Pinned Repositories
model-missing
Script to automatically add missing residues and refine loops with MODELLER
MSE
Just a personal repo to play around with molecular simulations.
paper-multimap-tfep-2023
Source code and input files associated to the paper "Multimap targeted free energy estimation"
tfep
A library to perform targeted free energy perturbation with normalizing flows.
tfep-revisited-2021
Source code and input files associated to the paper "Targeted free energy perturbation revisited: Accurate free energies from mapped reference potentials".
openmmtools
A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.
software-development
A primer on software development best practices for computational chemistry
yank
An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.
mlcolvar
A unified framework for machine learning collective variables for enhanced sampling simulations
openff-toolkit
The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation available at http://open-forcefield-toolkit.readthedocs.io
andrrizzi's Repositories
andrrizzi/tfep-revisited-2021
Source code and input files associated to the paper "Targeted free energy perturbation revisited: Accurate free energies from mapped reference potentials".
andrrizzi/tfep
A library to perform targeted free energy perturbation with normalizing flows.
andrrizzi/paper-multimap-tfep-2023
Source code and input files associated to the paper "Multimap targeted free energy estimation"
andrrizzi/model-missing
Script to automatically add missing residues and refine loops with MODELLER
andrrizzi/MSE
Just a personal repo to play around with molecular simulations.
andrrizzi/phd-thesis
andrrizzi/alchemical-best-practices
Best practice document for alchemical free energy calculations going to livecoms journal
andrrizzi/robots
Laboratory automation toolkits
andrrizzi/alchemy
Alchemical tools for OpenMM
andrrizzi/andrrizzi.github.io
Somewhat more than a cheat sheet that gets updated with me.
andrrizzi/benchmarksets
Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards
andrrizzi/clusterutils
Utilities for running parallel jobs with Torque/Moab and MPI
andrrizzi/conda-recipes
conda build recipes for the Omnia project
andrrizzi/goodiebag
andrrizzi/kinase-benchmark
Benchmark Yank against kinases and FDA approved inhibitors.
andrrizzi/mcce-charges
generating ligand charges
andrrizzi/mdtraj
A modern, open library for the analysis of molecular dynamics trajectories
andrrizzi/mlcvs
Machine learning collective variables for enhanced sampling
andrrizzi/openmm
OpenMM is a toolkit for molecular simulation using high performance GPU code.
andrrizzi/openmmmcmc
MCMC sampler classes for OpenMM
andrrizzi/openmmtools
Test systems for OpenMM
andrrizzi/openmoltools
andrrizzi/paper-microfluidics
Experiments with paper-based microfluidics
andrrizzi/repex
Python replica-exchange simulation facility for OpenMM.
andrrizzi/SAMPL6
Challenge inputs and details for the SAMPL6 challenge
andrrizzi/schema
Schema validation just got Pythonic
andrrizzi/yank
GPU-accelerated calculation of ligand binding affinities in implicit and explicit solvent using alchemical free energy methodologies