diff --git a/Cargo.toml b/Cargo.toml
index 446b56c..28bb3d0 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -27,11 +27,11 @@ categories = [
 readme = "README.md"
 
 [dependencies]
-thiserror = "1.0"
+thiserror = "2.0"
 rayon = { version = "1.8", optional = true }
-nalgebra = { version = "0.32", optional = true }
-itertools = "0.12"
-reqwest = { version = "0.12", features = ["json", "blocking"], optional = true }
+nalgebra = { version = "0.34", optional = true }
+itertools = "0.14"
+reqwest = { version = "0.13", features = ["json", "blocking"], optional = true }
 serde = { version = "1.0", features = ["derive"], optional = true }
 serde_json = { version = "1.0", optional = true }
 flate2 = { version = "1.0", optional = true }
@@ -39,7 +39,7 @@ tokio = { version = "1.0", features = ["rt-multi-thread", "sync", "time", "fs",
 futures = { version = "0.3", optional = true }
 
 [dev-dependencies]
-criterion = "0.5"
+criterion = "0.8"
 proptest = "1.4"
 tempfile = "3.9"
 codecov = "0.4"
diff --git a/pdbrust-python/Cargo.toml b/pdbrust-python/Cargo.toml
index 4209420..0a2d3a0 100644
--- a/pdbrust-python/Cargo.toml
+++ b/pdbrust-python/Cargo.toml
@@ -16,7 +16,7 @@ name = "_pdbrust"
 crate-type = ["cdylib"]
 
 [dependencies]
-pyo3 = { version = "0.24", features = ["extension-module"] }
+pyo3 = { version = "0.28", features = ["extension-module"] }
 pdbrust = { path = "..", features = ["filter", "descriptors", "quality", "summary", "gzip", "geometry", "dssp", "ligand-quality"] }
 numpy = { version = "0.24", optional = true }
 tokio = { version = "1.0", features = ["rt-multi-thread"], optional = true }