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.

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65 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 ...
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156 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/...
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499 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/
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29 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 ...
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20 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 ...
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18 views

How to specify input resfile for Rosetta?

I'm trying to run the following Rosetta command. ...
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805 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 ...
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1answer
52 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?
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54 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 ...
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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: ...
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1answer
25 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 ...
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2answers
48 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 ...
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1answer
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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: ...
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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: ...
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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 ...
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2answers
146 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 ...
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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 ...
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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?
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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 ...
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33 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.
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65 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 ...
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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 ...
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1answer
41 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 ...
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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: ...
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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 ...
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2answers
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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: ...
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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 ...
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60 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 ...
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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?
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40 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 ...
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46 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 ...
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1answer
29 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 ...
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39 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 ...
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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 ...
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3answers
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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.
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2answers
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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 ...
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0answers
21 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, ...
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1answer
68 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 ...
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1answer
63 views

Which is the amino acids classification when analyzing the solvent accessibility of a protein?

I came across an article which has defined 3 categories: Buried [A, L, F, C, G, I, V, W], Exposed [ R, K, Q, E, N, D] and Intermediate [M, S, P, T, H, Y] when analyzing the solvent accessibility of a ...
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1answer
60 views

Determining position of side chain hydrogen in glycine residues from coordinates of backbone atoms

I have a dataset of pdb-format protein structure decoys/models generated by tertiary structure prediction programs. Many of these are missing hydrogen atoms. Specifically, I'd like to determine the ...
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1answer
84 views

Label protein strucuture residues in Chimera

I have generated proteins structure of capsid protein of two strains of viruses. I have modeled them showing Columbic electrostatic potential. I have opened them in two separate windows for comparison....
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2answers
157 views

If I modify a PDB file with a specific mutation, how to minimize energy?

I have a series of proteins that are all phylogenetically related. Only one of this proteins is currently X-ray crystallized. Is it valid to modify the reference PDB file (I mean by hand) to match ...
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1answer
30 views

Finding new drug-protein targets/interactions using a known one as base

Given a known interaction of a molecule with some proteases (having X-rays images too) is it possible to predict interactions with other proteins either using their 3D structure or not? If anyone ...
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1answer
266 views

What are the differences between “Site” and “CONECT” in a PDB file

The CONECT section in a PDB file describes atomic connectivity. The SITE section describes (among other characteristics), ...
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610 views

Is there a standard way to clean a PDB file and re-number its residues?

Is there a pre-existing tool which will tidy up the numbering of a PDB file? Firstly, I would like to re-number the residues on inserts to make the icode an actual residue in the chain (by that I ...
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0answers
52 views

Can VMD change its cartoon representation for secondary structure according to trajectories?

I am using VMD to visualise the secondary structure of protein. The trajectories are from my Gromacs simulation. Firstly I use ...
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60 views

Can I batch output the graph of Secondary Structure in VMD Timeline analysis?

I am using the VMD software, and use "Extension - Analysis - Timeline - Calculate - Calc. Sec. Structure" to visualise the secondary structure of my trajectories. I need to screenshot to get the ...
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“No records to view” error in the “Drug and Drug Target Mapping” PDB's search engine

I'm using the "Drug and Drug Target Mapping" search engine (http://www.rcsb.org/pdb/ligand/drugMapping.do). I've noticed that there are some drugs (generic names) that if they appear in the query, the ...
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116 views

Cross-reference with PDB database

I have a list of several thousand proteins and their UNIPROT IDs. I'm looking for an efficient method of cross-referencing it against the PDB tertiary structure database, and get a list of those ...
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Protein fold pathfinding?

This is probably a long-shot since it would be so dependent upon the underlying folding algorithms. Are there known algorithms for mapping the path followed in a protein folding simulation when you ...