Benjamin Fry

boltz-generalized-covalent-modification. Enables using Boltz-1/1x to predict the structure of arbitrary covalent modifications / Non-Canonical Amino Acids. Covalent bonds are enforced. Also walks you through injecting a new residue into the CCD.

CARPdock. Fast gpu-accelerated rigid-rigid docking onto protein backbones without a sequence.

ProteinMPNN. Code for the ProteinMPNN paper

Machine-Learning-Fundamentals. A collection of Machine Learning models implemented from math to model in jupyter notebook.

apmth-207-problem-sets. Problem set solutions for Fall 2022 Applied Math 207 (Advanced Scientific Computing: Stochastic Methods for Data Analysis, Inference and Optimization) at Harvard

REINFORCEmers. Final Project for Harvard CS184: Introduction to Reinforcement Learning

CS475-Machine-Learning-Final-Project. Final project: Song recommendation algorithm from Spotify API and Million Playlist Dataset (MPD) https://www.aicrowd.com/challenges/spotify-million-playlist-dataset-challenge

Code-Notes. Notes taken in Typora in Markdown on programming and mathematics.

benf549.github.io. Personal Website / CV