Pinned Repositories
AF-cryptic-pocket
Cryptic pocket prediction using AlphaFold 2
alchemical_metadynamics
ALK_files_2021_PNAS
This GitHub repo has folders required for setting up the Molecular Dynamics simulations, Metadynamics simulations, and a description of the post-processing codes that were used in the Patil et. al. PNAS 2021
DailyBlog
Everyday work simple blog.
engauge-digitizer
Extracts data points from images of graphs
Enhanced_Sampling_Methods_Tutorials
Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..
funnel_maker
Funnel maker is a set of scripts that sets up funnel metadynamics simulations for protein-ligand binding with PLUMED and OpenMM.
funnel_metadynamics
Funnel Metadynamics MD Simulations
FunnelMetadynamicsAnalysis
A jupyter notebook for the analysis of Funnel Metadynamics simulation data.
shift
Yet another wrapper around SHIFTX+ for MD trajectories analysis but using MPI and HDF5
codebian's Repositories
codebian/AF-cryptic-pocket
Cryptic pocket prediction using AlphaFold 2
codebian/alchemical_metadynamics
codebian/ALK_files_2021_PNAS
This GitHub repo has folders required for setting up the Molecular Dynamics simulations, Metadynamics simulations, and a description of the post-processing codes that were used in the Patil et. al. PNAS 2021
codebian/DailyBlog
Everyday work simple blog.
codebian/engauge-digitizer
Extracts data points from images of graphs
codebian/Enhanced_Sampling_Methods_Tutorials
Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..
codebian/funnel_maker
Funnel maker is a set of scripts that sets up funnel metadynamics simulations for protein-ligand binding with PLUMED and OpenMM.
codebian/funnel_metadynamics
Funnel Metadynamics MD Simulations
codebian/FunnelMetadynamicsAnalysis
A jupyter notebook for the analysis of Funnel Metadynamics simulation data.
codebian/GromacsWrapper
GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2021 supported).
codebian/lipid_ionINTERACTION
Files related to the NMRlipids II project
codebian/masterclass-22-11
Files for PLUMED Masterclass-22-11
codebian/MATCH
codebian/metadynamics
codebian/metadynamics-1
Run metadynamics simulations and analyse free energy surfaces
codebian/metadynminer.py
Python package for efficient analysis of HILLS files generated by Plumed metadynamics simulations. Inspired by the Metadynminer package for R.
codebian/multipmd
Multiple path-metadynamics and PathMaps
codebian/multipmd-dna
Multiple-path-metadynamics applied to DNA base-pairing transitions
codebian/opes
Rethinking Metadynamics: From Bias Potentials to Probability Distributions
codebian/PAP-review-inputs
How one can use binary classifiers, variational auto-encoder, TICA, PCA, distance and dihedral order parameters as CVs in context of pepsin-like aspartic proteases e.g. BACE1 and plasmepsin-II.
codebian/papers
Material from papers from KULL centre
codebian/Perl2Python
Perl to Python code translator.
codebian/plotly.py
The interactive graphing library for Python (includes Plotly Express) :sparkles:
codebian/Plotting-MD-Metadynamics
Jupyter Notebook showing how to plot FES, histograms and time-series data using Matplotlib.
codebian/postmetad
Python package for post-processing PLUMED metadynamics and OPES simulations.
codebian/PythonDataScienceHandbook
Python Data Science Handbook: full text in Jupyter Notebooks
codebian/repository-summary
仓库/笔记 越来越多，本人一些质量还不错的项目/笔记汇总
codebian/rmsd
Calculate Root-mean-square deviation (RMSD) of two molecules, using rotation, in xyz or pdb format
codebian/ufedmm
Unified Free Energy Dynamics (UFED) simulations with OpenMM
codebian/zotero-pdf-background
a zotero plugin to set green pdf background to care your eyes