Questions tagged [protein-structure]

The 3-D structure of a protein in space. It can refer to secondary structures, such as alpha helices or beta sheets, or the 3-D coordinates of the atoms making up a protein.

Filter by
Sorted by
Tagged with
1
vote
1answer
16 views

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

I am going to screen a set of small molecules against a CYP450 2C9 protein target. The structure I am using exactly is 5A5I. Do I need to fill in missing side chains and loops before performing VLS? I ...
3
votes
1answer
30 views

Why is there a chloride ion in this 3D model?

Here we have a 3D model of a sequence that match with this sequence VVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIK in Blast the 3D structure is here Why is there a chloride ion in this 3D model?
1
vote
1answer
34 views

Outputting crunchable list of HBonds from Pymol

X-posted from the Main Stack Overflow because folks here are possibly more familiar with PyMol(?) I have been trying to assess the strength of an interface I want to mutate using Pymol. What I am ...
1
vote
1answer
23 views

Map gene IDs to protein structure if exist

I want to map some gene ids to their proteins structures if they exist. The genes are rows of this CSV. There are other information that may help also such as Product description but that may lead to ...
0
votes
0answers
20 views

Why is the output from the online DISOPRED portal and a local DISOPRED installation different?

I recently installed DISOPRED on a computer cluster to predict the intrinsic disorder in long (~800 residues) amino acid sequences. I followed instructions provided on an online blog, since I couldn't ...
0
votes
1answer
40 views

Methods to predict one connected structure from two known separate structures

Currently, I am facing such a question: how to predict one connected protein structures from two separate known structures? It should be different from the protein-protein docking method, which is ...
3
votes
1answer
70 views

CCP4 file to a Python 3 numpy array or similar workaround

I would like to merge together several ccp4 formatted density maps (and do a few minor things). So ideally I would like to open the ccp4/mrc files as numpy arrays in Python 3 and save the array as a ...
1
vote
1answer
23 views

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

I will be docking a small library of molecules that I have downloaded from PubChem using AutoDock. I thought why not minimize their energy before docking using ChemDraw. I am thinking; what is the ...
1
vote
1answer
39 views

Generate ligands candidates based on protein shape

Recent approaches to novel drug design using machine learning (ML) and deep learning, often involve generating hundreds of potential ligands which are later tested by docking with a target protein and ...
2
votes
1answer
38 views

Protein misfolding

I am looking for literature on protein and RNA mis-folding. I am on the computational/biophysics side, and what interests me are the practical applications: diseases caused by misfolding, drug ...
0
votes
1answer
60 views

Visualizing protein-ligand interactions with LIGPLOT or any other suitable software?

I have used DOCK software to dock 10 ligands into the protein structure. I want to generate a pdb file that contains all 10 binding modes of the ligands together with the protein. So all together in ...
1
vote
1answer
41 views

Extract autodocked protein-ligand connections programatically

I have 2 crystal structures, one for my protein and one for my ligand (I have several protein-ligand pairs). I am using AutoDock Vina to simulate docking, which returns another file of the ligand with ...
1
vote
2answers
94 views

Can I automate CLUSTALO and output alignment sequence identity?

I've detected homology between targets of ligands in drugbank and proteins in the proteome of a pathogen. I've parsed the output very rudimentary and calculated my query coverage. This exists in an ...
-3
votes
1answer
168 views

Are there any Sulfur Dioxide molecules in this structure?

Does the protein structure shown in the JSmol link have any Sulfur Dioxide molecules? 1 In the picture, the Sulfur element is yellow and Oxygen is red 2 https://www.viprbrc.org/brc/...
0
votes
1answer
503 views

What does the yellow mean in this image from Virus Pathogen Resource?

What does the yellow mean in this image? It's from https://www.viprbrc.org/brc/
1
vote
1answer
99 views

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

Hello I'm helping to develop a cloud docking tool for screening compounds, similar to Swissdock but with mass throughput and GPU optimizations. Specifically helping screen existing drugs against ...
1
vote
0answers
31 views

What's the difference between Procheck and Whatcheck?

I'm currently using Procheck to check a protein backbone. The process is: Determine backbone phi, psi, and omega angles Compare to known angle distributions to identify outliers, and angles in ...
0
votes
1answer
44 views

How to specify input resfile for Rosetta?

I'm trying to run the following Rosetta command. ...
13
votes
1answer
1k views

Is it possible for coronavirus or SARS to be synthetic?

I have heard several conspiracy theories regarding the origin of the new coronavirus, 2019-nCov. For example that the virus and/or SARS were produced in a laboratory or were some variant of Middle ...
1
vote
1answer
53 views

Searching for proteins by primary and secondary structure

I need to find peptides/proteins with a certain sequence of amino acids in a certain type of secondary structure. For example, "ALA PHE GLY" in alpha-helix. Is there any tool that does that?
2
votes
1answer
61 views

How to quickly and robustly convert between mmCIF and PDB?

There is already a question on PDB/CIF to MMTF, however what is a robust way to programmatically go between PDB and CIF files? For example I can use a python script from this gist that relies on ...
0
votes
1answer
42 views

Can foldx position-scan produce different result with different lists of mutations?

I am running foldx position scan for GFPmut2 (PDB: 6GO9) and I use a config file with the following template: ...
0
votes
1answer
28 views

pymol script to only select 5 chains within a distance from a reference and save the selection

I am generating 30 asymmetric units of a protein structure. Now, I want to select different combinations of 5 units which are 30 Angstroms away from the reference and save it as a different file. Here ...
1
vote
2answers
55 views

Protein model quality assessment

How do I perform protein model quality assessment? I will obtain predicted structures from DMPfold, I-Tasser, and Rosetta, what should be the next approach to select a structure from among this set ...
2
votes
1answer
30 views

What does final generated models with TM-score of DMPfold signify in “sequence.ema.txt” file?

So, my runs have finished and got 5 final models. I predicted TM-score of one model to understand the result. The output of "predict-tmscore.sh" for "final_1.pdb" is: ...
1
vote
1answer
58 views

Rosetta ab initio run gives 0.00 RMSD for generated 2000 models? (run still in progress)

I am running rosetta ab initio prediction using the command line: ...
1
vote
1answer
25 views

A program “PSICOV” “stopped” from a few days on Ubuntu 18.04?

I am running dmpfold, "seq2maps.sh" and from a few days the program is at the "PSICOV" stage: psicov -z 15 -o -d 0.03 tail-fiber-sequence.aln "ps aux" gives me ...
3
votes
2answers
197 views

Putting labels of different sizes on one PyMOl Object

I'm new to PyMol (and StackExchange!) and working on my first project. I have the structure of a protein as an object, called PolyA-M, and the idea is that the residues of it are shown as spheres of ...
3
votes
1answer
55 views

How many models should be generated by rosetta for denovo protein structure prediction?

How many models should be generated by rosetta for de novo protein structure prediction of a 382 long sequence? In the tutorial, it says 50,000 models but practically it takes a lot of time (weeks) to ...
0
votes
2answers
43 views

Can DMPfold and I-Tasser work well for de novo structure prediction of 1135 amino acid long sequence?

I am trying to perform de novo structure prediction of a 1135 long protein sequence; can DMPfold and I-Tasser work well for de novo structure prediction of 1135 amino acid long sequence?
0
votes
1answer
13 views

DMPfold: number of models produced using “10 500” feature in “run_dmpfold.sh”?

I ran this command: run_dmpfold.sh sequence.fasta sequence.21c sequence.map ./folder 10 500 From my previous discussion, I understand that I should run with ...
0
votes
1answer
37 views

Download protein structure from gene name

I have a list of gene name, I want to download and save each protein 3D structure corresponding to each gene name.
1
vote
1answer
72 views

From ensembl id to protein structure

Forgive me if this question is too trivial. I have a list of ~700 Ensembl ID. I need to extract the protein structures of each Ensembl id. How can I do this? Is there any script(python, R) so that ...
0
votes
1answer
31 views

DMPfold: Understand the run of DMPfold “run_dmpfold.sh”?

I ran dmpfold using this command: run_dmpfold.sh sequence.fasta sequence.21c sequence.map ./dmpfold-lysin 10 500 &> dmpfold-log.log It produced files like ...
2
votes
1answer
42 views

DMPfold: is it suitable to get 5000 models to compare with rosetta

I ran this command for 10 iteraions and 500 models. run_dmpfold.sh sequence.fasta sequence.21c sequence.map ./dmpfold-lysin 10 500 &> dmpfold-log.log I am ...
2
votes
2answers
55 views

Dmpfold error “No such file or directory: 'best_qdope.pdb'” when running “run_dmpfold.sh”?

I am running DMPfold, "seq2maps.sh" ran successfully, but whrn running "run_dmpfold.sh", it gives me this error: ...
1
vote
1answer
62 views

I have a list of protein targets. How to get structural data (atomic coordinate) from PDB?

I have a list of around 500 protein targets (human). I only have their protein symbols. As an example: EGFR AR FOXA1 CXCR3 ... I want to get structural data (atomic coordinate) from PDB (Protein ...
1
vote
2answers
91 views

DMPfold error while running protein structure prediction

I am using DMPfold to predict protein structure of a 382 residue protein sequence. All goes wel, and even the files are produced but during the "seq2maps.csh", I get this error in between: ...
4
votes
3answers
75 views

PDB codes for misfolded proteins?

I'm searching for PDB code examples for "healthy proteins" and misfolded ones, so I can compare the 3D structure. I'd prefer pairs of a "protein misfolding disease", but could be any. Can I find such ...
0
votes
2answers
61 views

What is the best way to start with Structural bioinformatics with zero prior experience? [closed]

My undergraduate thesis is on the topic "Ligand design from protein-protein interfaces" and my PI has asked me to learn the basics of Structural bioinformatics over the summer so that I'll be able to ...
1
vote
0answers
17 views

Possible evaluation or validation of predicted 3D protein structure generated by SCWRL4

I mutated a wild type protein structure using Scwrl4. How can I evaluate or validate the reliability of the predicted structure generated by Scwrl4?
0
votes
2answers
42 views

Evidence of emergence of “genuine” novel protein interactions by aa mutation [closed]

Anyone knows of an example of a protein that, without coming from a recent duplication event, underwent a mutation(s) that caused it to have a novel interaction with a new ligand, substrate, other ...
2
votes
1answer
51 views

Find similar proteins with similar tertiary structure?

I'm a mathematician studying knotted curves and am trying to find some applications of my work in proteins. Using https://www.rcsb.org/, how do I find proteins that have similar (but perhaps not the ...
3
votes
1answer
31 views

Proteins with one SS bond?

I would like to find proteins with exactly one SS bond. Is there a database where I can search this? I've tried advanced search on https://www.rcsb.org/, but no such option, at least I could not find ...
0
votes
1answer
41 views

Post docking evaluation

What to do after protein-ligand docking? Is there any necessary or enhancement step recommended after docking to validate the confirmation of highest score is the best? For your information, I am ...
1
vote
0answers
19 views

How to find Wild Type (WT) protein structure on Protein Data Bank (PDB)?

Currently, I am working on Galactose oxidase enzyme for protein docking and I am totally new to it. I have to study how mutation on specific residue will make mutated galactose oxidase better than the ...
4
votes
3answers
230 views

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

What is the reason for adding hydrogen and removing unnecessary water molecules from the protein structure before protein-ligand docking? FYI, the tools I used for docking is GOLD.
3
votes
2answers
100 views

Database for proteome-wide predictions of protein structures

Accuracies of protein structure predictors have improved quite a lot in recent years. Algorithms such as Rosetta have gotten robust enough to predict structures of large number of proteins. However, I ...
2
votes
0answers
24 views

What is a sensible forcefield choice for membrane proteins when using PDB2PQR?

I am generating PQR files for a membrane protein that is almost entirely buried in the membrane. There are no lipids in the structure. PDB2PQR has predefined options of amber, charmm, parse, tyl06, ...
1
vote
1answer
79 views

Reconstruct a protein's 3D structure from a pair-wise distance matrix

What is a good method to reconstruct a protein's 3D structure from a pair-wise distance matrix of residues? I think the question is self-explanatory. I know of this method but it seems that it uses ...