Questions tagged [protein-protein-interaction]

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Why is there a chloride ion in this 3D model?

Here we have a 3D model of a sequence that match with this sequence VVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIK in Blast the 3D structure is here Why is there a chloride ion in this 3D model?
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Could not parse String db protein interaction network PSI-MI XML file with GenerateDS Python parser

I want to get a list of all evidence types for interactions String db finds based on a list of gene names in order to filter in only those pieces of evidence I have confidence in. I downloaded a ...
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13 views

How do protein-protein interaction databases work?

I am a student and just trying to gain a base level understanding of PPI databases and how to interpret their data. For example, when inputing multiple genes into String, does it only give protein-...
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25 views

Error in ROSETTA flex ddG tutorial

I'm trying out the ROSETTA flex ddg tutorial (https://github.com/Kortemme-Lab/flex_ddG_tutorial). When running "Example 1" I get an output but with apparently empty folder. When running the "Analysis"...
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1answer
17 views

What's the difference between Barycenter Centrality and Closeness Centrality (Freeman)?

What's the difference between Barycenter Centrality and Closeness Centrality (Freeman)? Barycenter scores are calculated as 1 / (total distance from vertex v to all other vertices) in a strongly ...
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1answer
34 views

Outputting crunchable list of HBonds from Pymol

X-posted from the Main Stack Overflow because folks here are possibly more familiar with PyMol(?) I have been trying to assess the strength of an interface I want to mutate using Pymol. What I am ...
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2answers
16 views

Difference between PPI networks and Gene Co-expression networks

What exactly is the difference between protein-protein interaction (PPI) networks and gene co-expression networks? Based on my rudimentary understanding, PPIs are constructed from gene co-expression ...
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21 views

Can I pull a jackhmmer output file into ClustalO for pairwise alignments?

I'm still working on figuring out how to send ClustalO multiple jobs. I have a hmmer output and was looking to do a mixture of pairwise and local alignments on a subset of these. Is it possible to ...
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2answers
94 views

Can I automate CLUSTALO and output alignment sequence identity?

I've detected homology between targets of ligands in drugbank and proteins in the proteome of a pathogen. I've parsed the output very rudimentary and calculated my query coverage. This exists in an ...
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56 views

Mapping a disease integrome on the whole genome

I'm currently studying a disease which has complex traits (non mendelian disease). Very few data are available on humans. But data collected from cell/animal models have been used to identify human ...
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1answer
47 views

How to calculate lipophilicity of proteins?

The question says it all. I want to calculate lipophilicity of proteins to screen the compounds out for antigen-antibody interactions.
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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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61 views

What is the best way to start with Structural bioinformatics with zero prior experience? [closed]

My undergraduate thesis is on the topic "Ligand design from protein-protein interfaces" and my PI has asked me to learn the basics of Structural bioinformatics over the summer so that I'll be able to ...
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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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766 views

Receptor-ligand database

How can I find ligands of receptors (or vice versa)? For example, I want to find the receptors of IL-8 (CXCL8).
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1answer
110 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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1answer
156 views

Machine learning using protein-sequences

I'm participating in a bioinformatics machine-learning seminar at my university. The main task is predicting binary classification of protein-protein interactions using sequence data as input. One ...
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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 ...
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2answers
290 views

pvalue calculation of protein-protein network with permutation test

Note: this question has also been asked on Biostars I have performed a network recreation analysis based on the interactions of proteins from String db. I wanted to know if the interactions have ...