7

To make it crystal clear (and make than pun): Assignment: a 3D structure is known and the residues are assigned a secondary structure Prediction: an algorithm predicts from linear (primary) sequence what the secondary structure may be —often incorrectly. This can be homology based, covariance, deep learning etc. But most commonly just the vector norm of ...


5

You can use one of the UniProt Protein APIs. As you said you have your pdb entries in a text file line by line you can, like this example.txt containing: 1brr 4lzm 2dyi Using the commandline, you can use a little script like this to download the name, if it is available for the given pdb entry. while read line; do curl -X GET --header 'Accept:application/...


4

In general, if you simply want to extract that part of the PDB file, you could loop over it (it's plain text) and check the fields you're interested in: with open('2ly4.pdb') as pdb: for line in pdb: if line[:4] == 'ATOM': chain = line[21] res_idx = int(line[23:26]) if chain == 'A' and 1 <= res_idx <= 30: ...


3

comments from above fleshed out. Both: A graph network is a handy way to represent a molecule, but a matrix makes for fast maths. A graph network is a list of nodes (atoms), a list of edges, the connections between nodes and a list of properties associated with the nodes (symbol, name, index, residue index, residue number, chain, coordinates etc.) and ...


3

Here is an example how to do it using another Python library with another selection syntax. Requires pip install gemmi. import gemmi st = gemmi.read_structure('2ly4.pdb') subset = gemmi.parse_cid('/*/A/1-30').copy_structure_selection(st) subset.write_minimal_pdb('output.pdb')


3

By far the most accurate model right now should be AlphaFold, and there are open structures across several proteomes available at https://alphafold.ebi.ac.uk/.


3

If you go to the wwPDB ftp site https://ftp.wwpdb.org/ in your browser you can find the biological unit structures (and anything else available in the PDB). The caveat of course is that a biounit structure has to have been generated for your structure. By way of some examples, to get all biological units you could do (note the ftp instead of https in front ...


3

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 ordering the top N at \$100-250 each, should you spend \$1,000 or \$10,000? In the in silico step you have real time and CPU-time to factor in making this call even ...


3

CATH The CATH database classifies protein by fold: https://www.cathdb.info/ So the value from that is probably the most useful for you. Crystallographic conditions pH Salinity Dissolved Sugars Reducing Agent Concentration Your crystallising conditions do not mean much. They are a solution that is close to precipitating your protein but slowly enough for it ...


2

Molecular structures are 3D. The records (lines) in the PDB files are in so-called fixed column format. The fields don't need to be separated with blank characters, but they must be in specified columns. For example, the X coordinate is in columns 31-38. Here is the specification of the ATOM record from PDB v3.3. COLUMNS DATA TYPE FIELD ...


2

A contact map predictor will usually output the probability of a contact for every residue pair in a protein, often ommitting very close pairs (e.g. less than 6 residue separation). To calculate the L/n score, rank the predicted contacts descending by probability and look at the first L/n contacts. The fraction of these that are actually contacts in the ...


2

Assuming you can use R, have you tried with biomaRt? For example, using 2bhl (my PhD lover :D) library(biomaRt) ensembl <- useMart("ensembl",dataset="hsapiens_gene_ensembl") # get list of all available info filters <- listFilters(ensembl) attributes <- listAttributes(ensembl) getBM(attributes=c('hgnc_symbol','ensembl_gene_id','...


2

If you need to do it only once, for this one PDB file, it's easier to do it manually. When you open the file you can see it has 10 models from NMR. Do you want to extract a subset of one model or of all 10? In this file the residues are numbered according to the sequence. So you find the line where residue 31 begins in the first model: ATOM 500 N PRO A ...


2

PDBFixer and pyMutate are simple, lightweight, free and open-source. Both don't do any optimizing, though, so you may have to run some molecular dynamics afterward to get what would be the right "orientation". VMD would work for sure, I believe PyMOL too. They are both graphical interfaces but you can start them in text only mode (or just import ...


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

There is no consensus on how different programs do representations (example of NGL vs. PyMOL) or what they are called so there is not official way to store selections. Annotations can be REMARK lines, which have a specific format or simply lines after a hash at the bottom of the file get ignored by most viewers but that specific program may read. Here is a ...


2

Superposition https://michelanglo.sgc.ox.ac.uk/data/d6e427bb-a0cb-4a65-b988-b08237f5054a SwissModel https://swissmodel.expasy.org/repository/uniprot/Q969F8 SwissModel models are threaded against a template. In this case the homologue has 31% identity, which isn't great. The template is 6TP3 which has a rather high R_free of 0.32 and it's solved at 3 Å, ...


2

The data can be found here: https://bmrb.io/search/instant.php?term=2KB7 There is no link directly in the PBD as it is a one-to-many relationship. Clicking on the first value (a shifts dataset) you get somewhere in the middle a link to the actual dataset, which is a CIF like file with the following table: vvvvvvv 1 . 1 ...


2

The residue numbering in a PDB file mainly depend on the person who deposited it. There are usually reasons for how things are numbered, but ultimately you should look at PDB file, and check the details on how the structure was obtained. To give you an example, during my PhD I worked on a protein that had some missing residues at the N-terminus. That was ...


2

Yes, the letters are amino acids It's a schematic with a whole residue as a circle —possibly from Voet and Voet. Residue i is the one in focus, the reference. i-1 is the preceding residue. Have a gander at en.wikipedia.org/wiki/Turn_(biochemistry) where this type of relative notation is important. The diagram shows how secondary structure (helices, sheets ...


2

So you can install PyMOL as a standalone, but you can also install it as a bona fide Python 3 module via conda: conda install -c schrodinger -c conda-forge pymol-bundle It can be installed in other ways —apt-get or brew or even compiled, but the latter is excruciatingly painful. In your python notebook you can do: import pymol2 with pymol2.PyMOL() as pymol: ...


1

The documentation for the PDB module in biopython, which you have tagged, is very clear about how distances are measured between two given Cα atoms. To find out the secondary structure and interactions between strands of a sheet, you may want to look at the header of the PDB. This is the stuff before the ATOM/HETATM entries. SHEET entries are what you are ...


1

AlphaFold2 You are asking about how to hybridise different threaded models, but I would not give up on AF just yet as it can do complexes. AlphaFold2 is conceptually amazing, but does have some issues to such an extent that I blogged about common problems I was getting so many questions. Specifically, it models one protein chain in isolation. In the ...


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

Your title says holistic. This is a tad problematic as there's layers upon layers. Say, post-translation regulation, inhibiting metabolites, interacting protein etc. That is why when talking of an enzyme inhibitor, at the biochemical level one speaks in terms of k_i (inhibition constant), while at the cellular level ("holistic") one talks of IC50. ...


1

One way to get one of the many statistically possible paths is to start from the end and work backwards. This works with the maze puzzles on kids' menus, but also with proteins. To find how a ligand enters an active site, dynamic undocking uses tethered MD to pull a bound form out. Likewise for a protein folding starting from a folded state and lowering the ...


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