sbhakat Goto Github PK

gromacswrapper

GromacsWrapper is a python package that wraps system calls to Gromacs tools into thin classes. This allows for fairly seamless integration of the gromacs tools into python scripts. This is generally superior to shell scripts because of python’s better error handling and superior data structures. It also allows for modularization and code re-use. In addition, commands, warnings and errors are logged to a file so that there exists a complete history of what has been done.

gt4sd-core

GT4SD, an open-source library to accelerate hypothesis generation in the scientific discovery process.

hdx-md

Gromacs plugin which helps you to calculate distance of three nearest water molecules from an amide nitrogen. This allows identification of MD frames which can go HDX as per the criterion proposed by Halle and Persson https://www.pnas.org/doi/10.1073/pnas.1506079112

hk_dataminer

iaf

Code for reproducing key results in the paper "Improving Variational Inference with Inverse Autoregressive Flow"

iaf-vae

Pytorch Implementation of OpenAI's "Improved Variational Inference with Inverse Autoregressive Flow"

important-programmes

Histogram, bootstrapping and some analyses

information-bottleneck

demonstration of the information bottleneck theory for deep learning

infrequent-metadynamics

Prediction of transition time (kinetics) associated with aromatic ring flipping using infrequent metadynamics

intermol

Conversion tool for molecular simulations

latex-nihbiosketch

A LaTeX class implementing the new NIH Biographical Sketch Format

machine-learning-with-python

Practice and tutorial-style notebooks covering wide variety of machine learning techniques

masterclass-21-4

Repository of the data for PLUMED Masterclass 21.4

mastermsm

Python package for generating Markov state models

md-scripts

A collections of scripts for working molecular dynamics simulations

md2nmr

Compute NMR observables from MD trajectory data (chemical shifts and S2 order parameters)

medium_notebook

Repository containing notebooks of my posts on Medium

meta_pyemma_example

metadynamics trajectory analysis by pyemma

monthofjulia

Some code examples gathered during my Month of Julia.

mops

Compute Amide bond S2 order parameters from MD trajectories

mpro-rank-gen

Code for learning-to-rank using difference in molecular features, and for rule-based generation of a screening library

msm-ring-flipping

Predicting kinetics of aromatic side-chain flipping using Markov State Model

msmbuilder

:building_construction: Statistical models for biomolecular dynamics :building_construction:

msmbuilder2022

Statistical models for biomolecular dynamics

msmbuilder_codes_scripts

Analyzing large-scale MD simulations by MSM modeling and TPT analysis.

msms

Markov state models- GMM MSM

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.

penaunbindingpaper

penrose-steps-turtle-animation

Using Python's Turtle Module to Draw Penrose Steps.

plasmepsin-bace

This repo provides all details to repertory and validate the paper Flap dynamics in pepsin-like aspartic proteases: a computational perspective using Plasmepsin-II and BACE-1 as model systems (doi: https://doi.org/10.1101/2020.04.27.062539)