Samee Ullah's Projects
Implementation of Alpha Fold 3 from the paper: "Accurate structure prediction of biomolecular interactions with AlphaFold3" in PyTorch
Custom scripts for running AlphaFold in single sequence template mode using the EvoPro implementation
Exploring the conformational ensembles of protein-protein complexes with transformer-based generative neural networks
Rank binders by structure modeling
For managing BioNeMo Service Example notebooks
Facilitates searching, screening, and organizing large chemical databases
Python libraries for Google Colaboratory
DiffLinker: Equivariant 3D-Conditional Diffusion Model for Molecular Linker Design
Initial structures of the dithymine tetra peptide and the dA12
De novo drug design with deep interactome learning
EquiDock: geometric deep learning for fast rigid 3D protein-protein docking
A web app that finds possible binders of a protein using GPT language model.
ligandmpnn Colab NoteBook
A repository of update in molecular dynamics field by recent progress in machine learning and deep learning.
Modelling of Mycoplasma genitalium
List of papers about Proteins Design using Deep Learning
Multi-target de novo molecular generator conditioned on AlphaFold's latent protein embeddings.
Finetuning ProGen2 protein language model for generation of protein sequences from selected protein families.
🐙 Guides, papers, lecture, notebooks and resources for prompt engineering
Tutorials, cheat sheets, and other resources for computational methods for protein design.
Small_molecule_binder_design_use_pseudocycles
Combinatorial antibiotic generation
tanimoto-similarity
testing my blog