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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28 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
20 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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42 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
40 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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17 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
25 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
20 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
25 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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0answers
14 views

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
36 views

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
25 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 ...
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26 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
44 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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39 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
41 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
72 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
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 ...
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3 views

How do you select only alpha carbons in a graphical representation in VMD?

I am trying to select only alpha carbons for one protein, and I'm getting into a lot of trouble. My OS is Windows 10. The most recent thing I have tried is type in the Selected Atoms bar "name CA." I ...
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1answer
37 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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30 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
61 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
25 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 ...
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1answer
44 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
41 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
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/
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1answer
133 views

Algorithmic investigation of viral proteins for vaccine design [closed]

I wish to investigate how a virus could be attenuated through targeted mutagenesis by investigating its protein mutations in order to produce an efficacious vaccine. Are there examples where the ...
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0answers
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. ...
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0answers
71 views

How to get the GO information for all the human genes?

I would like to retrieve a list of all the human genes and their proteins’ functional classification. The Gene type attribute on ensembl.org is not specific ...
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2answers
213 views

How to translate amino acid sequences to Nucleotide sequences

I want to convert a list of fasta ( protein sequences) in a .text file into corresponding nucleotide sequences. A Google search gives me result of DNA to protein conversion but not vice versa. Also, I ...
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1answer
315 views

How to interpret the GROMACS MD Simulation RMSD Graph?

Hello brilliant researchers! After virtual screening, I performed MD Simulation via GROMACS to check the stability of the protein-top hit complex by following this tutorial http://www.mdtutorials.com/...
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1answer
144 views

How could I match atom orders between a .mol2 and a .pdb?

When I was drawing conformation of Autodock result, I noticed that Autodock generated pdbqt from dlg has some structural problem (e.g. Benzene ring missing), and wants to correct this. However I ...
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1answer
72 views

protein secondary structure matching/comparison scoring

I want to compare two secondary structures of aligned proteins. I do not know exactly how to do it well. Example: ...
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12 views

Search for XL-MS datasets

I am looking for human cross-linking mass spec datasets, where the exact residues that were crosslinked are stated. Any format, say csv, ...
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50 views

Is there a modern alignment tool tailored for transmembrane regions?

I am looking for a project or tool that allows programmatic pairwise alignments of proteins but that takes care with transmembrane regions of proteins. TM regions are traditionally too information ...
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1answer
132 views

Is there any tool for fuzzy sequence matching?

Note: this question was also asked on biostars are you aware of any tool that is able to perform error-tolerant pattern-matching search on protein FASTA files? For example, I want to know, which ...
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1answer
25 views

AutoDock 4 -soft docking

How could I turn on/off the smooth potential in AutoDock4? I need to do two docking. The first one is soft docking with smooth potential and the second is re-docking without the smooth potential.
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2answers
334 views

What value of reference RMSD after docking simulation from any starting coordinate would be considered outrageous to have?

I need to lightly verify a set of docking simulations from the reference RMSD of the outputs, and as we all know reference RMSD depends on the initial coordinates of the ligand set. What value of ...
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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 ...
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1answer
98 views

how to Know the longest ORF in Protein?

I have a protein Seq. and I want to know how to Know the longest ORF in this Protein? and if there is any tutorial for this process ??
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3answers
96 views

How to obtain the standard gene name

I have a list of genes and proteins extracted from literature. How can I convert them into standard gene names.
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1answer
34 views

Principle of TMT Tags in Multiplex Proteomics

I am new to proteomics research and analyzing mass-spec data. I am trying to learn more about the theory/principle of TMT tagging (a type of isobaric labeling) coupled with LC-MS/MS spectrometry. I ...
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1answer
40 views

Annotating conserved protein domains in bacterial assemblies

I understand the basic principles under which RPS-BLAST operates: search a protein (rpsblast) or nucleotide (rpstblastn) query ...
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1answer
52 views

How to predict protein binding to ligands?

I want to predict from protein sequence if the protein binds to metal, nuclear or small ligand. How can I do this ? Which features are relevant if I want to use them in a machine learning algorithm ?
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1answer
42 views

How can I predict if the binding site of a DNA-binding protein is located on the promoter sequence of a gene?

Is there any computational tool or any other method to predict if the binding site of DNA binding protein is actually located on a promoter sequence?
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1answer
55 views

Alternative splicing positions on protein

I have mass-spectrometry data (Human cellsanalyzed and annotated by MaxQuant). I want to find which peptides are covering positions of former splice junctions (on the mRNA sequence), based on protein ...
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2answers
30 views

How do i map subcellular localizations to lower the number of classes to predict

For a project, I want to predict the subcellular localization of some proteins. I am a student in software Informatics at the University of applied Science HEIG-VD. Subcellular localization ...
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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 ...
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1answer
55 views

How to allow “half windows” in biopython?

I am using Biopython to examine protein sequences including the Kyte and Doolittle hydrophobicity. However, for short sequences, this returns an empty value; the value is not allowed if the window ...
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1answer
40 views

How to find the position-specific weight matrix (PSWM) for a list of genes having different sizes?

Wiki has the algorithm for finding position-specific weight matrix (PSWM) for a list of nucleotide sequences having an equal number of nucleotide. How do we find the PSSM for a list of nucleotide ...
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1answer
30 views

How to interpret amino acid representation

What is the difference between C383S and C383A? For C383S, does it mean Cysteine(C) position 383 in the sequence and its next amino acid connect to it is Serine(S)?