codebian's repositories
AF-cryptic-pocket
Cryptic pocket prediction using AlphaFold 2
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.
GromacsWrapper
GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2021 supported).
lipid_ionINTERACTION
Files related to the NMRlipids II project
masterclass-22-11
Files for PLUMED Masterclass-22-11
metadynamics-1
Run metadynamics simulations and analyse free energy surfaces
metadynminer.py
Python package for efficient analysis of HILLS files generated by Plumed metadynamics simulations. Inspired by the Metadynminer package for R.
multipmd
Multiple path-metadynamics and PathMaps
multipmd-dna
Multiple-path-metadynamics applied to DNA base-pairing transitions
opes
Rethinking Metadynamics: From Bias Potentials to Probability Distributions
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.
papers
Material from papers from KULL centre
Perl2Python
Perl to Python code translator.
plotly.py
The interactive graphing library for Python (includes Plotly Express) :sparkles:
Plotting-MD-Metadynamics
Jupyter Notebook showing how to plot FES, histograms and time-series data using Matplotlib.
postmetad
Python package for post-processing PLUMED metadynamics and OPES simulations.
PythonDataScienceHandbook
Python Data Science Handbook: full text in Jupyter Notebooks
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
rmsd
Calculate Root-mean-square deviation (RMSD) of two molecules, using rotation, in xyz or pdb format
ufedmm
Unified Free Energy Dynamics (UFED) simulations with OpenMM
zotero-pdf-background
a zotero plugin to set green pdf background to care your eyes