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Recent Replies
Answer: Which tools do you recommend me use to get the maximum information of a protein
by
fileyfood
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For modeling, check out the [AlphaFold Server][1] for predicting protein structure.
[1]: https://alphafoldserver.com/
Answer: Tools for predicting protein function?
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fileyfood
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Have you read the [wikicrow entry][1] on the gene? Wikicrow is an LLM generated jumping off point, so while you should treat the informatio…
Answer: Map genome positions onto protein coordinates?
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fileyfood
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You can use [ensemble VEP][1] to get the protein coding changes.
You can then use [the Genomics 2 Proteins portal][2] to map these changes…
Answer: Online tool for creating figures of gene with its features
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fileyfood
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Yes, check out [the Genomics 2 Proteins portal.][1] The tool allow you to map any feature, including domains onto a protein structure and c…
Answer: Simple tools for creation of figures of gene and protein structure
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fileyfood
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Yes, check out [the Genomics 2 Proteins portal][1]. The tool allow you to map any feature, including domains onto a protein structure and c…
Answer: To create amino acid substitution in protein structure
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For more intensive analysis, you can consider MD simulations of the mutant protein where you relax the structure after mutation using tools…
Answer: Where Can I Get The Secondary Structure Of A Protein?
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[UniProt][1] will show the secondary structure for areas of the protein with available SIFTS secondary structures (from PDBs). If there is …
Answer: Database Of Structurally Derived Protein Features
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fileyfood
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A few databases that have protein structural features are [UniProt][1], [the RCSB PDB][2], and [the G2P portal][3]
Structural features fro…
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There is a tradeoff between speed and information for a mutation:
(1) Fast, visual: tools like MutationMapper[enter link description here]…
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For a quick visual analysis of how a mutation relates to or features in 3D, the [Genomics 2 Proteins portal][1] is designed for this purpos…
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You can start by visualizing protein structures in a variety of different tools, including offline tools like PyMOL (has an online version …
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The [Genomics 2 Proteins portal][1]'s Interactive Mapping module is designed for this purpose. You can upload sets of mutations or experime…
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The OP wanted to directly compare the Mutants (Analysis 3), and the analysis I have proposed for their consideration will do that, whilst c…
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Actually, I tried two methods—one with batch effect correction and one without—and the results were completely different.
In the UMAP witho…
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You cannot remove batch effects where they overlap perfectly with a biological condition of interest.
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