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assorted_md

assorted_scripts

assorted scripts, mostly related to MD or laziness

autodock_pipeline

bioem

GPU accelerating computing for Bayesian inference of electron microscopy images. BioEM is a publicly available software that enables the characterization of structural models with respect to individual electron microscopy images.

bioinformatics_scripts

assorted scripts associated with bioinformatics, mostly protein sequence analysis/manipulation

cryo_scripts

assorted scripts for dealing with cryoEM data

cryobias

cryojax

Cryo electron microscopy image simulation and analysis built on JAX.

cryojax_reweight

gnome_ui_scripts

A few scripts to tweak the gnome 3 ui. xdotool required.

gromacs_scripts

assorted scripts for working with gromacs

ion_solvation_openmm

Ion solvation free energy with spherical boundary conditions

mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics trajectories.

mdanalysis_scripts

assorted scripts for analysing molecular dynamics simulations.

miro-astore.github.io

A beautiful, simple, clean, and responsive Jekyll theme for academics

modeller_workflow

mutation_builder

workflow for building several missense mutations for protein analysis from a template system

namd2_scripts

Assorted scripts for working with namd.

namd_scripts

assorted scripts for running MD simulations in NAMD

openmm_workflow

assorted scripts for openmm

pdb2fasta

Take a PDB file and spit out protein sequence in 3 or 1 letter format

plumed_scripts

pyemma_scripts

scripts for analysing md trajectories with the pyemma libraries.

relion_scripts

searching_charmm

testing

thesis_template

a latex template you can use for your phd thesis.

vmd-cvs-github