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force_fields

Force fields in various formats

forcebalance

Systematic force field optimization.

frustratometer2

This repository contains the pipeline for running the frustratometer software

frustratometer_tools

genie

De Novo Protein Design by Equivariantly Diffusing Oriented Residue Clouds

gentrl

Generative Tensorial Reinforcement Learning (GENTRL) model

gmx_makecyclictop

This script makes a cyclic peptide or cyclic nucleotide topology file for GROMACS out of (specially prepared) linear molecule topology file

gremlin_cpp

GREMLIN - learn MRF/potts model from input multiple sequence alignment! Implementation now available in C++ and Tensorflow/Python!

gromacs-scripts

A collection of scripts which I have developed to use GROMACS, for both compute clusters and post-simulation analysis.

gromacs_examples

Examples showing how to run GROMACS molecular dynamics simulations

guthriesolv

Experimental small molecule hydration free energy dataset

haddocking.github.io

Webpage of the HADDOCK group

hlatools

A collection of tools to work with IMGT/HLA data

homework3

MATLAB code for ridge regression

ibm3202

Google Colab Tutorials for IBM3202

kernel-ridge-regression

first submit

kmeans-extension

lammps-charmm-helper-scripts

Python scripts to handle some LAMMPS-CHARMM script differences.

lasso

A R implementation of Lasso regression

latex

Some examples of LaTeX code I wrote.

loos

LOOS: a lightweight object-oriented structure analysis library

mabbot

Generates a random name for an antibody-based drug

machine-learning-for-proteins

Listing of papers about machine learning for proteins.

man

Codes and data for the paper entitled "Learning representations to predict intermolecular interactions on large-scale heterogeneous molecular association network"

manual

Gromacs Manual

manyfold

🧬 ManyFold: An efficient and flexible library for training and validating protein folding models

math-science-video-lectures

List of Science courses with video lectures

mcmg

MCMG_V1

merlot

Reconstruct the lineage topology of a scRNA-seq differentiation dataset.

merlot-scripts

Benchmark and plotting scripts for the MERLoT paper