raimondilab/precogx

A predictor of GPCR couplings with G-proteins/B-arrs using Transformers

precogx's Issues

show positions in the structure panel

VAR = IUPHAR should be renamed to IUPHAR/STRING or have another for STRING

Mutation label toggle in Structure Panel

Set scaling based on Marin (0 is yellow)

Remake Emax, LogRAi & GtoPdb tables with Gene name, UniProtKB Acc and ID

Input check

Hi everybody @raimondifranc @nataliarosa9 @maticmarin

I remember that @nataliarosa9 had shown us in the previous call input checks that she created (eg: only alphabets in FASTA etc). So here I am making a list of other checks that we have to make in the input.

We all can edit (add more items) this checkbox-list and request @nataliarosa9 to include them also:

• Input accepted only in FASTA formatted or precog format (eg: DRD1/F61P)
• If the input is FASTA, it cannot be more than 1024 residues long (correct @maticmarin?)
• Use cannot input more than 15 sequences in one go (counting both WT and MUT), right, @raimondifranc?

Add heatmap/contact under the sequence panel (with dropdown option)

Hey @maticmarin , could you share the contact map pairs? thx!

Show best G-protein by default for first input

HELP/ABOUT page

Remove distance label from Structure panel

Add snapshot button in Structure Panel

Features

• Add PCA panel
• Dropdown option in PCA panel to select G-protein/labels
• Update precogx script to include point mutations
• Update precogx webApp to include point mutations
• Automate GPCR seq SQL DB
• First GPCR automate on page load
• Show Bonds
• Add result URL

Structure of class B, C etc

Legend in Sequence Panel and increase the by default sequence length

Run PRECOGx on all GPCRs and store info in SQL DB

Hi Gurdeep,

yes, I think that 25 sequences is already pretty generous .... we should
also provide a refreshing page with the URL of the output, and possibly the
option to provide an email, in case the calculations will take a while.
We should probably also run the prediction for all the GPCR sequences at
least of the human GPCRome (and possibly from swissprot) and store this
information in a database (SQLite or MySQL), so to speed up the analysis
in those cases where a certain sequence was already analyzed or for the
mutation analysis case (the WT embeddings predictions should already be
there).

Talk to you on Thursday.
Best,
Francesco

On Tue, Dec 7, 2021 at 11:52 AM Gurdeep Singh @.***>
wrote:

Hi everybody @raimondifranc https://github.com/raimondifranc
@nataliarosa9 https://github.com/nataliarosa9 @maticmarin
https://github.com/maticmarin

I remember that @nataliarosa9 https://github.com/nataliarosa9 had shown
us in the previous call input checks that she created (eg: only alphabets
in FASTA etc). So here I am making a list of other checks that we have to
make in the input.

We all can edit (add more items) this checkbox-list and request
@nataliarosa9 https://github.com/nataliarosa9 to include them also:

• Input accepted only in FASTA formatted or precog format (eg:
  DRD1/F61P)
• If the input is FASTA, it cannot be more than 1024 residues long
  (correct @maticmarin https://github.com/maticmarin?)
• Use cannot input more than 25 sequences in one go (counting both WT
  and MUT), right, @raimondifranc https://github.com/raimondifranc?

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Originally posted by @raimondifranc in #14 (comment)

Remove the length bubble from Sequence panel

Example of classes B, C etc on home page

Accept all kinds of input format

• Gene name
• UniProt Acc
• UniProt ID
• FASTA seq from UniProt (both sp and tr)
• Accept "\n" lines
• Ignore '#' lines

Continous coloring scheme for assays and binary for IUPHAR

Re-color the PCA with grey and varying shades of green

Fix Structure view

Show AlphaFold monomers

Show scaled value of input for GPCRome

Structure panel features 07.12.2021

• Radius proportional to number of contacts the positions makes
• Change bond colors to red/blue to highlight enrichment/depletion
  - [ ] Use SIFT's XML files to map from UniProt to PDB residues
• Include B-arr structures as well

Not clickable with filtered columns (G-proteins)

Slider range

Hi @nataliarosa9 , could I ask you to please fix the aesthetics of the slider? I am bad at HTML/CSS stuff

• Add HTML/CSS to the slider
• Insert label "Log-Odds score >"
• Move it to the right-end of the panel

Thanks

Small yellow bubbles still visible in Structure of WT

BLASTp against PDB file-derived sequence and not PDB FASTA sequence

check structure mapping issues in the structure panel

Reduce the label size in structure

GPCR embeddings

/data/Users/marin/transformers/gpcr
This is the 33rd layer

PCA values for all GPCRs

Hi @maticmarin, I think you will have to re-run the train script in my directory to save the PCA matrix of all the GPCRs (at least class A) against all the best models (G-proteins). Please note that I removed > from your extract.sh as I am already saving the NumPy format.

Thanks!

PCA panel 07.12.2021

• Dropdown to show IUPHAR/Shedding/ebBRET-based coloring
• Dropdown to show either all 33 layers or the best one (G-protein specific)
• Always show GPCRome in the background (use grey or reduce opacity if the given GPCR is not in the selected label)
• Show also WT on PCA when showing for MUT
• Show GPCR name on hover
• Disable IUPHAR for some G-proteins like GoA and Barrs (instead show from STRING)
• Include B-arr too

Make firs and second column clickable

heatmap clickable to show on structure

select the assay and PCA dropdowns based on the last click

Results panel 07.12.2021

• Include IUPHAR/Shedding/ebBRET assay info also
• Show check-boxes
• Show download option
• Include B-arrs too

Automate BLASTp of PDB seq files (not FASTA) against GPCRDB sequences

Upload button on the home page

Hi @nataliarosa9
Could you also provide an upload button on the home page?

Move from Chain ID to Entity ID for 3D structures (adopt CIF format)

SCOP GPCR superfamily HMM

Hi @maticmarin, @raimondifranc
Could any of you paste here the path to the file?

thanks

Set Latest-3D workflow to every Friday at 15:30

Contacts panel 07.12.2021

• Center around zero
• Change color range to something else (red clashed with mutation color)

Order of labels in the heatmap

Contacts file

Hi @maticmarin, when you update the contacts file specific_position_score.txt, please remember to add Barrs too. Also, could you provide Superfamily numbering? (see here)

Thanks

Add Barr structure information to automated workflow

WT and MUT always overlap in the PCA panel

Though when you select only Wt and MUT individually, it works fine

Tool tip to show BW on hover in sequence panel

Increase BW label size in the structure panel

Limit number of sequences to 15 by default