Compare revisions

f741a518 · f741a518 · f741a518 · f741a518 · f741a518 · f741a518
--- a/content/3.defense-systems/sspbcde.md
+++ b/content/3.defense-systems/sspbcde.md
@@ -10,6 +10,9 @@ tableColumns:
    Activator: Direct
    Effector: Nucleic acid degrading
    PFAM: PF01507, PF01580, PF03235, PF07510, PF13182
+relevantAbstracts:
+    - doi: 10.1128/mBio.00613-21
+    - doi: 10.1128/mBio.00613-21
 ---

 # SspBCDE
@@ -34,83 +37,40 @@ The system was detected in 299 different species.
 Proportion of genome encoding the SspBCDE system for the 14 phyla with more than 50 genomes in the RefSeq database.


-## Structure

+## Structure
 ### SspBCDE
-
-Example 1:
-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /sspbcde/SspBCDE,SspBCDE__SspB,0,V-plddts_92.59451.pdb
---
-::
-
-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /sspbcde/SspBCDE,SspBCDE__SspC,0,V-plddts_85.51697.pdb
---
-::
-
-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /sspbcde/SspBCDE,SspBCDE__SspD,0,V-plddts_87.41069.pdb
---
-::
-
-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /sspbcde/SspBCDE,SspBCDE__SspE,0,V-plddts_88.74902.pdb
---
-::
-
-Example 2:
-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /sspbcde/SspBCDE,SspBCDE__SspB,0,V-plddts_92.59451.pdb
---
-::
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /sspbcde/SspBCDE,SspBCDE__SspC,0,V-plddts_85.51697.pdb
---
-::
+dataUrls:
+   - /sspbcde/SspBCDE.SspBCDE__SspC.1.V.cif
+   - /sspbcde/SspBCDE.SspBCDE__SspD.0.V.cif
+   - /sspbcde/SspBCDE.SspBCDE__SspE.0.V.cif
+   - /sspbcde/SspBCDE.SspBCDE__SspB.1.V.cif

-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /sspbcde/SspBCDE,SspBCDE__SspD,0,V-plddts_87.41069.pdb
 ---
 ::
+##### Example 2

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /sspbcde/SspBCDE,SspBCDE__SspE,0,V-plddts_88.74902.pdb
---
-::
+dataUrls:
+   - /sspbcde/SspBCDE.SspBCDE__SspH.1.V.cif
+   - /sspbcde/SspBCDE.SspBCDE__SspG.1.V.cif
+   - /sspbcde/SspBCDE.SspBCDE__SspF.1.V.cif
+   - /sspbcde/SspBCDE.SspBCDE__SspD.0.V.cif
+   - /sspbcde/SspBCDE.SspBCDE__SspC.1.V.cif
+   - /sspbcde/SspBCDE.SspBCDE__SspB.1.V.cif

-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /sspbcde/SspBCDE,SspBCDE__SspB,1,V-plddts_92.38727.pdb
---
-::
-
-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /sspbcde/SspBCDE,SspBCDE__SspC,1,V-plddts_84.03334.pdb
 ---
 ::

 ## Experimental validation
+
 <mermaid>
 graph LR;
    Xiong_2020[<a href='https://doi.org/10.1038/s41564-020-0700-6'>Xiong et al., 2020</a>] --> Origin_0
@@ -183,14 +143,4 @@ end
    style Title3 fill:none,stroke:none,stroke-width:none
    style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
---
-items:
-    - doi: 10.1128/mBio.00613-21
-    - doi: 10.1128/mBio.00613-21
-
---
-::

--- a/content/3.defense-systems/stk2.md
+++ b/content/3.defense-systems/stk2.md
@@ -10,6 +10,8 @@ tableColumns:
    Activator: Direct
    Effector: Other (protein modifying)
    PFAM: PF00069, PF07714
+relevantAbstracts:
+    - doi: 10.1016/j.chom.2016.08.010
 ---

 # Stk2
@@ -43,18 +45,22 @@ The system was detected in 29 different species.
 Proportion of genome encoding the Stk2 system for the 14 phyla with more than 50 genomes in the RefSeq database.


-## Structure

+## Structure
 ### Stk2
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /stk2/Stk2__Stk2-plddts_91.79541.pdb
+dataUrls:
+   - /stk2/Stk2__Stk2.cif
+
 ---
 ::

 ## Experimental validation
+
 <mermaid>
 graph LR;
    Depardieu_2016[<a href='https://doi.org/10.1016/j.chom.2016.08.010'>Depardieu et al., 2016</a>] --> Origin_0
@@ -89,13 +95,4 @@ end
    style Title3 fill:none,stroke:none,stroke-width:none
    style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
---
-items:
-    - doi: 10.1016/j.chom.2016.08.010
-
---
-::

--- a/content/3.defense-systems/thoeris.md
+++ b/content/3.defense-systems/thoeris.md
@@ -10,6 +10,9 @@ tableColumns:
    Activator: Signaling
    Effector: Nucleotide modifying
    PFAM: PF08937, PF13289, PF18185
+relevantAbstracts:
+    - doi: 10.1038/s41586-021-04098-7
+    - doi: 10.1126/science.aar4120
 ---

 # Thoeris
@@ -34,41 +37,35 @@ The system was detected in 298 different species.
 Proportion of genome encoding the Thoeris system for the 14 phyla with more than 50 genomes in the RefSeq database.


-## Structure

+## Structure
 ### Thoeris_I
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /thoeris/Thoeris_I,Thoeris_I__ThsA_new_grand,0,V-plddts_93.92302.pdb
---
-::
+dataUrls:
+   - /thoeris/Thoeris_I.Thoeris_I__ThsA_new_grand.0.V.cif
+   - /thoeris/Thoeris_I.Thoeris__ThsB_Global.0.V.cif

-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /thoeris/Thoeris_I,Thoeris__ThsB_Global,0,V-plddts_90.12702.pdb
 ---
 ::
-
 ### Thoeris_II
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /thoeris/Thoeris_II,Thoeris_II__ThsA_new_petit,0,V-plddts_88.7532.pdb
---
-::
+dataUrls:
+   - /thoeris/Thoeris_I.Thoeris__ThsB_Global.0.V.cif
+   - /thoeris/Thoeris_II.Thoeris_II__ThsA_new_petit.0.V.cif

-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /thoeris/Thoeris_II,Thoeris__ThsB_Global,0,V-plddts_93.32159.pdb
 ---
 ::

 ## Experimental validation
+
 <mermaid>
 graph LR;
    Doron_2018[<a href='https://doi.org/10.1126/science.aar4120'>Doron et al., 2018</a>] --> Origin_0
@@ -127,14 +124,4 @@ end
    style Title3 fill:none,stroke:none,stroke-width:none
    style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
---
-items:
-    - doi: 10.1038/s41586-021-04098-7
-    - doi: 10.1126/science.aar4120
-
---
-::

--- a/content/3.defense-systems/tiamat.md
+++ b/content/3.defense-systems/tiamat.md
@@ -48,18 +48,22 @@ The system was detected in 251 different species.
 Proportion of genome encoding the Tiamat system for the 14 phyla with more than 50 genomes in the RefSeq database.


-## Structure

+## Structure
 ### Tiamat
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /tiamat/Tiamat__TmtA-plddts_86.46392.pdb
+dataUrls:
+   - /tiamat/Tiamat__TmtA.cif
+
 ---
 ::

 ## Experimental validation
+
 <mermaid>
 graph LR;
    Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
@@ -87,3 +91,4 @@ end

 ---

+
--- a/content/3.defense-systems/uzume.md
+++ b/content/3.defense-systems/uzume.md
@@ -9,6 +9,8 @@ tableColumns:
    Sensor: Unknown
    Activator: Unknown
    Effector: Unknown
+relevantAbstracts:
+    - doi: 10.1016/j.chom.2022.09.017
 ---

 # Uzume
@@ -33,18 +35,22 @@ The system was detected in 87 different species.
 Proportion of genome encoding the Uzume system for the 14 phyla with more than 50 genomes in the RefSeq database.


-## Structure

+## Structure
 ### Uzume
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /uzume/Uzume__UzmA-plddts_94.2491.pdb
+dataUrls:
+   - /uzume/Uzume__UzmA.cif
+
 ---
 ::

 ## Experimental validation
+
 <mermaid>
 graph LR;
    Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
@@ -70,12 +76,4 @@ end
    style Title3 fill:none,stroke:none,stroke-width:none
    style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
-## Relevant abstracts

-::relevant-abstracts
---
-items:
-    - doi: 10.1016/j.chom.2022.09.017
-
---
-::
--- a/content/3.defense-systems/viperin.md
+++ b/content/3.defense-systems/viperin.md
@@ -55,18 +55,22 @@ The system was detected in 95 different species.
 Proportion of genome encoding the Viperin system for the 14 phyla with more than 50 genomes in the RefSeq database.


-## Structure

+## Structure
 ### Viperin
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /viperin/Viperin__pVip-plddts_95.08271.pdb
+dataUrls:
+   - /viperin/Viperin__pVip.cif
+
 ---
 ::

 ## Experimental validation
+
 <mermaid>
 graph LR;
    Bernheim_2020[<a href='https://doi.org/10.1038/s41586-020-2762-2'>Bernheim et al., 2020</a>] --> Origin_0
@@ -228,3 +232,4 @@ end
    style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>

+
--- a/content/3.defense-systems/wadjet.md
+++ b/content/3.defense-systems/wadjet.md
@@ -10,6 +10,8 @@ tableColumns:
    Activator: Direct
    Effector: Nucleic acid degrading
    PFAM: PF09660, PF09661, PF09664, PF09983, PF11795, PF11796, PF11855, PF13555, PF13558, PF13835
+relevantAbstracts:
+    - doi: 10.1126/science.aar4120
 ---

 # Wadjet
@@ -42,105 +44,47 @@ The system was detected in 1467 different species.
 Proportion of genome encoding the Wadjet system for the 14 phyla with more than 50 genomes in the RefSeq database.


-## Structure

+## Structure
 ### Wadjet_I
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /wadjet/Wadjet_I,Wadjet__JetA_I,0,V-plddts_85.26647.pdb
---
-::
-
-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /wadjet/Wadjet_I,Wadjet__JetB_I,0,V-plddts_87.82736.pdb
---
-::
-
-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /wadjet/Wadjet_I,Wadjet__JetC_I,0,V-plddts_84.15592.pdb
---
-::
+dataUrls:
+   - /wadjet/Wadjet_I.Wadjet__JetA_I.0.V.cif
+   - /wadjet/Wadjet_I.Wadjet__JetB_I.0.V.cif
+   - /wadjet/Wadjet_I.Wadjet__JetC_I.0.V.cif
+   - /wadjet/Wadjet_I.Wadjet__JetD_I.0.V.cif

-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /wadjet/Wadjet_I,Wadjet__JetD_I,0,V-plddts_93.08112.pdb
 ---
 ::
-
 ### Wadjet_II
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /wadjet/Wadjet_II,Wadjet__JetA_II,0,V-plddts_85.37749.pdb
---
-::
-
-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /wadjet/Wadjet_II,Wadjet__JetB_II,0,V-plddts_94.08089.pdb
---
-::
-
-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /wadjet/Wadjet_II,Wadjet__JetC_II,0,V-plddts_84.09293.pdb
---
-::
+dataUrls:
+   - /wadjet/Wadjet_II.Wadjet__JetD_II.0.V.cif
+   - /wadjet/Wadjet_II.Wadjet__JetC_II.0.V.cif
+   - /wadjet/Wadjet_II.Wadjet__JetB_II.0.V.cif
+   - /wadjet/Wadjet_II.Wadjet__JetA_II.0.V.cif

-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /wadjet/Wadjet_II,Wadjet__JetD_II,0,V-plddts_92.28569.pdb
 ---
 ::
-
 ### Wadjet_III
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /wadjet/Wadjet_III,Wadjet__JetA_III,0,V-plddts_80.48148.pdb
---
-::
-
-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /wadjet/Wadjet_III,Wadjet__JetB_III,0,V-plddts_80.7136.pdb
---
-::
-
-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /wadjet/Wadjet_III,Wadjet__JetC_III,0,V-plddts_83.96933.pdb
---
-::
-
-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /wadjet/Wadjet_III,Wadjet__JetD_III,0,V-plddts_91.07357.pdb
---
-::
-
-## Relevant abstracts
-
-::relevant-abstracts
---
-items:
-    - doi: 10.1126/science.aar4120
+dataUrls:
+   - /wadjet/Wadjet_III.Wadjet__JetD_III.0.V.cif
+   - /wadjet/Wadjet_III.Wadjet__JetA_III.0.V.cif
+   - /wadjet/Wadjet_III.Wadjet__JetB_III.0.V.cif
+   - /wadjet/Wadjet_III.Wadjet__JetC_III.0.V.cif

 ---
 ::
-
--- a/content/3.defense-systems/zorya.md
+++ b/content/3.defense-systems/zorya.md
@@ -10,6 +10,9 @@ tableColumns:
    Activator: Unknown
    Effector: Unknown
    PFAM: PF00176, PF00271, PF00691, PF04851, PF15611
+relevantAbstracts:
+    - doi: 10.1093/nar/gkab883
+    - doi: 10.1126/science.aar4120
 ---

 # Zorya
@@ -38,62 +41,38 @@ The system was detected in 310 different species.
 Proportion of genome encoding the Zorya system for the 14 phyla with more than 50 genomes in the RefSeq database.


-## Structure

+## Structure
 ### Zorya_TypeI
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /zorya/Zorya_TypeI,Zorya_TypeI__ZorC,0,V-plddts_85.7807.pdb
---
-::
+dataUrls:
+   - /zorya/Zorya_TypeI.Zorya_TypeI__ZorC.0.V.cif
+   - /zorya/Zorya_TypeI.Zorya_TypeI__ZorD.0.V.cif
+   - /zorya/Zorya_TypeII.Zorya__ZorA.0.V.cif
+   - /zorya/Zorya_TypeI.Zorya__ZorB.0.V.cif

-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /zorya/Zorya_TypeI,Zorya_TypeI__ZorD,0,V-plddts_80.74261.pdb
---
-::
-
-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /zorya/Zorya_TypeI,Zorya__ZorA,0,V-plddts_72.58295.pdb
---
-::
-
-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /zorya/Zorya_TypeI,Zorya__ZorB,0,V-plddts_88.9782.pdb
 ---
 ::
-
 ### Zorya_TypeII
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /zorya/Zorya_TypeII,Zorya_TypeII__ZorE,0,V-plddts_88.59937.pdb
---
-::
-
-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /zorya/Zorya_TypeII,Zorya__ZorA,0,V-plddts_77.19519.pdb
---
-::
+dataUrls:
+   - /zorya/Zorya_TypeII.Zorya__ZorA.0.V.cif
+   - /zorya/Zorya_TypeI.Zorya__ZorB.0.V.cif
+   - /zorya/Zorya_TypeII.Zorya_TypeII__ZorE.0.V.cif

-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /zorya/Zorya_TypeII,Zorya__ZorB,0,V-plddts_91.39341.pdb
 ---
 ::

 ## Experimental validation
+
 <mermaid>
 graph LR;
    Doron_2018[<a href='https://doi.org/10.1126/science.aar4120'>Doron et al., 2018</a>] --> Origin_0
@@ -145,14 +124,4 @@ end
    style Title3 fill:none,stroke:none,stroke-width:none
    style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
---
-items:
-    - doi: 10.1093/nar/gkab883
-    - doi: 10.1126/science.aar4120
-
---
-::

--- a/data/all_predictions_statistics_clean.csv
+++ b/data/all_predictions_statistics_clean.csv
--- a/data/all_predictions_statistics_clean.tsv
+++ b/data/all_predictions_statistics_clean.tsv
--- a/packages/df-wiki-cli/df_wiki_cli/meilisearch/__init__.py
+++ b/packages/df-wiki-cli/df_wiki_cli/meilisearch/__init__.py
@@ -161,6 +161,8 @@ def update_structure(
            "prediction_type",
            "plddts",
            "iptm+ptm",
+            "proteins_in_the_prediction",
+            "system_genes",
            "pDockQ",
        ]
    )
No results found