spiwokv/ptltsne-visualizations

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spiwokv/ptltsne-visualizations

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Visualizations of free energy surfaces calculated by parametric time-lagged tSNE metadynamics

metadynminer

Package for reading, analysis and visualization of metadynamics HILLS

anncolvar

Collective variables by artificial neural networks

tltsne

Time-lagged t-SNE of molecular trajectories

af2cv

Python script to convert Alphafold output to collective variable

metadynminer3d

Package for reading, analysis and visualization of metadynamics HILLS with 3 collective variables (addendum to metadynminer)

mc_syntax_for_Plumed

Syntax highlight of plumed.dat files in Midnight Commander

docking4structbioinf

Docking and virtual screening tutorial for Structural bioinformatics

Dockingtutorial

Protein-ligand docking and virtual screening tutorial

Rtutorial

Introduction to statistics and visualisation in R

homolmod4structbioinf

Homology modelling tutorial for Structural biology

FlyingGaussianTutorial

Flying Gaussian Tutorial

latticeprotein

Monte Carlo simulation of 3D lattice protein model

encodetraj

Autoencoders for molecular trajectory analysis

md4structbioinf

Molecular dynamics simulation tutorial for Structural biology

enminGromacs

Elastic network model in Gromacs

Fourier-Transform-Understanding-by-R

Fourier Transform: Understanding by R - toutorial

reweightfes

R package for on-the-fly and Tiwary reweighting of metadynamics and other biased molecular simulations

mdtsne

Barnes-Hut t-Distributed Stochastic Neighbor Embedding (t-SNE) for analysis of molecular dynamics trajectories