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andreasprlicandreasprlic
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updating legacy chemical component and atom names to current naming conventions.
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‎biojava-modfinder/src/main/resources/org/biojava/nbio/protmod/ptm_list.xml‎

Lines changed: 18 additions & 76 deletions
Original file line numberDiff line numberDiff line change
@@ -1,11 +1,15 @@
11
<?xml version="1.0" encoding="UTF-8"?>
22
<ProteinModifications>
33
<Revisions>
4-
<Revision>
5-
<Date>2016-05-10</Date>
6-
<Change>Added definition for PLP</Change>
7-
<Date>2011-08-12</Date>
8-
<Change>Added glycosylation entries 386-429</Change>
4+
<Revision>
5+
<Date>2016-06-10</Date>
6+
<Change>Updated legacy chemical component and atom names to current naming conventions. Removed two obsolete entires (CLE and CGL)</Change>
7+
</Revision>
8+
<Revision>
9+
<Date>2016-05-10</Date>
10+
<Change>Added definition for PLP</Change>
11+
<Date>2011-08-12</Date>
12+
<Change>Added glycosylation entries 386-429</Change>
913
</Revision>
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<Revision>
1115
<Date>2011-07-26</Date>
@@ -730,7 +734,7 @@
730734
<SystematicName>(R)-2-amino-3-selanylpropanoic acid</SystematicName>
731735
<CrossReference>
732736
<Source>PDBCC</Source>
733-
<Id>CSE</Id>
737+
<Id>SEC</Id>
734738
<Name>selenocysteine</Name>
735739
</CrossReference>
736740
<CrossReference>
@@ -745,7 +749,7 @@
745749
</CrossReference>
746750
<Condition>
747751
<Component component="1">
748-
<Id source="PDBCC">CSE</Id>
752+
<Id source="PDBCC">SEC</Id>
749753
</Component>
750754
</Condition>
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<Occurrence>natural</Occurrence>
@@ -1353,35 +1357,6 @@
13531357
<Category>modified residue</Category>
13541358
<Keyword>amidated carboxyl end</Keyword>
13551359
</Entry>
1356-
<Entry>
1357-
<Id>0045</Id>
1358-
<Description>A protein modification that effectively converts an L-leucine residue to L-leucine amide.</Description>
1359-
<SystematicName>(S)-2-amino-4-methylpentanamide</SystematicName>
1360-
<CrossReference>
1361-
<Source>PDBCC</Source>
1362-
<Id>CLE</Id>
1363-
<Name>leucine amide</Name>
1364-
</CrossReference>
1365-
<CrossReference>
1366-
<Source>RESID</Source>
1367-
<Id>AA0091</Id>
1368-
<Name>L-leucine amide</Name>
1369-
</CrossReference>
1370-
<CrossReference>
1371-
<Source>PSI-MOD</Source>
1372-
<Id>MOD:00100</Id>
1373-
<Name>L-leucine amide</Name>
1374-
</CrossReference>
1375-
<Condition>
1376-
<Component component="1">
1377-
<Id source="PDBCC">CLE</Id>
1378-
<Terminal>C</Terminal>
1379-
</Component>
1380-
</Condition>
1381-
<Occurrence>natural</Occurrence>
1382-
<Category>modified residue</Category>
1383-
<Keyword>amidated carboxyl end</Keyword>
1384-
</Entry>
13851360
<Entry>
13861361
<Id>0046</Id>
13871362
<Description>A protein modification that effectively converts an L-phenylalanine residue to L-phenylalanine amide.</Description>
@@ -3755,7 +3730,7 @@
37553730
<SystematicName>(R)-2-amino-2-carboxyethanesulfinic acid</SystematicName>
37563731
<CrossReference>
37573732
<Source>PDBCC</Source>
3758-
<Id>CSW</Id>
3733+
<Id>CSD</Id>
37593734
<Name>cysteine-S-dioxide</Name>
37603735
</CrossReference>
37613736
<CrossReference>
@@ -3770,7 +3745,7 @@
37703745
</CrossReference>
37713746
<Condition>
37723747
<Component component="1">
3773-
<Id source="PDBCC">CSW</Id>
3748+
<Id source="PDBCC">CSD</Id>
37743749
</Component>
37753750
</Condition>
37763751
<Occurrence>natural</Occurrence>
@@ -6788,8 +6763,8 @@
67886763
<Id source="PDBCC">SEC</Id>
67896764
</Component>
67906765
<Bond>
6791-
<Atom component="1">SEG</Atom>
6792-
<Atom component="2">SEG</Atom>
6766+
<Atom component="1">SE</Atom>
6767+
<Atom component="2">SE</Atom>
67936768
</Bond>
67946769
</Condition>
67956770
<Occurrence>hypothetical</Occurrence>
@@ -6997,7 +6972,7 @@
69976972
</Component>
69986973
<Bond>
69996974
<Atom component="1">SG</Atom>
7000-
<Atom component="2">SEG</Atom>
6975+
<Atom component="2">SE</Atom>
70016976
</Bond>
70026977
</Condition>
70036978
<Occurrence>natural</Occurrence>
@@ -9629,39 +9604,6 @@
96299604
<Occurrence>natural</Occurrence>
96309605
<Category>attachment</Category>
96319606
<Keyword>phosphoprotein</Keyword>
9632-
</Entry>
9633-
<Entry>
9634-
<Id>0290</Id>
9635-
<Description>A protein modification that effectively converts an L-cysteine residue to S-glutathionyl-L-cysteine.</Description>
9636-
<SystematicName>(2S)-2-amino-3-((2S)-2-((4R)-4-amino-4-carboxyl-1-oxobutyl)amino-3-(carboxylmethyl)amino-3-oxo-propyl)dithio-propanoic acid</SystematicName>
9637-
<CrossReference>
9638-
<Source>PDBCC</Source>
9639-
<Id>CGL</Id>
9640-
<Name></Name>
9641-
</CrossReference>
9642-
<CrossReference>
9643-
<Source>RESID</Source>
9644-
<Id>AA0229</Id>
9645-
<Name>L-cysteine glutathione disulfide</Name>
9646-
</CrossReference>
9647-
<CrossReference>
9648-
<Source>PSI-MOD</Source>
9649-
<Id>MOD:00234</Id>
9650-
<Name>L-cysteine glutathione disulfide</Name>
9651-
</CrossReference>
9652-
<CrossReference>
9653-
<Source>PDBCC</Source>
9654-
<Id>CGL</Id>
9655-
<Name>cystine-glutathione</Name>
9656-
</CrossReference>
9657-
<Condition>
9658-
<Component component="1">
9659-
<Id source="PDBCC">CGL</Id>
9660-
</Component>
9661-
</Condition>
9662-
<Occurrence>natural</Occurrence>
9663-
<Category>modified residue</Category>
9664-
<Keyword>disulfide bond</Keyword>
96659607
</Entry>
96669608
<Entry>
96679609
<Id>0291</Id>
@@ -9983,7 +9925,7 @@
99839925
<SystematicName>(2R)-2-amino-6-[(2R,3R)-3-methyl-3,4-dihydro-2H-pyrrol-2-ylcarbonyl]aminohexanoic acid</SystematicName>
99849926
<CrossReference>
99859927
<Source>PDBCC</Source>
9986-
<Id>PYH</Id>
9928+
<Id>PYL</Id>
99879929
<Name>N6-{[(2R,3R)-3-methyl-3,4-dihydro-2H-pyrrol-2-yl]carbonyl}-L-lysine</Name>
99889930
</CrossReference>
99899931
<CrossReference>
@@ -9998,7 +9940,7 @@
99989940
</CrossReference>
99999941
<Condition>
100009942
<Component component="1">
10001-
<Id source="PDBCC">PYH</Id>
9943+
<Id source="PDBCC">PYL</Id>
100029944
</Component>
100039945
</Condition>
100049946
<Occurrence>natural</Occurrence>

‎biojava-modfinder/src/test/java/org/biojava/nbio/protmod/structure/ProteinModificationParserTest.java‎

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -106,6 +106,8 @@ public static String[][] setUpShortTest() {
106106
//{"1Z2M",null}, distances are too big for the new cutoffs
107107
{"2O6N",null},
108108
{"1GA7",null},
109+
{"1ACD","AA0262"}, // test for CSD
110+
{"1AA6","AA0022"} , // test for SEC
109111

110112
};
111113
return strucs;

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