diff --git a/pyproject.toml b/pyproject.toml
index 86199fb19bd8aaf42263e3fb16d0f5d44127c9df..b5032f2d753fa3563f02cccc193e21e7b771137e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -29,7 +29,7 @@ dependencies = [
'lxml>=5.2',
'lxml-html-clean>=0.1.0',
'matid>=2.1.0',
- 'mdanalysis==2.5.0',
+ 'mdanalysis==2.7.0',
'networkx>=2.6.3',
'nptyping~=1.4.4',
'numpy>=1.22.4,<2.0.0',
diff --git a/requirements-dev.txt b/requirements-dev.txt
index c6b6423587dde299034379ce97c06f0d57ad6d32..481e6c62324e5ededca319d22c79014949d67540 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -22,7 +22,6 @@ bagit==1.8.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
basicauth==0.4.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
beautifulsoup4==4.12.3 # via -r requirements.txt, nomad-lab (pyproject.toml)
billiard==4.2.0 # via celery, -r requirements.txt
-biopython==1.84 # via mdanalysis, -r requirements.txt
bitarray==2.9.2 # via -r requirements.txt, nomad-lab (pyproject.toml)
blinker==1.8.2 # via flask, -r requirements.txt
build==1.2.1 # via nomad-lab (pyproject.toml)
@@ -70,7 +69,6 @@ gitdb==4.0.11 # via gitpython, -r requirements.txt
gitpython==3.1.43 # via mkdocs-git-revision-date-localized-plugin, -r requirements.txt, nomad-lab (pyproject.toml)
greenlet==3.0.3 ; (python_full_version < '3.13' and platform_machine == 'AMD64') or (python_full_version < '3.13' and platform_machine == 'WIN32') or (python_full_version < '3.13' and platform_machine == 'aarch64') or (python_full_version < '3.13' and platform_machine == 'amd64') or (python_full_version < '3.13' and platform_machine == 'ppc64le') or (python_full_version < '3.13' and platform_machine == 'win32') or (python_full_version < '3.13' and platform_machine == 'x86_64') # via sqlalchemy, -r requirements.txt
griddataformats==1.0.2 # via mdanalysis, -r requirements.txt
-gsd==3.3.1 # via mdanalysis, -r requirements.txt
gunicorn==21.2.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
h11==0.14.0 # via httpcore, uvicorn, -r requirements.txt
h5grove==1.3.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
@@ -114,8 +112,8 @@ markdown==3.7 # via mkdocs, mkdocs-click, mkdocs-material, pymdown-e
markupsafe==2.1.5 # via jinja2, mako, mkdocs, werkzeug, -r requirements.txt, nomad-lab (pyproject.toml)
matid==2.1.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
matplotlib==3.9.2 # via ase, asr, mdanalysis, phonopy, pymatgen, -r requirements.txt
-mda-xdrlib==0.2.0 # via pyedr, -r requirements.txt
-mdanalysis==2.5.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
+mda-xdrlib==0.2.0 # via mdanalysis, pyedr, -r requirements.txt
+mdanalysis==2.7.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
mergedeep==1.3.4 # via mkdocs, mkdocs-get-deps
mistune==3.0.2 # via m2r, -r requirements.txt
mkdocs==1.6.0 # via mkdocs-git-revision-date-localized-plugin, mkdocs-macros-plugin, mkdocs-material, mkdocs-redirects, nomad-lab (pyproject.toml)
@@ -139,11 +137,11 @@ mypy==1.0.1 # via nomad-lab (pyproject.toml)
mypy-extensions==1.0.0 # via mypy
names==0.3.0 # via nomad-lab (pyproject.toml)
netcdf4==1.6.5 # via -r requirements.txt, nomad-lab (pyproject.toml)
-networkx==3.3 # via matid, mdanalysis, pymatgen, -r requirements.txt, nomad-lab (pyproject.toml)
+networkx==3.3 # via matid, pymatgen, -r requirements.txt, nomad-lab (pyproject.toml)
nh3==0.2.18 # via readme-renderer
nomad-openbis==1.0.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
nptyping==1.4.4 # via -r requirements.txt, nomad-lab (pyproject.toml)
-numpy==1.26.4 # via ase, biopython, cftime, contourpy, griddataformats, gsd, h5grove, h5py, matid, matplotlib, mdanalysis, mrcfile, netcdf4, nptyping, pandas, phonopy, pyedr, pymatgen, rdkit, scikit-learn, scipy, spglib, tifffile, xarray, -r requirements.txt, nomad-lab (pyproject.toml)
+numpy==1.26.4 # via ase, cftime, contourpy, griddataformats, h5grove, h5py, matid, matplotlib, mdanalysis, mrcfile, netcdf4, nptyping, pandas, phonopy, pyedr, pymatgen, rdkit, scikit-learn, scipy, spglib, tifffile, xarray, -r requirements.txt, nomad-lab (pyproject.toml)
oauthenticator==15.1.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
oauthlib==3.2.2 # via jupyterhub, -r requirements.txt
openpyxl==3.1.5 # via -r requirements.txt, nomad-lab (pyproject.toml)
@@ -261,7 +259,7 @@ uncertainties==3.2.2 # via pymatgen, -r requirements.txt
unidecode==1.3.2 # via -r requirements.txt, nomad-lab (pyproject.toml)
uri-template==1.3.0 # via jsonschema, -r requirements.txt
urllib3==1.26.19 # via docker, elasticsearch, nomad-openbis, requests, -r requirements.txt
-uv==0.2.37 # via nomad-lab (pyproject.toml)
+uv==0.3.0 # via nomad-lab (pyproject.toml)
uvicorn==0.30.6 # via h5grove, -r requirements.txt, nomad-lab (pyproject.toml)
uvloop==0.20.0 ; platform_python_implementation != 'PyPy' and sys_platform != 'cygwin' and sys_platform != 'win32' # via uvicorn, -r requirements.txt
validators==0.18.2 # via -r requirements.txt, nomad-lab (pyproject.toml)
@@ -271,7 +269,7 @@ watchfiles==0.23.0 # via uvicorn, -r requirements.txt
wcwidth==0.2.13 # via prompt-toolkit, -r requirements.txt
webcolors==24.8.0 # via jsonschema, -r requirements.txt
webencodings==0.5.1 # via html5lib, -r requirements.txt
-websockets==12.0 # via uvicorn, -r requirements.txt
+websockets==13.0 # via uvicorn, -r requirements.txt
werkzeug==3.0.3 # via flask, -r requirements.txt
wrapt==1.16.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
xarray==2024.7.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
diff --git a/requirements.txt b/requirements.txt
index 6bb5c73d23d74114399fe7218fcf294f32a6a425..c960f435ae96ca8d341c58e1558c66d6e225314e 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -17,7 +17,6 @@ bagit==1.8.1 # via nomad-lab (pyproject.toml)
basicauth==0.4.1 # via nomad-lab (pyproject.toml)
beautifulsoup4==4.12.3 # via nomad-lab (pyproject.toml)
billiard==4.2.0 # via celery
-biopython==1.84 # via mdanalysis
bitarray==2.9.2 # via nomad-dos-fingerprints (dependencies/nomad-dos-fingerprints/pyproject.toml), nomad-lab (pyproject.toml)
blinker==1.8.2 # via flask
cachetools==5.5.0 # via nomad-lab (pyproject.toml)
@@ -58,7 +57,6 @@ gitdb==4.0.11 # via gitpython
gitpython==3.1.43 # via nomad-lab (pyproject.toml)
greenlet==3.0.3 ; (python_full_version < '3.13' and platform_machine == 'AMD64') or (python_full_version < '3.13' and platform_machine == 'WIN32') or (python_full_version < '3.13' and platform_machine == 'aarch64') or (python_full_version < '3.13' and platform_machine == 'amd64') or (python_full_version < '3.13' and platform_machine == 'ppc64le') or (python_full_version < '3.13' and platform_machine == 'win32') or (python_full_version < '3.13' and platform_machine == 'x86_64') # via sqlalchemy
griddataformats==1.0.2 # via mdanalysis
-gsd==3.3.1 # via mdanalysis
gunicorn==21.2.0 # via nomad-lab (pyproject.toml)
h11==0.14.0 # via httpcore, uvicorn
h5grove==1.3.0 # via nomad-lab (pyproject.toml)
@@ -95,8 +93,8 @@ mako==1.3.5 # via alembic
markupsafe==2.1.5 # via jinja2, mako, werkzeug
matid==2.1.0 # via nomad-lab (pyproject.toml)
matplotlib==3.9.2 # via ase, asr, mdanalysis, phonopy, pymatgen
-mda-xdrlib==0.2.0 # via pyedr
-mdanalysis==2.5.0 # via nomad-lab (pyproject.toml)
+mda-xdrlib==0.2.0 # via mdanalysis, pyedr
+mdanalysis==2.7.0 # via nomad-lab (pyproject.toml)
mistune==3.0.2 # via m2r
mmtf-python==1.1.3 # via mdanalysis
mongoengine==0.28.2 # via nomad-lab (pyproject.toml)
@@ -106,10 +104,10 @@ mpmath==1.3.0 # via sympy
mrcfile==1.5.3 # via griddataformats
msgpack==1.0.8 # via mmtf-python, nomad-lab (pyproject.toml)
netcdf4==1.6.5 # via nomad-lab (pyproject.toml)
-networkx==3.3 # via matid, mdanalysis, pymatgen, nomad-lab (pyproject.toml)
+networkx==3.3 # via matid, pymatgen, nomad-lab (pyproject.toml)
nomad-openbis==1.0.0 # via nomad-lab (pyproject.toml)
nptyping==1.4.4 # via nomad-lab (pyproject.toml)
-numpy==1.26.4 # via ase, biopython, cftime, contourpy, griddataformats, gsd, h5grove, h5py, matid, matplotlib, mdanalysis, mrcfile, netcdf4, nptyping, pandas, phonopy, pyedr, pymatgen, rdkit, scikit-learn, scipy, spglib, tifffile, xarray, nomad-dos-fingerprints (dependencies/nomad-dos-fingerprints/pyproject.toml), nomad-lab (pyproject.toml)
+numpy==1.26.4 # via ase, cftime, contourpy, griddataformats, h5grove, h5py, matid, matplotlib, mdanalysis, mrcfile, netcdf4, nptyping, pandas, phonopy, pyedr, pymatgen, rdkit, scikit-learn, scipy, spglib, tifffile, xarray, nomad-dos-fingerprints (dependencies/nomad-dos-fingerprints/pyproject.toml), nomad-lab (pyproject.toml)
oauthenticator==15.1.0 # via nomad-lab (pyproject.toml)
oauthlib==3.2.2 # via jupyterhub
openpyxl==3.1.5 # via nomad-lab (pyproject.toml)
@@ -208,7 +206,7 @@ watchfiles==0.23.0 # via uvicorn
wcwidth==0.2.13 # via prompt-toolkit
webcolors==24.8.0 # via jsonschema
webencodings==0.5.1 # via html5lib
-websockets==12.0 # via uvicorn
+websockets==13.0 # via uvicorn
werkzeug==3.0.3 # via flask
wrapt==1.16.0 # via nomad-lab (pyproject.toml)
xarray==2024.7.0 # via nomad-lab (pyproject.toml)