightAIDS@home?

I don't know that project's details, so cannot say officially, but undoubtedly it will be crystal structures of protein or models of point mutants based on structures of protein. Computer structure ...
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1 vote
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Which of these enzymes is a better target for virtual screening?

The ultimate choice stems from your individual interests and not a scientific reason... but having said that some pointer of issues may be handy. I am assuming that you want to make an inhibitor that ...
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