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alchemical-best-practices

Best practice document for alchemical free energy calculations going to livecoms journal

covid-19

Novel Coronavirus (COVID-19) Cases, provided by JHU CSSE

covid-moonshot

Scripts and input files associated with docking and free energy calculations for the COVID Moonshot

crem

CReM: chemically reasonable mutations framework

cryoem_synthetic_generation

Simulation of cryo-EM ensemble data from atomic models of molecules exhibiting continuous motions

examples

Example files for Colvars module: https://github.com/Colvars/colvars

flareplot

Visualizing temporal networks

fragment_expansion

Software tools for fragment-based drug discovery (FBDD)

g_mmpbsa

MM-PBSA method for GROMACS. For full description, please visit homepage:

haddock-antibody-antigen

The repository contains material to run the HADDOCK antibody-antigen modelling protocol

inflecs-free-energy-clustering-tutorial

Python tutorial for estimating and clustering free energy landscapes with InfleCS.

jidt

JIDT: Java Information Dynamics Toolkit for studying information-theoretic measures of computation in complex systems

mdbenchmark

Quickly generate, start and analyze benchmarks for GROMACS and NAMD simulations.

mdtraj

A modern, open library for the analysis of molecular dynamics trajectories

openbabel

Open Babel is a chemical toolbox designed to speak the many languages of chemical data.

pmf-calculation-using-umbrella-sampling-namd

pyrosetta.notebooks

Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design

pythondatasciencehandbook

Python Data Science Handbook: full text in Jupyter Notebooks

relion_optics_group_assigner

Simple scripts to add optics groups to existing RELION star files

replicaexchangewithhybridtempering

Scripts and code for REHT simulation (Paper: "High resolution ensemble description of metamorphic and intrinsically disordered proteins using an efficient hybrid parallel tempering scheme")

samplingpaper

Setup files and scripts to reproduce the sampling paper

sars-cov-2-proteins

spider

SPIDER (System for Processing Image Data from Electron microscopy and Related fields) is an image processing system for electron microscopy, especially usefull for single-particle reconstruction.

vfvs

VirtualFlow for Virtual Screening

vmd-analysis-tcl-scripts

Calculate the buried surface area of ligands in the protein-ligand complex.