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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19 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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48 views

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

I would like to find a list of all the human genes and their proteins’ functional classification. The Gene type attribute on ensembl.org is not specific enough, ...
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2answers
61 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
49 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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28 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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58 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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9 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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35 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
102 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
23 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
189 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
55 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
60 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
93 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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2answers
181 views

How to find common sequences among 6 multi-fasta files

I have 6 multi-fasta files, every of them contains ca 1500 sequences like that: ...
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21 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
37 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
46 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
28 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
38 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
41 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
30 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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8 views

How to define TMH boundaries from structures in OPM at the sequence level

I am trying to find which are the transmembrane residues in a given structure. OPM uses PPI to orient TMPs in a membrane space. OPM looks to have the boudnaries at the atomistic level from their ...
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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)?
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1answer
36 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
78 views

How do I perform a pathway related grouping of genes?

I have a list of gene names from the analysis of my mouse single seq data. I want to perform a simple grouping of the genes based on the pathways to which they belong or pathways through which they ...
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2answers
93 views

Database for proteome-wide predictions of protein structures

Accuracies of protein structure predictors have improved quite a lot in recent years. Algorithms such as Rosetta have gotten robust enough to predict structures of large number of proteins. However, I ...
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1answer
45 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 ...
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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
61 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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0answers
624 views

Searching for start and stop codons for protein sequencing of contigs

I need to convert contigs into their respective protein sequences given a reference genome (i.e. I need to take a substring, whose position is already known on the string, and I need to locate the ...
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1answer
101 views

How to calculate Gene Ontology terms in python

I am testing different Protein-Protein Interaction networks alignment tools. I observed that all alignment tools show some ...
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0answers
83 views

How to assign the best gap penalty and gap extension penalty using BLOSUM65

For an assignment I must do a pairwise optimal local alignment using BLOSUM65 and five protein sequences. The algorithm I want to use is the Smith-Waterman. Context protein sequencing using Blastp: ...
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1answer
71 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
278 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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3answers
82 views

How to get the product of a CDS

I need the name of the protein in /product="protein_name" using bash commands. Beware, there is a lot of whitespace between lines. ...
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2answers
55 views

Genomic coordinates of predicted binding pocket

I would like to know the genomic coordinates of a proteins ligand-binding pocket. For example, on this PDB page you can see that there is xray crystallography data for how CYP2C9 interacts with two ...
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1answer
128 views

How to calculate Moreau-Broto autocorrelation, Moran autocorrelation, Geary autocorrelation from protein (amino acid) sequences?

I want to code Moreau-Broto autocorrelation, Moran autocorrelation, Geary autocorrelation in Python 3.6 from the scratch for amino acid sequences without using any package. Unfortunately, I have not ...
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1answer
61 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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2answers
10k views

How to scale the size of heat map and row names font size?

I have an expression data matrix (120X15; 15 samples and 120 genes), my heatmap looks blurred and raw names (gene names) looks very small and can not read. How can I improve my scripts? Here is the ...
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24 views

What is the most efficient method to identify a protein that has undergone post-translational modifications by an enzyme?

I am in the process of conducting research on a wide array of proteins that are all post-translationally modified by the human enzyme GSK-3beta. What is the best to show (using peer-reviewed research ...
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1answer
94 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
58 views

Determining position of side chain hydrogen in glycine residues from coordinates of backbone atoms

I have a dataset of pdb-format protein structure decoys/models generated by tertiary structure prediction programs. Many of these are missing hydrogen atoms. Specifically, I'd like to determine the ...
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1answer
78 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
35 views

Automating download of results of Drug and Drug Target Mapping

The drug and drug target mapping tool shows the top 3 PDB IDs for each drug based on the drug target sequence similarity search and ligand id search. Is there a way to get all the PDB ids of the drug-...
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2answers
142 views

If I modify a PDB file with a specific mutation, how to minimize energy?

I have a series of proteins that are all phylogenetically related. Only one of this proteins is currently X-ray crystallized. Is it valid to modify the reference PDB file (I mean by hand) to match ...
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1answer
101 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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2answers
123 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....