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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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How to choose docking score cutoff?

I made a virtual screening of a large database (~5M) and want to filter ligand structures for further more accurate screening (from Schrodinger HTVS to SP resolution). My next step is to define a ...
Nurlybek Amangeldiuly's user avatar
3 votes
1 answer
589 views

How do you calculate the top L/5 score?

I am currently investigating how to predict protein structure and contact map predictions. There, I see things like top L/5 and top L/2 scores as a way to evaluate the contact map. What formulas do ...
musako's user avatar
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How can atomic RMS differences / atomic RMS distributions help us understand the structure of a protein?

For example, I have a paper that says: "the atomic RMS distribution about the mean coordinate positions is 0.41 +/- 0.04 A for the backbone atoms and 0.82 +/- 0.04 A for all atoms" And I ...
Ig009's user avatar
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Get protein names corresponding to PDB ID

I have a list of about 4000 PDB IDs and would like to get the actual names of the proteins (e.g. lactate dehydrogenase, cytochrome c). I tried the batch header section at the Protein Databank Download ...
David's user avatar
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How to see if a gene is the product of copy number variation?

Copy number variation (CNV) is a phenomenon in which sections of the genome are repeated and the number of repeats in the genome varies between individuals.Copy number variation is a type of ...
Spartan 117's user avatar
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1 answer
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How many entries in PDB have SS bonds?

Is there a way to figure out what percentage of entries in PDB have SS bonds? In addition, what other types of bonds in PDB may be worth looking into (not H bonds)?
Jake B.'s user avatar
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1 answer
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How does sequence alignment help with protein folding prediction? [closed]

I've been seeing using sequence alignment to help with prediction of protein folding, but am unable to understand why. Google returns other research papers for these search terms, hence I'm hoping the ...
pohjie's user avatar
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What programs account for structural alignment of different parts of distant homologs which have significant structural differences?

If there is a need to perform structural alignment of different parts of distant homologs, which program one should use? Since distant homologs often have significant structural changes, meaning the ...
TRakesh's user avatar
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2 answers
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How are different forcefields developed/evaluated?

The Rosetta software can use a variety of different energy functions: Ref2015 GenPot Beta-Nov16 How are these energy functions developed and validated? Is it common to do a single protein design ...
Seanny123's user avatar
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B-factor analysis in nanobodies

I am doing my research on nanobodies. Currently, I am trying to do a comparison study of the flexibility of CDR loops using B-factor values. I would like to know if there is any statistical analysis ...
anmaklaksh's user avatar
1 vote
2 answers
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Delete chains from a protein

We have a docking target protein with multiple chains (A,B and C). However, I just need chain A. How can I delete the 2 other chains from the docking target protein.
ibio_rep1's user avatar
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Issues with AutoDock Vina

I am trying to use AutoDock Vina to do docking however I am getting this error. I would really appreciate any help as I have not been able to resolve this error despite trying numerous times.
ibio_rep1's user avatar
1 vote
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How to implement SEG (Wootton and Federhen ,1993) algorithm?

I want to implement SEG in my MATLAB environment and I'm relying on Wootton and Federhen (1993) Reading the article I cannot succeed to understand what kind of process I have to implement in order to ...
Spartan 117's user avatar
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261 views

Extract only the amino acid residues on the surface of protein structure data

I'd like to use protein structure data from PDBs visualized by Chimera to do two things. I'd be happy to learn the appropriate tools and methods. ・Mapping information about amino acids present on ...
farinelli's user avatar
1 vote
1 answer
90 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 ...
Nurlybek Amangeldiuly's user avatar
3 votes
1 answer
62 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?
Dare to ask-I dnt mind punishm's user avatar
1 vote
1 answer
144 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 ...
LauraCZD's user avatar
1 vote
1 answer
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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 ...
BND's user avatar
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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 ...
Moing Gude's user avatar
4 votes
1 answer
639 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 ...
Matteo Ferla's user avatar
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1 answer
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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 ...
Linda's user avatar
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2 votes
1 answer
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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 ...
Jim Eric Skogman's user avatar
2 votes
1 answer
59 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 ...
Roger V.'s user avatar
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1 answer
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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 ...
djordje's user avatar
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1 answer
317 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 ...
Zac R.'s user avatar
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2 answers
236 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 ...
Mike 's user avatar
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-2 votes
1 answer
218 views

Are there any Sulfur Dioxide molecules in this structure?

Does the protein structure shown in the JSmol link have any Sulfur Dioxide molecules? In the picture, the Sulfur element is yellow and Oxygen is red (see here) https://www.viprbrc.org/brc/...
Andy's user avatar
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1 answer
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What does the yellow mean in this image from Virus Pathogen Resource?

What does the yellow mean in this image of a SARS (coronavirus) protease from the Virus Pathogen resource database? It's from https://www.viprbrc.org/brc/
Andy's user avatar
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1 vote
1 answer
2k 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 ...
Paul Shen's user avatar
1 vote
0 answers
225 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 ...
Seanny123's user avatar
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1 answer
390 views

How to specify input resfile for Rosetta?

I'm trying to run the following Rosetta command. ...
Seanny123's user avatar
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1 vote
1 answer
124 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?
user75619's user avatar
  • 123
4 votes
1 answer
3k 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 ...
James's user avatar
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1 answer
279 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: ...
WYSIWYG's user avatar
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1 answer
494 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 ...
shome's user avatar
  • 147
1 vote
2 answers
70 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 ...
DanielSebas's user avatar
2 votes
1 answer
59 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: ...
DanielSebas's user avatar
1 vote
1 answer
133 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: ...
DanielSebas's user avatar
1 vote
1 answer
30 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 ...
DanielSebas's user avatar
3 votes
2 answers
1k 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 ...
A. King's user avatar
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3 votes
1 answer
106 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 ...
DanielSebas's user avatar
0 votes
2 answers
66 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?
DanielSebas's user avatar
0 votes
1 answer
14 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 ...
DanielSebas's user avatar
0 votes
1 answer
86 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.
Pratik Dutta's user avatar
1 vote
1 answer
180 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 ...
Pratik Dutta's user avatar
0 votes
1 answer
36 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 ...
DanielSebas's user avatar
2 votes
1 answer
53 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 ...
DanielSebas's user avatar
2 votes
2 answers
101 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: ...
DanielSebas's user avatar
1 vote
1 answer
271 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 ...
entropy's user avatar
  • 23
1 vote
2 answers
241 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: ...
DanielSebas's user avatar