codebian

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/shift

Yet another wrapper around SHIFTX+ for MD trajectories analysis but using MPI and HDF5

codebian/gmx_tutorials_livecoms

LiveCoMS GROMACS Tutorials Paper

codebian/gridmat-md

GridMAT-MD membrane analysis program

codebian/kinase-metadynamics

To run metadynamics simulations using openMM (based on Peter Eastman's script)

codebian/meta_pyemma_example

metadynamics trajectory analysis by pyemma

codebian/metadyn_view

Tool for fast and lightweight vizualization of metadynamic results

codebian/nmrlipids.blogspot.fi

Files related to the nmrlipids.blogspot.fi

codebian/NMRlipidsIVotherHGs

NMRlipids IV project

codebian/openmm_metadynamics

toy metadynamics example

codebian/SML_CV

Using supervised machine learning to build collective variables for accelerated sampling

codebian/tf_metadynamics

Using neural networks for enhanced sampling in computational biophysics

codebian/tica_metadynamics

Efficient sampling of protein mutants via transfer learning from the wild-type simulation

codebian/tica_metadynamics_paper_1

Accelerating MD and MSM by running Metadynamics along tICA coordinates

codebian/vde_metadynamics

Enhanced protein mutational sampling using time-lagged variational autoencoders