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1. markovmodel/PyEMMA markovmodel/PyEMMA Public archive

   🚂 Python API for Emma's Markov Model Algorithms 🚂

   Python 338 126

2. binding_HREMD binding_HREMD Public

   Hamiltonian replica exchange plugin (for ACEMD) for binding free energy calculations for protein-protein interaction (https://www.nature.com/articles/s41467-017-01163-6)

   C 2

3. Tutorial_Patch-clamp_data Tutorial_Patch-clamp_data Public

   Forked from JanMuench/Tutorial_Patch-clamp_data

   Code for "Bayesian inference of kinetic schemes for ion channels by Kalman filtering" https://elifesciences.org/articles/62714

   Python

4. Tutorial_Bayesian_Filter_cPCF_data Tutorial_Bayesian_Filter_cPCF_data Public

   Forked from JanMuench/Tutorial_Bayesian_Filter_cPCF_data

   Code for "Bayesian inference of kinetic schemes for ion channels by Kalman filtering" https://elifesciences.org/articles/62714

   Python

5. simplex simplex Public

   🎆 Tools for building core set MSMs in TICA or VAMP space (https://arxiv.org/abs/1811.12551)

   Jupyter Notebook 6

6. Reorder small molecule atoms in PDB ... Reorder small molecule atoms in PDB file to match the order in template PDB file. Uses RDKit.

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   import numpy as np

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   import rdkit.Chem

   3

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   def reorder_atoms(mol_pdb_fname, template_pdb_fname, output_pdb_fname):

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    from rdkit.Chem import rdmolfiles