Alternatives and similar repositories for pdbfixer

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

• Discngine / fpocket
  fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scien…
  ☆419Updated last year
• pablo-arantes / making-it-rain
  Cloud-based molecular simulations for everyone
  ☆459Updated last month
• chemosim-lab / ProLIF
  Interaction Fingerprints for protein-ligand complexes and more
  ☆455Updated last week
• pharmai / plip
  Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Schake,…
  ☆615Updated last month
• 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.
  ☆285Updated last month
• jensengroup / propka
  PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.
  ☆324Updated last year
• haddocking / pdb-tools
  A dependency-free cross-platform swiss army knife for PDB files.
  ☆435Updated 2 months ago
• prody / ProDy
  A Python Package for Protein Dynamics Analysis
  ☆515Updated last week
• rdk / p2rank
  P2Rank: Protein-ligand binding site prediction from protein structure based on machine learning.
  ☆366Updated 2 months ago
• Pymol-Scripts / Pymol-script-repo
  Collected scripts for Pymol
  ☆502Updated 4 months ago
• gnina / gnina
  A deep learning framework for molecular docking
  ☆807Updated last month
• AngelRuizMoreno / Jupyter_Dock
  Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting f…
  ☆273Updated 2 years ago
• forlilab / Meeko
  Interface for AutoDock, molecule parameterization
  ☆313Updated this week
• openmm / openmmforcefields
  CHARMM and AMBER forcefields for OpenMM (with small molecule support)
  ☆335Updated 2 weeks ago
• lightdock / lightdock
  Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm
  ☆367Updated 2 months ago
• MolecularAI / REINVENT4
  AI molecular design tool for de novo design, scaffold hopping, R-group replacement, linker design and molecule optimization.
  ☆625Updated last week
• wallnerlab / DockQ
  DockQ is a single continuous quality measure for Protein, Nucleic Acids and Small Molecule Docking Models
  ☆345Updated last month
• ccsb-scripps / AutoDock-GPU
  AutoDock for GPUs and other accelerators
  ☆539Updated 2 months ago
• maabuu / posebusters
  Plausibility checks for generated molecule poses.
  ☆342Updated last week
• zrqiao / NeuralPLexer
  NeuralPLexer: State-specific protein-ligand complex structure prediction with a multi-scale deep generative model
  ☆314Updated 2 months ago
• RosettaCommons / PyRosetta.notebooks
  Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design
  ☆633Updated last year
• williamgilpin / pypdb
  A Python API for the RCSB Protein Data Bank (PDB)
  ☆332Updated 6 months ago
• MolecularAI / Reinvent
  ☆364Updated 6 months ago
• PDB-REDO / dssp
  Application to assign secondary structure to proteins
  ☆228Updated last week
• ccsb-scripps / AutoDock-Vina
  AutoDock Vina
  ☆863Updated 2 months ago
• volkamerlab / teachopencadd
  TeachOpenCADD: a teaching platform for computer-aided drug design (CADD) using open source packages and data
  ☆936Updated 2 weeks ago
• Acellera / htmd
  HTMD: Programming Environment for Molecular Discovery
  ☆268Updated last week
• baker-laboratory / rf_diffusion_all_atom
  Public RFDiffusionAA repo
  ☆455Updated last year
• openforcefield / openff-toolkit
  The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation avai…
  ☆371Updated last week
• LPDI-EPFL / masif
  MaSIF- Molecular surface interaction fingerprints. Geometric deep learning to decipher patterns in molecular surfaces.
  ☆705Updated last year