Questions tagged [proteins]

Questions relating to proteins, the chains of amino acids that form three-dimensional structures carrying important functions of life. Protein sequence, structure, similarity, domains, etc.

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Convert .smp from CDD into HMM file

Is there a method or tool to convert a .smp file from CDD (Protein Domain File) into a HMM file? I downloaded the CDD files from the FTP site and am more familiar with domain searching with the HMMer ...
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1answer
25 views

Holistic enzyme activity determination with computation [closed]

I'm currently working on a program which will determine the activity difference between an original enzyme and a variant with just 1 or 2 variants. Of course, I'm not talking about the "kinetic ...
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1answer
22 views

How to get 2d/3d structural coordinates from a PDB file?

Is there a way we can get 2d/3d structural coordinates like in (x/y/z) manner from a pdb file. I have looked a believe that the coordinates are in below line: ...
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Do proteins move inside the cell? [closed]

Do proteins move inside the cell and how fast do they move or move? Please support your answer with articles or books.
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1answer
27 views

Extract features from fasta sequences and train the classifier

I am new to the bioinformatics field. I have positive and negative protein sequences for acetylation PTM. Now, I want to train a classifier, say SVM. What will be the next step? How can I convert ...
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13 views

phosphosite nomenclature and conversion (phosphoproteomics)

I have a dataset containing the following kind of phosphorylation sites nomenclature: ...
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2answers
107 views

Why GAG protein HIV-1 (virus) is in Staphylococcus sp. SS21 and in Klebsiella quasipneumoniae (Bacteria)?

I am one ignorant... Why GAG protein HIV-1 (virus) is in Staphylococcus sp. SS21 and in Klebsiella quasipneumoniae (Bacteria)? These are the links in GenBank: ...
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Java Protein Comparison Visualisation

I have project where I am required to build a visual analytics tool into an existing Java project to visually compare and analyse protein sequences from SwissProt, GenBank, EMBL etc. (downloaded from ...
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1answer
64 views

What unit is the length of a protein measured in?

Sorry if this question is obvious - I'm not familiar with proteomics so I'm not sure of the standard units. In this paper, it talks about using the length of a protein to calculate the NSAF value. ...
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2answers
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How can I convert Protein ID to PDB ID?

I have a list of Protein ID such as Q9S9U6, A2XLL2, Q06402. What name is this ID? UniProtKB ID? And how can I get PDB ID from this list? Is its PDB ID only one? I'm using Python. Get a list of PDB ids ...
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1answer
100 views

What origins for virus HIV1?

What origins for virus HIV1? This is the alignment of a small part of the POL protein of the HIV1 virus GenBank KU749412.1, with the POL protein of the Visna virus GenBank L06906.1 ...
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How can I get properties from each one letter amino acid?

Im using python and wish to get properties from each one letter amino acid? I mean M(Met) => Density:1.340, MW:149.21... The RDkit methods atom.GetSymbol(), atom.GetDegree() permit this and I am ...
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1answer
53 views

Align the HIV-1 Gag protein with the Gag protein of Visna virus

Align the HIV-1 Gag protein with the Gag protein of Visna virus Background Visna virus is a lentivirus causing encephalitis in sheep The problem is align the follow two protein Gag of viruses HIV-1 (...
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2answers
32 views

Functional Annotation vs Functional Enrichment--which one should I use for Network Analysis?

I am currently working on a network pharmacology project where I am supposed to find out the possible diseases our drug might have an effect on. I am not a bioinformatics student, so my knowledge in ...
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5 views

Mutated residue number shown wrong in foldX yasara

I am trying to mutate phenylalanine 274 position in Uracil DNA glycosylase with alanine. The pDB file has the protein starting from 82nd residue. After the repair the console shows FA161A. The residue ...
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1answer
50 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 ...
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1answer
54 views

Mining documents for nucleotide and peptide sequences

The text mining literature has an emphasis on identifying and normalizing gene names, mutations, pathways, concepts, and so on. I haven't been able to find much, however, on methods for extracting ...
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Python/Biopython - Replace amino acid residue on MSA with “z” from a list of unaligned positions

I'm trying to programmatically replace a set of amino acid residues on an MSA with a "Z" from a list of unaligned positions. Any ideas on how I could do this? Input: a list of unaligned ...
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36 views

Please help me with my command!

I am looking for a command to count the total number of unique proteins in a file. For instance I wrote a command to BLAST XYZ proteins as query against the DLY proteins as a database to determine the ...
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1answer
60 views

amino acids substitution probability [closed]

I'm looking for the probabilities of amino acid substitutions in protein sequences. A matrix of probabilities for every combination of amino acids (something like BLOSUM or PAM matrices but more ...
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1answer
37 views

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)?
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23 views

Error while splitting PDBQT file

I am trying to split to a pdbqt file containing 178 compounds into individual pdbqt files. I have been using the Autodock Vina_split.exe file to split the multiple entry file however I keep running ...
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2answers
43 views

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 ...
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1answer
47 views

PDB residue numbering

The residue numbering in PDB (in my understanding) coincides with UniProtKB align. However, this might not be consistent with that in PDB fasta file. To complicate it further, UniProtKB align can be a ...
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1answer
31 views

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 ...
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1answer
61 views

Modifying protein_scale in ProteinAnalysis in SeqUtil in Biopython?

Is there a way to give weight arguments to each of the residues when using protein_scale in the ProteinAnalysis module of Bio.SeqUtils.ProtParam? I thought this would be done with the window and edge ...
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1answer
65 views

Seurat DE t.test

I am new to the Seurat package and was looking at the tutorials on the Seurat website and am just curious to know if there is any way to perform a t.test for the expression of a specific gene between ...
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1answer
83 views

Identification of starting point for the synthesis of a protein

identify where is the starting point for the synthesis of a protein in the DNA For indentify a starting point in RNA or DNA my function search all ATG or M in the sequece and report the linear ...
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1answer
103 views

Human Herpes Virus, fusion motif in protein vs. SARS-CoV-2?

Is it possible that the fusion with cell propriety of Human Herpes virus, I see X14112.1 in GenBank is due to protein UL36 (tegument of virus) starting in linear position 2685 ??? ...
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1answer
26 views

Calculating Isoelectric point from a multifasta file

I need to calculate Isoelectric point from a multifasta file, is there any python code or web tool that allows me to do that?
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1answer
108 views

How do I convert an Excel file (.xlsx) to an .smi file format?

How do I convert an Excel file(.xlsx) to .smi file format? The original file I have is an excel file containing over 27,000 ligands. I am going to using the Padel Descriptor software to calculate the ...
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1answer
26 views

Is it possible to predict protein-ligand binding kinetics using machine learning? [closed]

I would like to work on a project that involves the prediction of protein-ligand binding kinetics. What might be the feature that is relevant for the prediction?
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1answer
36 views

Do I need to remove water molecules before protein-ligand docking?

I am going to screen small molecules against a protein target. Do I need to remove all the solvent molecules before performing VLS?
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Residue coevoution from position wise residue preferences rather than multiple sequence alignments

Hello experts in residue coevolution analysis of proteins, I am looking for a way to calculate residue coevolution (coupling scores) between all pairs of residues of a protein. The issue is that ...
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0answers
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Is there a software that can predict protein-DNA binding?

Is there any software that, given a DNA sequence as input, can predict what protein/ type of protein can bind to the DNA. The sequence of interest is a potential transcriptional regulator, I want to ...
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0answers
30 views

Available Protein sequence alignment dataset and HMM model

It may better to move the question here. I am new to biology and I find my algorithm may be used in the Protein sequence alignment, since it is a henced HMM model. I find that people use HMM to ...
2
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1answer
129 views

MSA (protein) with biopython or something else?

I am very new to bioinformatics (and python in general), but I would like to use python to more efficiently analyse enzymes both in terms of structure and functio, using Jupiter notebook. I would like ...
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1answer
46 views

how to evaluate neural networks

I have made some architectures of neural networks in order to classify proteins in three categories. I have calculated true positive, true negative, false negative, false positive, Mathews, ...
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0answers
74 views

How can I interpret multiple alignment results?

I would like to ask how I can interpret objectively multiple alignment results. I have used JALVIEW and TCOFFEE. I would like to ask if consistency score plays any role in the interpretation? I ...
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1answer
48 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 ...
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1answer
178 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 ...
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1answer
42 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 ...
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1answer
43 views

Finding discriminating positions for a sequence alignment column

I don't have any theoretical background in biology, so forgive me if my question is a bit.. well..dumb. I'm trying to use a Monte Carlo approach to find the discriminating position of a given sequence ...
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0answers
91 views

What exactly does each of InterPro, PANTHER, Pfam bring to the table individually in classifying a protein?

I would be very grateful if somebody could sketch out the methods Pfam and PANTHER use to assign a family to a given protein and how they are different. My (cursory) understanding is that InterpProp ...
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1answer
102 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 ...
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1answer
30 views

How to filter the PDB for single-domain proteins with full length 3D-structures solved

I am trying to reproduce a machine learning model that has been developed here. As one of the datasets, they use single-domain proteins with full length 3D-structures solved. Since I don't have a ...
2
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1answer
63 views

Translating a genome sequence into possible frames

I have a sequence below from MYC gene about which I need to translate the sequence in all possible frames AND identify (for each frame) which codons are actually used in MYC ...
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1answer
47 views

Identifying proteins in a concatenated protein sequences [closed]

I have a 120-concatenated protein sequence in a fasta file. I would like to split by proteins. How can I identify each protein?
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1answer
506 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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24 views

What are the meanings of these transcript ids?

I have three types of transcripts for Rosa chinensis "Old Blush" homozygous genome v2.0 from GDR genome browser. ...