griffithlab · susannasiebert · Aug 28, 2026 · Aug 28, 2026 · Sep 17, 2026 · Sep 17, 2026
diff --git a/docs/pvacbind/features.rst b/docs/pvacbind/features.rst
@@ -165,12 +165,6 @@ for a variety of additional algorithms.
      - Immunogenicity
      - yes
      - yes
-   * - Pickpocket
-     - 1.1
-     - MHC Class I
-     - Binding
-     - yes
-     - yes
    * - SMM
      - 1.0
      - MHC Class I

diff --git a/docs/pvacfuse/features.rst b/docs/pvacfuse/features.rst
@@ -165,12 +165,6 @@ for a variety of additional algorithms.
      - Immunogenicity
      - yes
      - yes
-   * - Pickpocket
-     - 1.1
-     - MHC Class I
-     - Binding
-     - yes
-     - yes
    * - SMM
      - 1.0
      - MHC Class I

diff --git a/docs/pvacseq/features.rst b/docs/pvacseq/features.rst
@@ -169,12 +169,6 @@ for a variety of additional algorithms.
      - Immunogenicity
      - yes
      - yes
-   * - Pickpocket
-     - 1.1
-     - MHC Class I
-     - Binding
-     - yes
-     - yes
    * - SMM
      - 1.0
      - MHC Class I

diff --git a/docs/pvacseq/frequently_asked_questions.rst b/docs/pvacseq/frequently_asked_questions.rst
@@ -82,7 +82,9 @@ There are a number of factors that determine the number of IEDB calls to be made
   already a consensus method between NetMHC, NetMHCpan, and PickPocket.
   If NetMHCcons is chosen, you may want to omit the underlying prediction
   methods. Likewise, if you want to run NetMHC, NetMHCpan, and PickPocket
-  individually, you may want to skip NetMHCcons.
+  individually, you may want to skip NetMHCcons. Note that PickPocket is no
+  longer a prediction algorithm supported by IEDB, so it's been removed as
+  an algorithm in pVACtools.
 
 - ``--downstream-sequence-length`` parameter value
 

diff --git a/docs/pvacsplice/features.rst b/docs/pvacsplice/features.rst
@@ -167,12 +167,6 @@ for a variety of additional algorithms.
      - Immunogenicity
      - yes
      - yes
-   * - Pickpocket
-     - 1.1
-     - MHC Class I
-     - Binding
-     - yes
-     - yes
    * - SMM
      - 1.0
      - MHC Class I

diff --git a/docs/pvacvector/getting_started.rst b/docs/pvacvector/getting_started.rst
@@ -19,7 +19,7 @@ Here is an example of how to run pVACvector with a pVACseq output TSV:
    <example_data_dir>/input.tsv \
    Test \
    HLA-A*02:01,HLA-B*35:01 \
-   MHCflurry MHCnuggetsI MHCnuggetsII NNalign NetMHC PickPocket SMM SMMPMBEC SMMalign \
+   MHCflurry MHCnuggetsI MHCnuggetsII NNalign NetMHC SMM SMMPMBEC SMMalign \
    <output_dir> \
    -e1 8,9,10 \
    -e2 15 \
@@ -33,7 +33,7 @@ In this example pVACvector is run with an input FASTA file:
    <example_data_dir>/input.fa \
    Test \
    HLA-A*02:01,HLA-B*35:01 \
-   MHCflurry MHCnuggetsI MHCnuggetsII NNalign NetMHC PickPocket SMM SMMPMBEC SMMalign \
+   MHCflurry MHCnuggetsI MHCnuggetsII NNalign NetMHC SMM SMMPMBEC SMMalign \
    <output_dir> \
    -e1 8,9,10 \
    -e2 15

diff --git a/pvactools/lib/aggregate_all_epitopes.py b/pvactools/lib/aggregate_all_epitopes.py
@@ -134,7 +134,7 @@ def get_best_mut_line(self, df, key):
 
     def determine_used_ic50_algorithms(self):
         headers = pd.read_csv(self.input_file, delimiter="\t", nrows=0).columns.tolist()
-        potential_algorithms = ["NetMHCpan", "NetMHC", "NetMHCcons", "PickPocket", "SMM", "SMMPMBEC", "MHCflurry", "MHCnuggetsI", "NetMHCIIpan", "SMMalign", "NNalign", "MHCnuggetsII", "TLBind"]
+        potential_algorithms = ["NetMHCpan", "NetMHC", "NetMHCcons", "SMM", "SMMPMBEC", "MHCflurry", "MHCnuggetsI", "NetMHCIIpan", "SMMalign", "NNalign", "MHCnuggetsII", "TLBind"]
         prediction_algorithms = []
         for algorithm in potential_algorithms:
             if "{} MT IC50 Score".format(algorithm) in headers or "{} IC50 Score".format(algorithm) in headers:
@@ -152,7 +152,7 @@ def determine_used_binding_score_algorithms(self):
 
     def determine_used_binding_percentile_algorithms(self):
         headers = pd.read_csv(self.input_file, delimiter="\t", nrows=0).columns.tolist()
-        potential_algorithms = ["NetMHCpan", "NetMHC", "NetMHCcons", "PickPocket", "SMM", "SMMPMBEC", "MHCflurry", "MHCnuggetsI", "NetMHCIIpan", "SMMalign", "NNalign", "MHCnuggetsII", "MixMHCpred", "TLBind"]
+        potential_algorithms = ["NetMHCpan", "NetMHC", "NetMHCcons", "SMM", "SMMPMBEC", "MHCflurry", "MHCnuggetsI", "NetMHCIIpan", "SMMalign", "NNalign", "MHCnuggetsII", "MixMHCpred", "TLBind"]
         prediction_algorithms = []
         for algorithm in potential_algorithms:
             if "{} MT Percentile".format(algorithm) in headers or "{} Percentile".format(algorithm) in headers:

diff --git a/pvactools/lib/prediction_class.py b/pvactools/lib/prediction_class.py
@@ -834,11 +834,6 @@ class NetMHCcons(IEDBMHCI):
     def iedb_prediction_method(self):
         return 'netmhccons'
 
-class PickPocket(IEDBMHCI):
-    @property
-    def iedb_prediction_method(self):
-        return 'pickpocket'
-
 class MHCII(PredictionClass, metaclass=ABCMeta):
     @property
     def needs_epitope_length(self):