Hot answers tagged

3

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, one being the N of the K in your ligand and the other the O of the E of your protein. Full syntax and examples here: https://pymolwiki.org/index.php/Distance If ...


2

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 protein residues protonation state. The best part is that you can use PDB2PQR web server and they will give you the corresponding CLI arguments for each option you ...


2

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 collision energy of a water molecule at 37°C as that is RT ($\frac{k_b\cdot T}{N_A}$, wiki)under a Maxwell–Boltzmann distribution. A salt bridge –2 kcal/mol (...


2

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 corresponds to the correct conformation, the docking algorithm sometimes fails to find it. Try several times and see for yourself. Note that the probability of failing to ...


1

the tutorials video on youtube Gromacs has great written documentation, so I'd suggest referring to that directly. I can also use GROMACS if that gives me the results. Gromacs works fine with a DNA-ligand system. There are different Amber forcefields, proteins are generally used with AMBER99SB-ILDN simply because it has the longest name and is one of the ...


1

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. Also there are online drawing tools everywhere, where you can download a SMILES (see below). Chemical formula is the wrong way to go, unless you are "...


1

I normally use PyMOL. In PyMOL you can generate a model of a sequence of DNA with the command fnab — a sister command to the better known fab, which makes a protein sequence of a given secondary structure. I've not encountered that site, but it says it uses experimental data, which is a better approach. Side note 1 OP is asking for DNA, but if anyone ...


1

maybe you can use the "per-residue interaction scores" (wich is available via Schrödinger). On the other hand,to show if a Docking Pose is really "better" you could show specific interactions rather than the complete big molecule.. e.g. an important salt bridge is missing. (hydrogen bonds are not that important, due to the fact that they ...


1

NB. This is a long comment as opposed to an answer which requires a colossal working chunk of code. Control Science is all about controls failing. A great control for docking is the barnase-barnstar complex (PDB:1BRS): both small, but form a strong interactions. If this is done, the RMSD against the original structure is very meaningful and useful. RMSF A ...


1

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 that loading all 1e6 into memory crashes your system. What is the fraction of unreadable compounds in RDKit? And does it matter? These are likely failing ...


1

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 is choosen. (select Ligand and save selection. then use the function on that selections) But be aware that for Docking comparison you probably don't want to ...


Only top voted, non community-wiki answers of a minimum length are eligible