Soren
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How do I create Protein Ligand images
3 votes

Yes, PyMol is one of the best programs for rendering IMO. Usually, you would create folder with your PDB file and a file that contains all the commands to create your image like shown here. You can ...

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How I can change the name of multiple files at once in R or terminal?
3 votes

If your filenames do not contain blank spaces, you can do it with a for-loop in bash: Make a test run with echo so that the command is only printed but not yet executed: for i in *.vcf; do echo mv $...

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Running MaxQuant on Linux
2 votes

I have been running MaxQuant quite frequently on Linux. I would use conda to create a dedicated environment and install mono. # create the environment conda create -n maxquant -c conda-forge mono # ...

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How to convert a SDF molecular structure file to a pandas dataframe with Python?
Accepted answer
2 votes

It is easily done with RDKit: from rdkit.Chem import PandasTools fn = '/mypath/dataset.sdf' df = PandasTools.LoadSDF(fn, embedProps=True, molColName=None, smilesName='smiles')

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What is the best way to drop alignment artifacts in sequence objects in biopython?
2 votes

I think the .ungap() is what I was looking for. def read_fasta_file(fn): with open(fn,'r') as file: fasta_sequences = SeqIO.parse(file, 'fasta') sequences = pd.DataFrame([{ ...

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predict the IC50 after using Schrodinger suite Glide tool for docking
Accepted answer
2 votes

I don't think it is possible just from the docking scores. Docking scores are designed to give you an estimate of the binding affinity (entalphy), but they do not take entropic contributions into ...

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median normalization for proteomics
Accepted answer
2 votes

The kind of normalization depends on what you what to explore. So, there is no absolute answer to this. Different normalizations highlight different aspects of your dataset. There is a nice paper for ...

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Principle of TMT Tags in Multiplex Proteomics
Accepted answer
2 votes

TMT stands for tandem-mass-tag. The idea is to tag different samples with one of the tags then pool all samples together and run them through the mass spectrometer together. Then the reporter groups ...

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Is there a Python package to convert InChi to molecular structures?
2 votes

Slightly modified Matteos answer: import requests def get_smiles_from_inchikey(inchikey): r = requests.get(f'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/{inchikey}/property/...

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Post docking evaluation
2 votes

You can run a Molecular Dynamics simulation to see if the pose is stable and whether the protein changes/adapts it’s conformation. You can calculate the ligand efficiency, the docking score divided ...

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Asking for Docking programme
2 votes

Autodock-Vina is a free molecular docking solution. You need to generate different input conformations for each ligand though, e.g. with RDKit. Here is a link to tutorial

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Can a gff file be converted to a fasta file?
2 votes

I extracted the sequence contained in the gff file into a separate file and added a header according to the fasta file format specifications. I named that file ERS654933.fasta and then used prokka to ...

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Reproducible PyTorch Model
1 votes

There is this nice function from Kaggle: def seed_everything(seed=1234): random.seed(seed) os.environ['PYTHONHASHSEED'] = str(seed) np.random.seed(seed) torch.manual_seed(seed) ...

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Getting System.IO.FileNotFoundException with MaxQuant running on Linux with mono
1 votes

...seems the mqpar file was not compatible with the maxquant version. Make sure the mqpar.xml file shows the same version number as the MaxQuant binary. MaxQuant is not really made for the command ...

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Why does a missing label 11plex TMT shows up at almost 50% intensity compared to other labels?
1 votes

The developers answered along these lines: This might be a normalization artefact. Reporter is normalizing the ratios so that the median is 1. So, if the label is almost not present the noise gets ...

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How to export peptide-shaker data from commandline?
1 votes

You have to start PeptideShaker calling java with the -cp argument an input project file and provide a comma/space-separated list of integers for the reports you want to export: java -cp ...

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Rdkit.Chem.Draw.savefig() creates empty figures
1 votes

For some reason you have to set bbox_inches to tight. Without that rdkit does not fit the molecule into the canvas and might plot an empty figure. fig.savefig('mol.jpeg', bbox_inches='tight')

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How to see effect of point mutation in PyMOL?
0 votes

You could run a molecular dynamics simulation for example with Gromacs or Charm. The problem with pymol is that the structure is static and you don't know how much tension that point mutation creates. ...

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How to run MaxQuant in command line mode?
0 votes

You can now install MaxQuant (v. 1.6.10.43) with anaconda: conda install -c bioconda maxquant and to run MaxQuant simply with: maxquant.sh mqpar.xml Reference

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How to use pyopenms.FeatureFindingMetabo() for peak picking in pyOpenMS?
0 votes

My minimal procedure based on the code that @deeenes shared for a single file. Comments to improve this solution are highly appreciated: files = list_of_filenames feature_map = oms.FeatureMap() ...

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Can Maven (mass spectrometry software) read mzML files?
0 votes

No, Maven still can read only mzXML files.

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

The molecular docking programs usually tread the target structure as rigid. It does not know which atom belongs to the receptor and which is bulk water. So, if you keep the water in the structure the ...

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