Questions tagged [protein-protein-interaction]
The protein-protein-interaction tag has no usage guidance.
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Which molecular interaction (MI) terms refer to dierct binary interaction detection techniques?
I am currently researching protein pairs that engage in direct binary interactions. My primary sources of information are databases such as STRING, where experimental evidence is often annotated with ...
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Protein-Protein Simulation using Gromacs
Can we do protein-protein simulation through Gromacs? if yes, can anyone teach me the correct procedure to get this done.
Thank you,
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ProteinPromt installation
i dont know how to build/pull this container (https://codebase.helmholtz.cloud/proteinprompt/ProteinPrompt) can you advice me how to install it?
EDIT:
My soft - Ubuntu 20.04 lts
Thanks to @M__ I ...
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How can I extract the Protein distance map data in Julia?
I calculated the distance between C-alphas using Julia,
but there is no way to extract distance map data from Julia.
I don't even know the data file form, png or csv or etc.
I don't want to extract it ...
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Why do we need to find minimum energy in a protein chain?
High–quality protein backbone reconstruction from alpha carbons using Gaussian mixture models
The above research paper is about a software tool for reconstructing a protein's main chain model only ...
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How can I clean a PDB file using VMD or NAMD?
I have 3884 PDB files generated by pd2_ca2main. PD2 CA2main is server for reconstructing the backbone of Calpha proteins using Gaussian mixture models.
All of these files have duplicate atoms or ...
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Cytoscape for coloring the nodes in the network
I need to color different categories of the proteins in the interaction network automatically. Is there any way to color each category with a different color in cytoscape? or R?
My input is 2 column ...
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What is coarse-grained modeling of proteins?
I need beginner-level study materials for coarse-grained modeling of proteins.
Can anyone supply me with entry level resources besides the Wikipedia article?
Background
Coarse grain protein modelling ...
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Build protein-protein interaction prediction deep learning model
I'm an undergraduate biology student and my thesis is on designing a deep learning architecture to predict whether two proteins interact or not given their primary sequences. I have read some papers ...
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743
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PyMol: Output Polar Contacts Between Chains to Text File
I am new to PyMOL but have a very specific task that I need to do.
I have a PDB structure file of protein homo-oligomer, and I want to use PyMol to determine polar contacts between chain A and all ...
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Why isn’t ace2 included in SARS‑CoV‑2 PPI map?
I'm doing my master's thesis on drug repositioning for SARS‑CoV‑2 using AI more specifically network medicine,
I found only one human protein-protein interactions (PPIs) map from Gordon et al.
The ...
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How to access XL-MS raw data and databases?
I'm looking for databases and/or raw data of protein mass spectrometry experiments.
After reviewing xlinkdb and Proxl, I was curious to learn about other alternatives and options that allow users to ...
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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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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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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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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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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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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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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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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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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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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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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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"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 ...
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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 ...
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