Mahmoud Ebrahimkhani's Projects
A 3D Generative Model for Structure-Based Drug Design (NeurIPS 2021)
An antibody-specific language model focusing on NGL prediction
A curated list of awesome AI and Bioinformatics.
Open source code for AlphaFold.
A GitHub repository with Jupyter notebooks for training & testing a CGAN to transform the anatomy of the aorta & velocity metrics from 4D flow MRI using deep learning techniques. Ideal for medical imaging researchers & practitioners
Use of state of the art Convolutional neural network architectures including 3D UNet, 3D VNet and 2D UNets for Brain Tumor Segmentation and using segmented image features for Survival Prediction of patients through deep neural networks.
Protein language model trained on coding DNA
Implementation of the Paper "Learning Continuous and Data-Driven Molecular Descriptors by Translating Equivalent Chemical Representations" by Robin Winter, Floriane Montanari, Frank Noe and Djork-Arne Clevert.
A conditional generative adversarial network model for image generation
ct_aortic_anatomy_to_pc_mri_flow_conversion
Molecular generative model based on conditional variational autoencoder for de novo molecular design
This repository contains the Python and MATLAB scripts associated with the project titled "A deep learning approach to using wearable seismocardiography (SCG) for diagnosing aortic valve stenosis and predicting aortic hemodynamics obtained by 4D flow MRI".
Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology
✌🏻 Antigen-Specific Antibody Design and Optimization with Diffusion-Based Generative Models for Protein Structures (NeurIPS 2022)
Python implementation of a denoising diffusion probabilistic model (DDPM) for predicting the binding affinity of a protein-ligand complex.
Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking
A Euclidean diffusion model for structure-based drug design.
Docking_py is a python library allowing a simplified use of the Smina, vina, qvina2 and qvinaw docking software. Docking_py can be easily automatize and scripted.
De Novo Drug Design with RNNs and Transformers
3D molecular fingerprints
A modular framework for neural networks with Euclidean symmetry
A deep learning framework for molecular docking
Geometric Vector Perceptron --- a rotation-equivariant GNN for learning from biomolecular structure
Geometric Vector Perceptrons --- a rotation-equivariant GNN for learning from biomolecular structure
Release for Improved Denoising Diffusion Probabilistic Models