Alternatives and similar repositories for gemmi

Users that are interested in gemmi are comparing it to the libraries listed below

• jensengroup / propka
  PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.
  ☆320Updated last year
• Amber-MD / cpptraj
  Biomolecular simulation trajectory/data analysis.
  ☆158Updated 2 weeks ago
• openmm / openmmforcefields
  CHARMM and AMBER forcefields for OpenMM (with small molecule support)
  ☆330Updated 2 weeks ago
• Amber-MD / pytraj
  Python interface of cpptraj
  ☆184Updated 9 months ago
• openforcefield / openff-toolkit
  The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation avai…
  ☆365Updated this week
• scanberg / viamd
  Visual Interactive Analysis of Molecular Dynamics
  ☆310Updated last week
• choderalab / openmmtools
  A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.
  ☆298Updated last month
• openmm / pdbfixer
  PDBFixer fixes problems in PDB files
  ☆594Updated last month
• choderalab / pymbar
  Python implementation of the multistate Bennett acceptance ratio (MBAR)
  ☆274Updated 2 weeks ago
• mittinatten / freesasa
  C-library for calculating Solvent Accessible Surface Areas
  ☆162Updated 3 months ago
• Acellera / htmd
  HTMD: Programming Environment for Molecular Discovery
  ☆268Updated 4 months ago
• Electrostatics / pdb2pqr
  PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.
  ☆156Updated 7 months ago
• alanwilter / acpype
  OFFICIAL: AnteChamber PYthon Parser interfacE
  ☆236Updated 4 months ago
• Becksteinlab / GromacsWrapper
  GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2024 supported).
  ☆181Updated last month
• choderalab / yank
  An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.
  ☆187Updated 2 years ago
• chemosim-lab / ProLIF
  Interaction Fingerprints for protein-ligand complexes and more
  ☆446Updated 2 months ago
• Valdes-Tresanco-MS / gmx_MMPBSA
  gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.
  ☆278Updated 3 months ago
• Electrostatics / apbs
  Software for biomolecular electrostatics and solvation calculations
  ☆114Updated last year
• rlabduke / reduce
  Reduce - tool for adding and correcting hydrogens in PDB files
  ☆156Updated 5 months ago
• marrink-lab / vermouth-martinize
  Describe and apply transformation on molecular structures and topologies
  ☆126Updated last week
• Acellera / moleculekit
  MoleculeKit: Your favorite molecule manipulation kit
  ☆226Updated last week
• openmm / openmm-torch
  OpenMM plugin to define forces with neural networks
  ☆213Updated 8 months ago
• prody / ProDy
  A Python Package for Protein Dynamics Analysis
  ☆506Updated last week
• ParmEd / ParmEd
  Parameter/topology editor and molecular simulator
  ☆439Updated 2 months ago
• Discngine / fpocket
  fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scien…
  ☆396Updated last year
• westpa / westpa
  WESTPA: The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis
  ☆207Updated 3 weeks ago
• mdtraj / mdtraj
  An open library for the analysis of molecular dynamics trajectories
  ☆673Updated this week
• pemsley / coot
  Software for macromolecular model-building
  ☆151Updated last week
• molmod / openmm-tutorial-msbs
  OpenMM tutorial for the MSBS course
  ☆177Updated last week
• avirshup / py3dmol
  ☆130Updated 9 years ago