Proteopedia:Development: Difference between revisions

Line 2:

* [[Proteopedia:Wishlist]]

* [[Proteopedia:Problems]]

==Rehovot, March 2023==

(12-20 March) ''[[User:Angel_Herraez|AH]], [[User:Jaime_Prilusky|JP]]'' and [[User:Joel_L._Sussman|JS]]:

=== Sequence Tool ===

This widget reads the information in any pdb- or mmcif-formatted file included in a Proteopedia page and parses its content to display the protein sequence (for all chains) alongside the JSmol 3D-view panel.

The sequence includes information combined from both the COORD and SEQRES records in the PDB file, hence including physical gaps, numbering gaps, sequence microheterogeneity and inserted residues.

The visitor of the page may interactively explore the structure and the sequence:

* A click on a letter in the sequence listing will display the full information of that residue and will highlight it in the 3D structure view.

* A click on any atom in the 3D view will highlight the matching residue in the sequence listing.

* A search box accepts a residue number, or a residue letter, or a partial sequence; matches will be displayed on both the sequence and the structure.

This tool is included in all pages automatically generated in Proteopedia for any new structure

deposited in the Protein Data Bank (seeded pages) and may be included at will in user-generated

pages. Documentation is at [[Seqtool]]

=== Colouring schemes for AI-predicted structures ===

Procedures were developed to apply several colouring schemes in the 3D structure view that reflect the reliability or uncertainty in the coordinates of each residue in predicted 3D protein structures coming form several platforms and databases, namely:

* [https://robetta.bakerlab.org RoseTTAFold], with RMSD data for each atom or residue.

* [https://alphafold.ebi.ac.uk AlphaFold], with pLDDT score for each atom or residue.

* [https://esmatlas.com/about#fold ESMFold], with pLDDT score for each atom or residue.

The functionality for applying these colour schemes was added through buttons in the SAT, and it is offered automatically depending on which data source provides the uploaded structure files.

The colour reference (legend) is automatically included below the caption area under the 3D view, for any new scene that was created using the colouring option.

===Prediction of structure===

A new area inside 'load molecule' section of SAT allows to enter a raw or Fasta-formatted protein

sequence, sends it to the ESMfold server and retrieves the resulting predicted structure into

Proteopedia. The structure is also loaded on SAT, ready for preparing a scene.

==Alcalá, Spain, March 2021==

Proteopedia:Development: Difference between revisions

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@@ Line 2: / Line 2: @@
 * [[Proteopedia:Wishlist]]
 * [[Proteopedia:Problems]]
+==Rehovot, March 2023==
+(12-20 March) ''[[User:Angel_Herraez|AH]], [[User:Jaime_Prilusky|JP]]'' and [[User:Joel_L._Sussman|JS]]:
+=== Sequence Tool ===
+This widget reads the information in any pdb- or mmcif-formatted file included in a Proteopedia page and parses its content to display the protein sequence (for all chains) alongside the JSmol 3D-view panel.
+The sequence includes information combined from both the COORD and SEQRES records in the PDB file, hence including physical gaps, numbering gaps, sequence microheterogeneity and inserted residues.
+The visitor of the page may interactively explore the structure and the sequence:
+* A click on a letter in the sequence listing will display the full information of that residue and will highlight it in the 3D structure view.
+* A click on any atom in the 3D view will highlight the matching residue in the sequence listing.
+* A search box accepts a residue number, or a residue letter, or a partial sequence; matches will be displayed on both the sequence and the structure.
+This tool is included in all pages automatically generated in Proteopedia for any new structure
+deposited in the Protein Data Bank (seeded pages) and may be included at will in user-generated
+pages. Documentation is at [[Seqtool]]
+=== Colouring schemes for AI-predicted structures ===
+Procedures were developed to apply several colouring schemes in the 3D structure view that reflect the reliability or uncertainty in the coordinates of each residue in predicted 3D protein structures coming form several platforms and databases, namely:
+* [https://robetta.bakerlab.org RoseTTAFold], with RMSD data for each atom or residue.
+* [https://alphafold.ebi.ac.uk AlphaFold], with pLDDT score for each atom or residue.
+* [https://esmatlas.com/about#fold ESMFold], with pLDDT score for each atom or residue.
+The functionality for applying these colour schemes was added through buttons in the SAT, and it is offered automatically depending on which data source provides the uploaded structure files.
+The colour reference (legend) is automatically included below the caption area under the 3D view, for any new scene that was created using the colouring option.
+===Prediction of structure===
+A new area inside 'load molecule' section of SAT allows to enter a raw or Fasta-formatted protein
+sequence, sends it to the ESMfold server and retrieves the resulting predicted structure into
+Proteopedia. The structure is also loaded on SAT, ready for preparing a scene.
 ==Alcalá, Spain, March 2021==