sbhakat

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tutorials

 2  0
Various tutorials about MD setup and analysis, protein-ligand docking, machine learning and lots of other interesting things.

bayesian-flow-networks

 1  0
This is the official code release for Bayesian Flow Networks.

MasterMSM

 1  0
Python package for generating Markov state models

MonthOfJulia

 1  0
Some code examples gathered during my Month of Julia.

sklearn-sfa

 1  0
This project provides Slow Feature Analysis as a scikit-learn-style package.

time-from-biased-simulations-tools

 1  0
Simple tools for obtaining time from biased molecular dynamics simulations

Time-Series-Transformer

 1  0
A data preprocessing package for time series data. Design for machine learning and deep learning.

vmd-python

 1  0
Installable VMD as a python module
CMake

HDX-MD

 1  0
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
Jupyter Notebook

AF-cryptic-pocket

 21  2
Cryptic pocket prediction using AlphaFold 2

Plotting-MD-Metadynamics

 10  2
Jupyter Notebook showing how to plot FES, histograms and time-series data using Matplotlib.

PAP-review-inputs

 4  3
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.

BPTI-TICA-waterdynamics

 2  0
tICA to capture local loop motion. Describes how to analyse loop movement using TICA and how to run PT-Metad using TIC vectors

Classifier-CV-sampling

 2  0
Binary classifier as CV in enhanced sampling

Plasmepsin-bace

 2  0
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)

Play-data-MD

 2  1
Repo for Play with Real Data competition https://sdat.ir/en/playdata

MSM-ring-flipping

 1  1
Predicting kinetics of aromatic side-chain flipping using Markov State Model
MATLAB

Infrequent-metadynamics

 3  1
Prediction of transition time (kinetics) associated with aromatic ring flipping using infrequent metadynamics
Python

Funnel-metadynamics

 2  0
This repo is designed to give initial files to perform Funnel metadynamics as described in the paper Resolving the problem of trapped water in binding cavities: prediction of host–guest binding free energies in the SAMPL5 challenge by funnel metadynamics (https://link.springer.com/article/10.1007/s10822-016-9948-6)

colvar

 1  0
A package that allows you to read COLVAR output from Plumed and access data

Important-programmes

 1  0
Histogram, bootstrapping and some analyses