Awesome Protein Representation Learning

Source code for "Learning protein sequence embeddings using information from structure" - ICLR 2019

Code for AAAI 2024 paper "PSC-CPI: Multi-Scale Protein Sequence-Structure Contrasting for Efficient and Generalizable Compound-Protein Interaction Prediction"

pmUE (Protein Modelling Unreal Engine) - a repo for constructing a molecule visualizer plugin in Unreal

Large-Scale Computational Modeling of H5 Influenza Variants Against HA1-Neutralizing Antibodies

noodle-strut is an interactive 3D printing structural support module for PyMOL

Hybridized distance- and contact-based hierarchical protein folding

Designed for batch submission of multiple target sequences using a single structural template in SwissModel

StrBio@UAM

Protein Structure Prediction Toolkit A Python-based tool to fetch, parse, and analyze protein 3D structures using PDB IDs. It downloads .pdb files from RCSB, extracts chain and residue information using BioPython, and sets the foundation for future integration with AlphaFold2 and structural analysis tools.

AI/ML Graduate Student @ ASU | Scientific Developer @ Cadence | Specializing in GenAI, CUDA, Protein Modeling & Deep Learning

Integrated Bioinformatics and Computer-Aided Drug Design (CADD) workflow for identifying conserved therapeutic targets and potential inhibitors against Mpox virus.

Structural Bioinformatics Course @UAM

Protein–ligand interaction prediction using Metropolis simulations and machine learning models across molecular datasets

Learning project for protein modeling and BioAI using Python, Biopython, and ESM models

Multi-phase peptide ML pipeline for hemolysis prediction, generative design, and closed-loop optimization, built on transformers and modern PyTorch tooling.

Visualizing the 6KIX Histone Protein using PyMOL – includes annotated movie scenes.

Local-first protein modeling workbench for building, validating, and handing off AlphaFold-style structure-prediction jobs.

Trajectory database for 14 Molecular dynamics simulations systems of ANT(3″)-Ia aminoglycoside nucleotidyltransferase from A. baumannii & S. aureus | Git LFS · Schrödinger Maestro & Desmond

Codon optimization and structural modeling of perchlorate-reducing enzymes for Martian regolith bioremediation.