Pinned Loading

1. spink7-klk5-md-pipeline-v3 spink7-klk5-md-pipeline-v3 Public

   Paper Project 4: SPINK7-KLK5 molecular dynamics pipeline V3 – an end-to-end molecular dynamics pipeline for SPINK7-KLK5 binding free energy computation w/ OpenMM, AMBER ff14SB, & TIP3P; SMD/Jarzyns…

   Jupyter Notebook 1

2. the-lock-and-key the-lock-and-key Public

   Week 21 Project 1: Physics-based rigid-body molecular docking engine with an AutoDock4-calibrated five-term scoring function, soft-core Lennard-Jones potentials, binding-pocket carving, Monte Carlo…

   Python 1

3. the-motif-sculptor the-motif-sculptor Public

   Week 20 Project 3: Constrained inverse folding framework for transplanting catalytic motifs onto novel protein scaffolds; uses structure-conditioned message-passing neural networks (MPNNs) w/ locke…

   Python 1

4. the-digital-mutator the-digital-mutator Public

   Week 20 Project 2: In silico deep mutational scanning simulator powered by a structure-conditioned MPNN; predicts fitness effects of all single amino acid substitutions from backbone geometry & val…

   Python 1

5. the-sequence-whisperer the-sequence-whisperer Public

   Week 20 Project 1: Pure NumPy ProteinMPNN-lite inverse folding engine — predicts amino acid sequences from protein backbone structures using SE(3)-invariant message-passing neural networks; feature…

   Python 1

6. the-mini-fold the-mini-fold Public

   Week 19 Project 3: A pedagogical implementation of AlphaFold2's Invariant Point Attention (IPA) for peptide structure prediction; pure NumPy inference engine with 6 pretrained models (PyTorch GPU +…

   Python 1