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Merge pull request #166 from pszgaspar/master
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2024 Nov update
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pszgaspar authored Nov 5, 2024
2 parents 555c4c5 + 0638353 commit 2474238
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9 changes: 9 additions & 0 deletions release_notes/2024-11-06.html
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@@ -0,0 +1,9 @@
<ul class="release-notes">
<li class="gpcrdb">Odorant receptors (human + model organisms)</li>
<li class="gpcrdb"><a href="https://gpcrdb.org/mapper/">Data Mapper</a> (map own data onto GPCR plots)</li>
<li class="gpcrdb">Physiological ligand-GPCR <a href="https://gpcrdb.org/structure/ligand_complex_models">complex models</a> (AF2-Multimer and RoseTTAFold)</li>
<li class="gpcrdb"><a href="https://gpcrdb.org/structure/structure_similarity_search">Structure Similarity Search</a> (<a href="https://search.foldseek.com/search">Foldseek</a>)</li>
<li class="gpcrdb"><a href="https://gpcrdb.org/ligand/ligand_by_name">Ligand search tool</a> (by name, database ID, structure) updated</li>
<li class="gpcrdb">Inactive-/active-state GPCR <a href="https://gpcrdb.org/structure/homology_models">models</a> (AF2 and AF2-Multistate) updated</li>
<li class="all">Minor bug and performance fixes</li>
</ul>
22 changes: 22 additions & 0 deletions residue_data/unnatural_amino_acids.yaml
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Expand Up @@ -53,6 +53,7 @@ HOH: X
OCA: X
NAG: X
' ZN': X
ZN: X
MES: X
WF1: X
P42: X
Expand All @@ -69,3 +70,24 @@ DTY: X
CY3: X
BAL: X
NLN: X
'004': X
TY5: X
A1D: X
HYP: X
XZA: X
NMM: X
OH: X
XT9: X
DSN: X
SEP: X
NIT: X
FC0: X
NAL: X
HYP: X
XZA: X
2ML: X
PHA: X
PLM: X
MED: X
TPO: X

Binary file modified structure_data/annotation/GPCRdb_structure_info.xlsx
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10 changes: 10 additions & 0 deletions structure_data/annotation/all_anomalies.yaml
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Expand Up @@ -17169,3 +17169,13 @@ orn4c_human:
UniProt: orn4c_human
Xtal Templ: orn4c_human
Xtalised: NoXtal
e7fel0_danre:
7x44: 7x44
UniProt: e7fel0_danre
Xtal Templ: e7fel0_danre
Xtalised: NoXtal
q76sf8_hhv8:
7x44: 7x44
UniProt: q76sf8_hhv8
Xtal Templ: q76sf8_hhv8
Xtalised: NoXtal
2 changes: 2 additions & 0 deletions structure_data/annotation/arrestins.csv
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Expand Up @@ -11,3 +11,5 @@ PDB UniProt ChainID Note
7SRS arrb1_human C
8JRU arrb1_bovin A
8JRV arrb1_human A
8WRZ arrb1_human A
8WU1 arrb1_human C
64 changes: 64 additions & 0 deletions structure_data/annotation/fusion_proteins.csv
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Expand Up @@ -450,3 +450,67 @@ PDB Name
8W77 BRIL
8W8B BRIL
8W8Q BRIL
8FY8 BRIL
8FYE BRIL
8FYL BRIL
8FYT BRIL
8FYX BRIL
8IKJ BRIL
8J9O BRIL
8JH7 BRIL
8JHC BRIL
8JPN BRIL
8JPP BRIL
8JT6 BRIL
8JT8 BRIL
8K8J BRIL
8K9K BRIL
8K9L BRIL
8RLN BRIL
8RQQ BRIL
8TH3 BRIL
8TH4 BRIL
8UHB BRIL
8W1V T4-Lysozyme
8WKY GlgA glycogen synthase
8WKZ GlgA glycogen synthase
8WRZ BRIL
8X2K BRIL
8X5X BRIL
8X5Y BRIL
8X63 BRIL
8X64 BRIL
8XQL Exo-alpha-sialidase
8XQN Exo-alpha-sialidase
8XQO Exo-alpha-sialidase
8XQP Exo-alpha-sialidase
8XQR Exo-alpha-sialidase
8XQS Exo-alpha-sialidase
8XQT Exo-alpha-sialidase
8XVE Exo-alpha-sialidase
8XVH Exo-alpha-sialidase
8XVI Endoglucanase H
8XVJ Endoglucanase H
8XVJ BRIL
8XVK Endoglucanase H
8XVK BRIL
8XVL Endoglucanase H
8XVL BRIL
8YKY Exo-alpha-sialidase
8YRG BRIL
8YZK BRIL
8ZBE LgBiT
8ZCJ LgBiT
8ZFJ LgBiT
8ZFJ BRIL
8ZMF BRIL
8ZMG BRIL
8ZSJ BRIL
8ZSP BRIL
8ZSS BRIL
8ZSV BRIL
9CBL T4-Lysozyme
9CBM T4-Lysozyme
9D3G BRIL
9F33 GFP
9F34 GFP
245 changes: 243 additions & 2 deletions structure_data/annotation/g_proteins.csv
Original file line number Diff line number Diff line change
Expand Up @@ -183,7 +183,7 @@ PDB Alpha_UniProt Alpha_ChainID Beta_UniProt Beta_ChainID Gamma_UniProt Gamma_Ch
7P02 gnas2_human A gbb1_human B gbg2_human G Gs-Gi1 chimera
7RMG gnaq_human A gbb1_human B gbg2_human G Gs-Gq chimera
7RMH gnas2_human A gbb1_human B gbg2_human G
7RMI gnaq_human A gbb1_human B gbg2_human G Gs-Gq chimera
7RMI gnas2_human A gbb1_human B gbg2_human G Gs-Gq chimera
7VUG gnai1_human A gbb1_human B gbg2_human C
7VUH gnas2_human A gbb1_human B gbg2_human G
7VUI gnas2_human A gbb1_human B gbg2_human G
Expand Down Expand Up @@ -666,7 +666,7 @@ PDB Alpha_UniProt Alpha_ChainID Beta_UniProt Beta_ChainID Gamma_UniProt Gamma_Ch
8U26 gnas2_human A gbb1_human B gbg2_human G
8W87 gnas2_human A gbb1_human B gbg2_human G
8W88 gnas2_human A gbb1_human B gbg2_human G
8W89 gnas2_human A gbb1_human B gbg2_human G
8W89 gnai2_human A gbb1_human B gbg2_human G
8W8A gnai2_human A gbb1_human B gbg2_human G
8W8B gnai1_human A gbb1_human B gbg2_human G
8W8Q gnas2_human A gbb1_human B gbg2_human G
Expand All @@ -684,3 +684,244 @@ PDB Alpha_UniProt Alpha_ChainID Beta_UniProt Beta_ChainID Gamma_UniProt Gamma_Ch
8WRB gnai1_human A gbb1_human B gbg2_human C
8XBH gnai1_human A gbb1_rat B gbg2_bovin G
7V9L gnas2_human A gbb1_rat B gbg2_bovin Y
8FY8 gnai1_human A gbb1_human B gbg2_human G
8FYE gnai1_human A gbb1_human B gbg2_human G
8FYL gnai1_human A gbb1_human B gbg2_human G
8FYT gnai1_human A gbb1_human B gbg2_human G
8FYX gnai1_human A gbb1_human B gbg2_human G
8GAG gnai1_human A gbb1_human B gbg2_human C
8GDZ gnas2_human A gbb1_human B gbg2_human G
8GE1 gnas2_human A gbb1_human B gbg2_human G
8GE2 gnas2_human A gbb1_human B gbg2_human G
8GE3 gnas2_human A gbb1_human B gbg2_human G
8GE4 gnas2_human A gbb1_human B gbg2_human G
8GE5 gnas2_human A gbb1_human B gbg2_human G
8GE6 gnas2_human A gbb1_human B gbg2_human G
8GE7 gnas2_human A gbb1_human B gbg2_human G
8GE8 gnas2_human A gbb1_human B gbg2_human G
8GE9 gnas2_human A gbb1_human B gbg2_human G
8GEA gnas2_human A gbb1_human B gbg2_human G
8GEB gnas2_human A gbb1_human B gbg2_human G
8GEC gnas2_human A gbb1_human B gbg2_human G
8GED gnas2_human A gbb1_human B gbg2_human G
8GEE gnas2_human A gbb1_human B gbg2_human G
8GEF gnas2_human A gbb1_human B gbg2_human G
8GEG gnas2_human A gbb1_human B gbg2_human G
8GEH gnas2_human A gbb1_human B gbg2_human G
8GEI gnas2_human A gbb1_human B gbg2_human G
8GEJ gnas2_human A gbb1_human B gbg2_human G
8GFV gnas2_human A gbb1_human B gbg2_human G
8GFW gnas2_human A gbb1_human B gbg2_human G
8GFX gnas2_human A gbb1_human B gbg2_human G
8GFY gnas2_human A gbb1_human B gbg2_human G
8GFZ gnas2_human A gbb1_human B gbg2_human G
8GG0 gnas2_human A gbb1_human B gbg2_human G
8GG1 gnas2_human A gbb1_human B gbg2_human G
8GG2 gnas2_human A gbb1_human B gbg2_human G
8GG3 gnas2_human A gbb1_human B gbg2_human G
8GG4 gnas2_human A gbb1_human B gbg2_human G
8GG5 gnas2_human A gbb1_human B gbg2_human G
8GG6 gnas2_human A gbb1_human B gbg2_human G
8GG8 gnas2_human A gbb1_human B gbg2_human G
8GG9 gnas2_human A gbb1_human B gbg2_human G
8GGA gnas2_human A gbb1_human B gbg2_human G
8GGB gnas2_human A gbb1_human B gbg2_human G
8GGC gnas2_human A gbb1_human B gbg2_human G
8GGE gnas2_human A gbb1_human B gbg2_human G
8GGF gnas2_human A gbb1_human B gbg2_human G
8I7V gnai1_human A gbb1_human C gbg2_human D
8I7W gnai1_human B gbb1_human C gbg2_human D
8IED gnao_human C gbb1_human C gbg2_human Y
8IKL gna13_human A gbb1_human B gbg2_human Y
8IQ4 gnas2_human A gbb1_human B gbg2_human G
8IQ6 gnas2_human A gbb1_human B gbg2_human G
8IU2 gnai1_human A gbb1_human B gbg2_bovin G
8IY9 gnao_human A gbb1_human B gbg2_human G
8IYH gnao_human B gbb1_human A gbg2_human G
8IYW gnao_human B gbb1_human C gbg2_human G
8IZ4 gnai1_human A gbb1_human B gbg2_human C
8J20 gnai1_human C gbb1_human A gbg2_human E
8J21 gnai1_human C gbb1_human A gbg2_human E
8J22 gnai1_human B gbb1_human A gbg2_human D
8J23 gnai1_human B gbb1_human C gbg2_human D
8J24 gnai1_human C gbb1_human B gbg2_human F
8J6I gnai1_human A gbb1_human B gbg2_human G
8J6J gnai1_human A gbb1_human B gbg2_human G
8J6L gnai1_human A gbb1_human B gbg2_human G
8J9N gnaq_human C gbb1_human D gbg2_human E Gq-Gs chimera
8JBF gnaq_human C gbb1_rat D gbg2_bovin G
8JBG gnaq_human C gbb1_rat D gbg2_bovin G
8JBH gnaq_human C gbb1_rat D gbg2_bovin G
8JER gnao_human A gbb1_human B gbg2_human G
8JGB gnai1_human A gbb1_human B gbg2_human G
8JGF gnaq_human A gbb1_human B gbg2_human G
8JGG gnai1_human A gbb1_human B gbg2_human G
8JHB gnas2_human A gbb1_human B gbg2_human C
8JHI gnas2_human A gbb1_human B gbg2_human C
8JHN gnao_human A gbb1_human B gbg2_human G
8JPN gnai1_human A gbb1_human B gbg2_human G
8JPP gnas2_human A gbb1_human B gbg2_human G
8JT6 gnai1_human A gbb1_human B gbg2_human G
8JXT gnai1_human B gbb1_human C gbg2_human D
8JXV gnai1_human B gbb1_human C gbg2_human D
8JXW gnai1_human B gbb1_human C gbg2_human D
8JXX gnai1_human B gbb1_human C gbg2_human D
8K8J gnas2_human A gbb1_human B gbg2_human G
8K9K gnai3_macaque A gbb1_human B gbg2_human G
8K9L gnai3_macaque A gbb1_human B gbg2_human G
8KFX gnai1_human A gbb1_human B gbg2_human C
8KFY gnai1_human A gbb1_human B gbg2_human C
8KFZ gnai1_human A gbb1_human B gbg2_human C
8KGG gna13_human A gbb1_human B gbg2_human G
8PJK gnai1_human A gbb1_human B gbg2_human G
8PKM gnai1_human A gbb1_human B gbg2_human G
8POK gnas2_human B gbb1_human C gbg2_human D
8QJ2 gnas2_human B gbb1_human C gbg2_human G
8SMV gnas2_human A gbb1_human B gbg2_human G
8SZG gnaq_human C gbb1_human D gbg2_human E
8SZH gnai3_human C gbb1_human D gbg2_human E
8SZI gnai3_human C gbb1_human D gbg2_human E
8T3O gnaq_human A gbb1_human B gbg2_human G
8T3Q gnaq_human A gbb1_human B gbg2_human G
8T3S gnaq_human A gbb1_human B gbg2_human G
8T3V gnaq_human A gbb1_human B gbg2_human G
8TZQ gnao_human B gbb1_human A gbg2_human C
8U02 gnao_human B gbb1_human A gbg2_human C
8U4N gnai1_human A gbb1_human B gbg2_human C
8U4O gnai1_human A gbb1_human B gbg2_human C
8U4P gnai1_human A gbb1_human B gbg2_human C
8U4Q gnai1_human A gbb1_human B gbg2_human C
8U8F gnas2_human A gbb1_human B gbg2_human G
8UGY gnai1_human A gbb1_human B gbg2_human G
8UH3 gnai1_human A gbb1_human B gbg2_human G
8UHB gnas2_human C gbb1_human B gbg2_human G
8UNL gnas2_human A gbb1_human B gbg2_human G GTP bound, Class A
8UNM gnas2_human A gbb1_human B gbg2_human G GTP bound, Class B
8UNN gnas2_human A gbb1_human B gbg2_human G GTP bound, Class C
8UNO gnas2_human A gbb1_human B gbg2_human G GTP bound, Class D
8UNP gnas2_human A gbb1_human B gbg2_human G GTP bound, Class E
8UNQ gnas2_human A gbb1_human B gbg2_human G GTP bound, Class F
8UNR gnas2_human A gbb1_human B gbg2_human G GTP bound, Class G
8UNS gnas2_human A gbb1_human B gbg2_human G GTP bound, Class H
8UNT gnas2_human A gbb1_human B gbg2_human G GTP bound, Class I
8UNU gnas2_human A gbb1_human B gbg2_human G GTP bound, Class J
8UNV gnas2_human A gbb1_human B gbg2_human G GTP bound, Class K
8UNW gnas2_human A gbb1_human B gbg2_human G GTP bound, Class L
8UNX gnas2_human A gbb1_human B gbg2_human G GTP bound, Class M
8UNY gnas2_human A gbb1_human B gbg2_human G GTP bound, Class N
8UNZ gnas2_human A gbb1_human B gbg2_human G GTP bound, Class O
8UO0 gnas2_human A gbb1_human B gbg2_human G GTP bound, Class P
8UO1 gnas2_human A gbb1_human B gbg2_human G GTP bound, Class Q
8UO2 gnas2_human A gbb1_human B gbg2_human G GTP bound, Class R
8UO3 gnas2_human A gbb1_human B gbg2_human G GTP bound, Class S
8UO4 gnas2_human A gbb1_human B gbg2_human G GTP bound, Class T
8UWL gnaq_human B gbb1_human C gbg2_human D Gi2-mini-Gq chimera
8V6U gnaq_human B gbb1_human C gbg2_human D Gi2-mini-Gq chimera
8VY7 gnai1_human A gbb1_human B gbg2_human C
8VY9 gnat3_human A gbb1_human B gbg2_human C
8WA3 gnas2_human A gbb1_human B gbg2_human G
8WG7 gnas2_human A gbb1_human B gbg2_human G
8WG8 gnas2_human A gbb1_human B gbg2_human G
8WOG gnai1_human C gbb1_human D gbg2_human E
8WP1 gnai1_human C gbb1_human D gbg2_human E
8WSS gnai1_human A gbb1_human B gbg2_human G
8WST gnaq_human A gbb1_human B gbg2_human G
8WW2 gnas2_human A gbb1_human B gbg2_human G
8WZ2 gnaq_human A gbb1_rat B gbg2_bovin G
8X16 gnai1_human A gbb1_rat B gbg2_bovin C
8X17 gnai1_human A gbb1_rat B gbg2_bovin C
8X2K gnas2_human B gbb1_human C gbg2_human D
8X79 gnas2_human A gbb1_human B gbg2_human G
8X7A gnas2_human A gbb1_human B gbg2_human G
8X8L gnai1_human A gbb1_human B gbg2_human G
8X8N gnai1_human A gbb1_human B gbg2_human G
8XBE gnai1_human B gbb1_rat C gbg2_bovin D
8XGM gnai1_human C gbb1_human B gbg2_human G
8XGR gnat1_bovin A gbb1_rat B gbg2_bovin G
8XIO gnai1_human B gbb1_human C gbg2_human G
8XIP gnai1_human B gbb1_human C gbg2_human G
8XIQ gnai1_human B gbb1_human C gbg2_human G
8XIR gnai1_human B gbb1_human C gbg2_human G
8XJK gnaq_human A gbb1_human B gbg2_human C
8XJL gnaq_human A gbb1_human B gbg2_human C
8XJM gnaq_human A gbb1_human B gbg2_human C
8XJN gnaq_human A gbb1_human B gbg2_human C
8XJO gnaq_human A gbb1_human B gbg2_human C
8XOF gnaq_human A gbb1_human B gbg2_human G
8XOG gnaq_human A gbb1_human B gbg2_human G
8XOH gnaq_human A gbb1_human B gbg2_human G
8XOI gnaq_human A gbb1_human B gbg2_human G
8XOJ gnaq_human A gbb1_human B gbg2_human G
8XOR gnaq_human A gbb1_rat B gbg2_bovin C
8XOS gnai1_human A gbb1_rat B gbg2_bovin C
8XQL gnat3_human A gbb1_human B gbg2_human C
8XQN gnai1_human A gbb1_human B gbg2_human C
8XQO gnai1_human A gbb1_human B gbg2_human C
8XQP gnat3_human A gbb1_human B gbg2_human C
8XQR gnat3_human A gbb1_human B gbg2_human C
8XQS gnai1_human A gbb1_human B gbg2_human C
8XQT gnai1_human A gbb1_human B gbg2_human C
8XVE gnas2_human A gbb1_human B gbg2_human G
8XVH gnas2_human A gbb1_human B gbg2_human G
8XVI gnas2_human A gbb1_human B gbg2_human G
8XZF gnai1_human A gbb1_human B gbg2_human G
8XZG gnai1_human A gbb1_human B gbg2_human G
8XZH gnai1_human A gbb1_human B gbg2_human G
8XZI gnai1_human A gbb1_human B gbg2_human G
8XZJ gnai1_human A gbb1_human B gbg2_human G
8Y52 gnaq_human A gbb1_human B gbg2_human G
8Y53 gnaq_human A gbb1_human B gbg2_human G
8YKV gnai1_human A gbb1_rat B gbg2_bovin G
8YKW gnai1_human A gbb1_rat B gbg2_bovin G
8YKX gnai1_human A gbb1_rat B gbg2_bovin G
8YKY gnat3_human A gbb1_human B gbg2_human C
8YRG gnaq_human B gbb1_human C gbg2_human D Gs-min-Gq chimera
8YUT gnas2_human A gbb1_human B gbg2_human G
8YUU gnai1_human A gbb1_human B gbg2_human G
8YUV gnai1_human A gbb1_human B gbg2_human G
8YW3 gnas2_human A gbb1_human B gbg2_human G
8YW4 gnas2_human A gbb1_human B gbg2_human G
8YW5 gnas2_human A gbb1_human B gbg2_human G
8YY8 gnas2_human A gbb1_human B gbg2_human C
8ZBE gnai1_human B gbb1_rat C gbg2_mouse D
8ZCJ gnai1_human B gbb1_rat C gbg2_bovin D
8ZFJ gnas2_human A gbb1_human B gbg2_human G
8ZH8 gnaq_human A gbb1_rat B gbg2_bovin G
8ZJD gnaq_human A gbb1_human B gbg2_human G
8ZJE gnaq_human A gbb1_human B gbg2_human G
8ZPS gnas2_human A gbb1_human B gbg2_human G
8ZPT gnaq_human A gbb1_human B gbg2_human G
8ZQE gnai1_human A gbb1_human B gbg2_human C
8ZR5 gnas2_human A gbb1_human B gbg2_human G
8ZRK gnas2_human A gbb1_human B gbg2_human G
8ZSJ gnas2_human A gbb1_human B gbg2_human G
8ZSP gnas2_human A gbb1_human B gbg2_human G
8ZSS gnas2_human A gbb1_human B gbg2_human G
8ZSV gnas2_human A gbb1_human B gbg2_human G
9ASB gnaq_human A gbb1_human B gbg2_human G
9AUC gnas2_human A gbb1_human B gbg2_human G
9AVG gnas2_human A gbb1_human B gbg2_human G
9AVL gnai3_human A gbb1_human B gbg2_human G
9AXF gnaq_human A gbb1_human B gbg2_human G Gq-Gs-Gi chimera
9AYF gnai1_human A gbb1_human B gbg2_human G
9BKJ gnas2_human A gbb1_human B gbg2_human G Gs-Gi chimera
9BKK gnas2_human A gbb1_human B gbg2_human G
9BQJ gnai1_human A gbb1_human B gbg2_human C
9CBL gnai1_human A gbb1_human B gbg2_human G
9CBM gnai1_human A gbb1_bovin B gbg2_bovin G
9ERX gnai1_human A gbb1_human B gbg2_human C
9F33 gnao_human A gbb1_rat B gbg2_human C
9F34 gnao_human A gbb1_rat B gbg2_human C
9IIX gnat3_human D gbb1_human B gbg2_human C
9IJ9 gnai1_human A gbb1_human B gbg2_human C
9IJD gnas2_human A gbb1_rat B gbg2_bovin C
9IJE gnas2_human A gbb1_rat B gbg2_bovin C
8IKG gnai1_human A gbb1_human B gbg2_human C
8IKH gnai1_human A gbb1_human B gbg2_human C
8JJP gnai1_human C gbb1_human B gbg2_human G
8K3Z gnai1_human C gbb1_human B gbg2_human G
8K4O gnai1_human C gbb1_human B gbg2_human G
8K4P gnai1_human C gbb1_human B gbg2_human G
8K6M gnai2_human A gbb1_human B gbg2_human C
8K6N gnai2_human A gbb1_human B gbg2_human C
8K6O gnai2_human A gbb1_human B gbg2_human C
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