Felipe Engelberger's repositories
PDB_Energy_Analysis-v-0
Interactive Tool-set for Analysis of Energetic Changes caused by Protein Mutations
AF_Cluster
Predict multiple protein conformations using sequence clustering and AlphaFold2.
antibody_benchmark
Antibody-Antigen Docking and Affinity Benchmark
EigenFold
EigenFold: Generative Protein Structure Prediction with Diffusion Models
esm
Evolutionary Scale Modeling (esm): Pretrained language models for proteins
MLDE
A machine-learning package for navigating combinatorial protein fitness landscapes.
paper-qa
LLM Chain for answering questions from documents with citations
Asyrp_official
official repo for Asyrp : Diffusion Models already have a Semantic Latent Space (ICLR2023)
ColabFold
Making Protein folding accessible to all!
conditional-flow-matching
Conditional Flow Matching: Simulation-Free Dynamic Optimal Transport
ConformalLLM
Extending Conformal Prediction to LLMs
e3nn_profiling
Collection of experiments for profiling e3nn
ltt
Learn then Test: Calibrating Predictive Algorithms to Achieve Risk Control
OmegaFold
OmegaFold Release Code
personal-timeline
A public release of TimelineBuilder for building personal digital data timelines.
PIPPack
Implementation of Protein Invariant Point Packer (PIPPack)
RetroExplainer
RetroExplainer: A chemical knowledge and deep-leaning guided molecular assembly approach for retrosynthesis prediction with quantitative interpretability
sake
Spatial Attention Kinetic Networks with E(n)-Equivariance
se3_diffusion
Implementation for SE(3) diffusion model with application to protein backbone generation
tape-neurips2019
Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology. (DEPRECATED)
TensorRT
NVIDIA® TensorRT™, an SDK for high-performance deep learning inference, includes a deep learning inference optimizer and runtime that delivers low latency and high throughput for inference applications.
ThermoMPNN
GNN trained to predict changes in thermodynamic stability for protein point mutants
Topics-In-Modern-Statistical-Learning
Materials for STAT 991: Topics In Modern Statistical Learning (UPenn, 2022 Spring) - uncertainty quantification, conformal prediction, calibration, etc