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Jack Nicoludis's Projects

colabdesign icon colabdesign

Making Protein Design accessible to all via Google Colab!

evcouplings icon evcouplings

Evolutionary couplings from protein and RNA sequence alignments

eve icon eve

Official repository for the paper "Large-scale clinical interpretation of genetic variants using evolutionary data and deep learning". Joint collaboration between the Marks lab and the OATML group.

gamd-openmm icon gamd-openmm

Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calculations of biomolecules. It works by adding a harmonic boost potential to smooth the potential energy surface and reduce system energy barriers. http://miao.compbio.ku.edu/GaMD/

hivclassifier icon hivclassifier

Insight Health Data Science project on predicting HIV infection state from microbiome data

openfold icon openfold

Trainable PyTorch reproduction of AlphaFold 2

pangolin icon pangolin

Pangolin is a deep-learning method for predicting splice site strengths.

plmc icon plmc

Inference of couplings in proteins and RNAs from sequence variation

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