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task-structure-prep

Here are 9 public repositories matching this topic...

Scindices / openmm--pdbfixer

PDBFixer fixes problems in PDB files

status-active role-library lang-python interface-cli domain-structural-biology task-file-io entity-protein interface-api status-published status-packaged-pypi status-packaged-conda scope-focused domain-molecular-simulation task-structure-prep method-rule-based interface-gui ecosystem-openmm

Updated Mar 10, 2026
Python

Scindices / project-gemmi--gemmi

macromolecular crystallography library and utilities

status-active lang-python lang-cpp interface-cli domain-structural-biology task-file-io task-structure-analysis method-chemoinformatics entity-protein interface-api status-published status-packaged-pypi status-packaged-conda method-statistics role-toolkit scope-swissknife task-structure-prep entity-crystal domain-crystallography

Updated Jul 24, 2026
C++

Scindices / biotite-dev--hydride

Adding hydrogens to molecular models

status-active role-library lang-python interface-cli domain-structural-biology entity-protein entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda scope-focused method-physics task-structure-prep method-rule-based

Updated Nov 24, 2025
Python

Scindices / Electrostatics--pdb2pqr

PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.

status-active lang-python interface-cli role-application domain-structural-biology entity-protein interface-api status-published status-packaged-pypi status-packaged-conda scope-focused method-physics method-statistics task-structure-prep task-charge-assignment domain-computational-chemistry

Updated Apr 26, 2026
Python

Scindices / jensengroup--propka

PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.

status-active lang-python interface-cli role-application domain-structural-biology entity-protein interface-api status-published status-packaged-pypi status-packaged-conda scope-focused method-physics entity-complex method-statistics task-structure-prep task-charge-assignment domain-computational-chemistry

Updated Jul 14, 2026
Python

Scindices / rlabduke--reduce

Reduce - tool for adding and correcting hydrogens in PDB files

status-active lang-cpp interface-cli role-application domain-structural-biology entity-protein status-published status-packaged-conda scope-focused method-physics entity-nucleic-acid task-structure-prep method-rule-based

Updated Jan 5, 2026
C++

Scindices / haddocking--pdb-tools

A dependency-free cross-platform swiss army knife for PDB files.

status-active lang-python interface-cli domain-structural-biology task-file-io task-structure-analysis method-chemoinformatics entity-protein interface-api status-published status-packaged-pypi status-packaged-conda role-toolkit scope-swissknife entity-nucleic-acid task-structure-prep method-rule-based

Updated Jun 10, 2026
Python

Scindices / m3g--packmol

Packmol - Initial configurations for molecular dynamics simulations

status-active lang-python interface-cli role-application entity-protein entity-small-molecule status-published status-packaged-pypi status-packaged-conda scope-focused method-physics domain-molecular-simulation task-structure-prep task-system-model entity-crystal lang-fortran

Updated May 27, 2026
Fortran

Scindices / cctbx--cctbx_project

Computational Crystallography Toolbox

status-active lang-python lang-cpp interface-cli domain-structural-biology task-file-io task-structure-analysis entity-protein interface-api status-published status-packaged-conda method-physics method-statistics role-toolkit scope-swissknife task-structure-prep entity-crystal domain-crystallography

Updated Jul 29, 2026
Python

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