sarisabban

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Duke university

https://www.youtube.com/user/SariSabban

Sari Sabban's repositories

RamaNet

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

Language:PythonMIT47 3 1

RosettaDesign

RosettaDesign using PyRosetta

Language:PythonMIT27 3 1

Notes

Personal Notes

Language:PythonMIT21 5 2

VaxDesign

A script that computationally designs a vaccine

Language:PythonMIT16 40

Pose

A bare metal Python library for building and manipulating protein molecular structures

Language:PythonGPL-2.011 30

RosettaAbinitio

A bash script for an automated Rosetta Abinitio folding simulation on an HPC

Language:ShellMIT11 10

Rg

A small python script that calculates the Radius of Gyration (Rg) of a protein.

Language:PythonMIT8 10

RMSD

Calculate the RMSD between two protein structures

Language:PythonMIT800

SinfNet

A collection of datasets and neural networks for microorganism image classification

Language:HTMLMIT8 3 2

ProtLSTM

An LSTM neural network to generate novel protein sequences

Language:PythonMIT4 10

DeepPhase

Protein Crystal Classification Using Machine Learning

Language:PythonMIT2 20

btc

A simple Bitcoin (BTC) ticker

Language:PythonMIT100

Coronavirus

Live Coronavirus Tracker

Language:PythonMIT1 20

FragQuality

Measures the RMSD for each fragment at each protein structure's position and plots the lowest RMSD fragment for each position

Language:PythonMIT1 10

MiraMar

De novo cyclic protein polypeptide design using reinforcement learning.

Language:PythonGPL-2.0100

PDBclean

A small script that cleans the PDB database

Language:PythonMIT1 10

ReNumb

Renumbers a PDB protein structure starting at residue 1 and chain A

Language:PythonMIT1 10

CoreAnalyse

This script points out if a protein's core has polar amino acids.

Language:PythonMIT010

CoreRefine

This script generates a Resfile that allows better core packing of a protein.

Language:PythonMIT010

DiffusionModel

Generic U-Net based diffusion model written in tensorflow

Language:Jupyter Notebook020

Frags

Generate Fragment Picking and PSIPRED secondary structure prediction.

Language:PythonMIT010

ilmbot

A Twitter bot for the twitter account of my podcast ILM FM

Language:PythonMIT020

InstaMediaGET

A small script that parses an instagram account and gets all the video or image URLs.

Language:PythonMIT020

IRCbot

A simple IRC bot that posts a notice when talked to

Language:PythonMIT010

PDBAnalyse

A script that uses Machine Learning to analyse all protein structures in the Protein DataBank (PDB) database

Language:PythonMIT000

ProtLayers

This script calculates the different layers (Surface, Boundery, Core) of a protein then opens Pymol to highlight them.

Language:PythonMIT000

ProtVR

Visualise a Protein in Virtual Reality

Language:PythonMIT010

RefineAssist

This script will calculate the solvent-accessible surface (SASA) for each amino acid within a protein and point out which amino acids are in the wrong layer.

Language:PythonMIT020

Slice

Get Part of a Protein

Language:PythonMIT000

XtalPredSubmit

A script that submits a query to the XtalPred server for protein crystallisability prediction

Language:PythonMIT000