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Questions tagged [protein-database]

A file containing protein sequences together with corresponding metadata

Classical protein-databases are text files containing a large number of protein-sequences.

Protein sequences are represented as strings of uppercase letters, each corresponding to a different aminoacid. Each protein sequence is preceeded by a header line containing metadata (protein reference number, name, description...).

The standard fasta format looks like: 

>P31946|1433B_HUMAN 14-3-3 protein beta/alpha OS=Homo sapiens GN=YWHAB PE=1 SV=3
MTMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSS
YEILNSPEKACSLAKTAFDEAIAELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGDEGD
AGEGEN
>P62258|1433E_HUMAN 14-3-3 protein epsilon OS=Homo sapiens GN=YWHAE PE=1 SV=1
MDDREDLVYQAKLAEQAERYDEMVESMKKVAGMDVELTVEERNLLSVAYKNVIGARRASW
YYKMKGDYHRYLAEFATGNDRKEAAENSLVAYKAASDIAMTELPPTHPIRLGLALNFSVF
YYEILNSPDRACRLAKAAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDMQGDGE
EQNKEALQDVEDENQ
>.........................................................

A great amount of work in Bioinformatics relates with storing (annotating), searching and analyzing the sequences in these databases.

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Downloading all the PDB files available for a protein all at once

I want to download all the 7000 suggestions of the PDB files of that specific protein in RCSB, How should I proceed? I know that there is a download option beside each, but is there any shortcut to download all in one set?
SAMIRA
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Cytoscape Diffusion Algorithm

Can anyone tell me what diffusion algorithm is used by the tool diffusion in Cytoscape? Also, I found a plugin genemania in Cytoscape, does it do the same thing? I wish to get heat scores for the proteins in my network by providing a subset of…
Nazifa Ahmed Moumi
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How to extract chain-IDs from PDB files?

I have all the PDB files stored on my local hard disk. The files are in pdbXXXX.ent.gz format. I have a python program that reads a text file which must be in the following format: pdb_id chain_id resolution How can I prepare this plain text file…
user366312
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How can I identify acceptor and donor atoms using BioPython?

I know how to traverse through structures, models, chains, residues, and atoms in a protein chain using BioPython (which is very easy). How can I identify donor and acceptor atoms in a chain by traversing?
user366312
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Modeller script build_profile.py doesnt get the correct output

9 for protein structure modelling, by the way it runs on python2.3, i made the installation previously, when i run the script the output isnt rigth it should be an aligment of all the protein sequences and y only get the fist sequence and nothing…
alex
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How to create undirected (i)graph in R for protein-interaction data with tissue information?

I am new to bioinformatics in general and would really appreciate some help and tips with the project Im working on. My data of protein-protein interactions is stored in a table (in MySQL) with binary information about tissue-specificity. Now I am…
bi.nb21
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Importing PDB (Protein Data Bank) files directly into Unreal Engine 4

I am building a project that will use Unreal Engine 4 to display protein models. Currently I cannot find a way to directly import PDB (Protein Data Bank) files directly into Unreal. Ideally I would like to have the PDB files converted into FBX files…
Mortamass
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Hybridization of Atoms in a Protein (Biopython)

I want to find the hybridization of atoms (sp2, sp3) in a protein for a project. I am using biopython and I am struggling to code this. I couldn't find any existing code for this purpose. Is there an easy method to find the hybridizations? Note: I…
MathPanda
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How do I make a python dictionary from a string?

I am collecting protein sequence ids from this website: https://www.uniprot.org/ I've written this code: url = 'https://www.uniprot.org/uploadlists/' params = { 'from': 'ID', 'to': 'UPARC', 'format': 'tab', 'query': 'P00766 P40925' } data =…
Gabriel
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T-test comparing multiple columns to other columns

I am relatively new to R and need some help with my data analysis. In the attached table, Master Protein Accession column consists of a list of proteins that are increased or decreased in the cortex(C) under three conditions, i.e., control (C),…
Rizwan
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How to realize Multisequence Alignment with BioPython

I have multiple strings representing protein sequences ( for example ADADAAA,ADADDDCDAA and ACCC), I want to realize MSA on those such that resulting sequences have the same length. Biopython documentation seems only to explain how to handle…
nprime496
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How to plot the free energy landscape of protein structure?

I understand the question is not appropriate for this platform, but I can try if I can get some hints, I've been trying to plot the free energy landscape of a protein structure ("Chignolin"). I'm completely run out of ideas how to do that!! I've MD…
user12298516
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Unable to run python code which intends to show superimposed protein

we made a function superimpose which takes 7 arguments (PDB_id_1, Chain_id_1, Res_1, PDB_id_2, Chain_id_2, Res_2, out filename) . Then we have extracted the respective coordinates of the respective atoms from the mentioned residues in the input for…
Anas Jamshed
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How to add a Chain, Residues and atoms in pdb file?

I want to add a chain with all the residues and one carbon-alpha atom per residue using the OpenMM. Here the link of instances can be used openMM documentation . Currently I have one chain in my pdb file pdb file. Here is what I've tried: from…
user12298516
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extracting binding data in PDB files

pull out PDB binding data I want to pull out residue and hetatom coordinates in PDB files and make an evaluation of what the contact residues are. I then want to compare these residues against alignments. If these residues are conserved in an…
Mike
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