hongmeiyin Goto Github PK

protein_folding

Protein structure prediction ab initial using Monte Carlo sampling, Metropolis criterion, PyRosetta’s FastRelax and an energy eval using RMSD.

psi-blastexb

PSI-BLAST with a new sequence weighting algorithm

psiblastparser

parses psi Blast files

pymol-script-repo

Collected scripts for Pymol

pyrmsd

pyRMSD is a small Python package that aims to offer an integrative and efficient way of performing RMSD calculations of large sets of structures. It is specially tuned to do fast collective RMSD calculations, as pairwise RMSD matrices.

pyrosetta

My working copy of PyRosetta, and associated files

pyrosetta-basic

learn about pyrosetta

pyrosetta-help

Some scripts that I keep using over and over.

pyrosetta-mutagenesis-

Tutorial on how to use PyRosetta to mutate residues with automatic packing of rotamers. Also covers adding ligans in PyRosetta

pyrosetta-practice-and-workspace

pyrosetta-protocols

pyrosetta-study

PyRosetta is an interactive Python-based interface to the powerful Rosetta molecular modeling suite. It enables users to design their own custom molecular modeling algorithms using Rosetta sampling methods and energy functions. PyRosetta was created at Johns Hopkins University by Jeffrey J. Gray, Sergey Lyskov, and the PyRosetta Team.

pyrosetta_onboarding

pyRosetta exercises for 2021 UCSF Biophysics Onboarding

pyrosetta_project

MHC binding project for PyRosetta bootcamp

pyrosetta_protein_mutations_ddg

pyrosetta_pymol_interface

An interface for using PyRosetta via pymol

pyrosetta_routines

Routines or scripts written in PyRosetta

pyrosetta_scripts

pyrosetta scripts

pyrosetta_training

BIOF 096 Rosetta for Molecular Modeling and Design

pyrosetta_tutorial_20420

pyrosetta_viewer3d

Display PackedPose objects, Pose objects, or PDB files within a Jupyter notebook and Google Colab

pyrosettabook

others work with pyrosetta

pyrosettainteractivelabs

Interactive Jupyter notebooks to demonstrate essential protein design concepts

pyrosettaproject

pyrosettascripts_demo

Demonstration python-rosettascripts integration repo.

pyrosettautilityscripts

Some useful scripts for PyRosetta

pytorch-tutorial

PyTorch Tutorial for Deep Learning Researchers

pytorch_tutorial

《Pytorch模型训练实用教程》中配套代码

ramanet

Preforms De novo protein design using machine learning and PyRosetta to generate a novel protein structure

replace-ligand

Example of how to replace a ligand with a similar in Rdkit and Pyrosetta