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3d-featurizer-metalloenzyme

This repository houses my 3D featurizer of metallo-enzyme proteins. It takes in PDB files and the center of mass of binding site metals/metals

6250-project

NLP for healthcare

auto-c-to-cuda

Code for master's thesis

bert-as-service

Mapping a variable-length sentence to a fixed-length vector using BERT model

biograkn

BioGrakn Knowledge Graph

bipspi

Partner specific prediction of protein binding sites

colabfold

Making Protein folding accessible to all via Google Colab!

deepmind-research

This repository contains implementations and illustrative code to accompany DeepMind publications

dlaicourse

Notebooks for learning deep learning

hbind

Calculates hydrogen-bond interaction tables for protein-small molecule complexes, based on protein PDB and protonated ligand MOL2 structure input. Raschka, Wolf, et al. (2018) J. Computer-Aided Molec. Design

kaggle-rcic-1st

1st Place Solution for Kaggle Recursion Cellular Image Classification Challenge -- https://www.kaggle.com/c/recursion-cellular-image-classification/

keract

Activation Maps (Layers Outputs) and Gradients in Keras.

lightdock

Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm

mask_rcnn

Mask R-CNN for object detection and instance segmentation on Keras and TensorFlow

medium-tutorials

This is a repository for my medium tutorials

notebooks

A collection of Jupyter notebooks.

patentscope

Gem to allow easy access to data from the WIPO PATENTSCOPE Web Service

pdb-tools

A dependency-free cross-platform swiss army knife for PDB files.

plip

Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files

prodigy-cryst

Contacts-based classifier of biological and crystallographic interfaces

protein-recognition-index

Calculates the Protein Recognition Index (PRI), measuring the similarity between intermolecular H-bonding features in a given protein-ligand complex and the H-bond trends observed in diverse protein-ligand complexes. Raschka, Wolf et al. (2018) JCAMD

publishing_python_packages_talk

Resources and slides from the talk "Publishing (Perfect) Python Packages on PyPI"

readme-template

README.md available as a template for any Aras Community Project

readme-template.md

A README template for anyone to copy and use.

rosetta

sequery

Sequery is a tool to search the sequences of the protein structures in the Protein Data Bank (PDB) for a particular pattern of residues, which may include exact matches and acceptable substitutions based on a user-specified amino acid substitution matrix and/or a numerical threshold.

siteinterlock

A toolkit for predicting the binding mode of small molecules interacting with proteins based on interfacial rigidification, as assessed by graph theoretic constraint counting on the covalent and noncovalent bond network. Raschka et al. (2016) Proteins: Structure, Function, and Bioinformatics

spark-vs

Structure-Based Virtual Screening in Spark

trrosetta

A package to predict protein inter-residue geometries from sequence data

varcode

Library for manipulating genomic variants and predicting their effects