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amber-scripts

This repository will contain script related to AMBER installation and analysis

bash-scripts

This contain various Bash utilities

bootstrapping_tutorial

Jupyter notebook tutorial on bootstrapping (and other related methods) for resampling and calculating uncertainties from correlated timeseries data.

cpptraj

Biomolecular simulation trajectory/data analysis.

deep-learning-slow-modes

Supporting data for the manuscript "Deep learning the slow modes for rare events sampling"

deepchem

Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology

enhanced_sampling_methods_tutorials

Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..

gass

Globally Accelerated Sliced Sampling

gromacs-scripts

Gromacs molecular dynamics simulation analysis scripts

infrequent-mtd

introtodeeplearning

Lab Materials for MIT 6.S191: Introduction to Deep Learning

machine-learning

This folder contains various useful python scripts

mlcolvar

A unified framework for machine learning collective variables for enhanced sampling simulations

oddt

Open Drug Discovery Toolkit

python

This repository contains small python codes

rdkit-scripts

This is for the scripts of RDkit

stringmethod

Python implementation of the string method to compute the minimum energy path between two points on a 2-dimensional energy landscape.

tass-avibactam-unbinding

aThis repository contains all the essential files needed to reproduce avibactam unbinding form class C-beta lactamase using Temperature Accelerated Sliced Sampling method.

tcl_vmd_scripts

Some of useful tcl scripts to analyse data from VMD

workshop_for_free-energy_calculations

Resources & Study materials are available presented at workshop FECCBS organised at IIT Kanpur, by Prof. Nisanth Nair