akos-bio1 Goto Github PK

2019_sdasd

Codes for ribosome profiling study of SD-ASD interaction

abfe_workflow

This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.

cho_cell_microprotein_analysis

dash-tree

Partial Charge assignment for Molecular Dynamics

dynamicbind

repo for DynamicBind: Predicting ligand-specific protein-ligand complex structure with a deep equivariant generative model

espfit-experiment

Workspace for espfit

mace

MACE - Fast and accurate machine learning interatomic potentials with higher order equivariant message passing.

mace-md

mace-off23-sc

mdtraj

An open library for the analysis of molecular dynamics trajectories

oligopool_riboseq

openmm-rna

a reimplementation of work by seetin et al. for RNA tertiary structure prediction

openmm_mmgbsa

polymer_examples

Example polymers for testing.

polymerist

Polymer-Oriented LibrarY of Monomer-Expression Rules and In-silico Synthesis Tools

refit-espaloma

Refit espaloma with energies and forces

simple-simulate-complex

Simple protein-ligand complex simulation with OpenMM

vanilla-espaloma-experiment

Vanilla MD simulation of protein-ligand complex using espaloma-0.3

wasp_simulations

Repository for housing minimal reproducing scripts and chemical structures for water-soluble polymer (WaSP) MD studies