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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59 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
66 views

De novo motif discovery in protein sequences

I am trying to build a features matrix to be used for Random Forest based classification. I'd like to add, as features, short motifs which are common to all the protein sequences belonging to a ...
2
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1answer
132 views

How can the Autocovariances, autocorrelations, and autocorrelation coefficients be calculated from a Protein Amino Acid Sequence?

Given a normal protein sequence with the 20 standard amino acids, how can the 'Autocovariances', 'autocorrelations', and 'autocorrelation coefficients' of the sequence be calculated? What is meant by ...
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1answer
119 views

Download proteomes from NCBI based only on binomial names

I'm trying to download around 2000 proteomes from NCBI, but all I have is the genus and species e.g: lophodermium_seditiosum trichoderma_harzianum Does anyone know ...
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1answer
127 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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1answer
48 views

Proteins that cannot form biofilm?

I am trying to build a machine learning training set for bacterial protein sequences that form biofilm, and that cannot. I collected the positive sequences from the GO ontology website but for ...
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1answer
83 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 ...
2
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1answer
150 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 ...
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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2answers
636 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
68 views

API/website for blasting peptide sequence against database of all plant proteomes

I would like to blast a peptide sequence against all available plant proteome databases, i.e. a blastp metaproteome analysis. What tools are available? Which ...
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2answers
257 views

Protein expression units?

I'm starting for protein expression analysis. In gene expression, we have TPM, RPKM etc. However, all I can see for protein expression is: "High", "Medium", "Low" and "Not detected". https://www....
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1answer
139 views

Searching for protein motifs with MEME

I am trying to look for motifs in a set of proteins returned by a mass spec experiment using MEME. The experiment was carried out in the yeast Candida albicans. Does anyone know if it is worth ...
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0answers
115 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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0answers
100 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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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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80 views

What is the difference between Assignment and Prediction?

I am absolutely new to Structural Bioinformatics (I only started last week). I am working on the secondary structure assignment/prediction (actually I am not sure) of proteins using ML. When it comes ...
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1answer
38 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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1answer
74 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
56 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
436 views

Comparing two multi-fasta files of the same set of proteins with parser - to find and count mutations after treatment

My task is to count the mutations occurred in several proteins after a treatment. The sequences are all present in the two files in the same order. I opened both files with the FASTA parser (...
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1answer
41 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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1answer
49 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
44 views

Download program for ΔG for TM insertion

I am trying to calculate the ΔG of TM insertion for many protein sequences. Has anyone come across the source code or a programmatic version for the von Heijne ΔG for TM insertion? The web server is ...
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1answer
76 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
19 views

Retrieval of metadata of a batch of 3953 sequence data from GISAID database

Can we retrieve metadata (such as date of collection of sequence data, location, etc.) for a batch of 3953 GISAID accessions from the GISAID database? I am not very comfortable with GISAID. I am more ...
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1answer
65 views

How to calculate RMSD and binding energy from the already docked ligand-receptor

I have the following PDB file that looks like this. It is downloadable here. This PDB already contains ligand and receptor together. The red molecule is the ligand and the yellow is the receptor. They'...
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1answer
44 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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1answer
119 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
48 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
222 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
88 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
53 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
132 views

How to predict the distance between two residues in a protein sequence

I have some protein sequences and I need to predict the physical distance between each two residues in the protein when folded correctly in 3 dimensions; I need to predict this distances just by ...
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1answer
232 views

Filtering out all seqs with mutations of list2 from list1

I have 2 lists, list1 and list2, of protein sequences of the same given gene in different strains. In ...
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0answers
12 views

How to find disease association of disgenet with string db in homo sapiens

I want to work string-db to read the protein-protein interaction from it and I look up disease association from disgenet but the Ids do not seem to match-up and I do not know what to do. for example ...
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0answers
18 views

Why ace2 is not included in SARS-COV-2 PPIN map?

I'm doing my master's thesis on drug repositioning for sars-cov-2 using AI more specificaly network medicine, I found only one PPIN map from Gordon et al. but it doesn't include the ace2 protein which ...
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0answers
26 views

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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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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0answers
29 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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0answers
17 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
39 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
33 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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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
81 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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0answers
25 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
13 views

Finding the conserved region of protein in a given set of Kingdom

We have to find the conserved region of proteins in a given set of kingdom and we have to give more weightage to distantly related organism. What approach I should take to solve this problem?
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1answer
499 views

Extract certain fields using from GenBank file using Bash script

I need to extract certain lines from a GenBank file on Linux. Input file: ...
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1answer
43 views

Installing Rostlab's PredictProtein

I am trying to install Rostlab's PredictProtein in a Virtual Machine as detailed here https://rostlab.org/owiki/index.php/How_to_Run_The_PredictProtein_Machine_Image_with_VirtualBox: Download ...
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0answers
12 views

“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 ...