Yusuf Adeshina's repositories
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
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.
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