panernie Goto Github PK

ahtpeptidefusion

alphafold

Open source code for AlphaFold.

apbs-pdb2pqr

APBS - software for biomolecular electrostatics and solvation

boltzmann-machine-dca

Implementation of direct coupling analysis (DCA) for proteins using a Boltzmann machine algorithm.

chemshell-qmmm-protein-setup

MM and QM/MM setup for a metalloprotein using GROMACS, Chemshell and ORCA (Using the CHARMM forcefield (both in GROMACS and with Chemshell) and the ORCA code as QM code for Chemshell.)

controlnet

Let us control diffusion models!

ddgscan

Scripts and facilities for in-silico mutagenesis with FoldX, Rosetta and ABAUCS1/2

duivy

some scripts for analysis of MD and CADD. And some tutorials.

esm

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

gitskills

gmx_mmpbsa

gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.

gromacs_ff

Trusted force field files for gromacs

learngit

oligomerization-state_and_contact-map

paratemp

A package for molecular dynamics analysis and parallel tempering in GROMACS

peptide_docking_with_af2_and_rosettafold

Code and data used in https://doi.org/10.1101/2021.08.01.454656

pyautofep_gromacs_fep

pymol-script-repo

Collected scripts for Pymol

pytorch-book

PyTorch tutorials and fun projects including neural talk, neural style, poem writing, anime generation (《深度学习框架PyTorch：入门与实战》)

swarm-cg

Swarm-CG: Automatic Parametrization of Bonded Terms in MARTINI-based Coarse-Grained Models of Simple to Complex Molecules via Fuzzy Self-Tuning Particle Swarm Optimization

tensorflow-yolov3

🔥 TensorFlow Code for technical report: "YOLOv3: An Incremental Improvement"

ttclust

clusterize molecular dynamic trajectories (amber, gromacs, charmm, namd, pdb...)

watvina

implicit or explicit water model based docking with Autodock vina engine. supporting pharmacophore /position constrained docking