jacknicoludis

Principal Scientist and Group Leader, Computational Structural Biology

@Genentech

Pinned Repositories

HIVClassifier
Insight Health Data Science project on predicting HIV infection state from microbiome data
Language:Jupyter Notebook10
ChimeraX_MDTraj_Viewer
A ChimeraX trajectory loader based on the mdtraj package
Language:Python00
ColabDesign
Making Protein Design accessible to all via Google Colab!
Language:Python00
EVcouplings
Evolutionary couplings from protein and RNA sequence alignments
Language:Jupyter Notebook00
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.
Language:Python00
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/
Language:Python00
openfold
Trainable PyTorch reproduction of AlphaFold 2
Language:Python00
Pangolin
Pangolin is a deep-learning method for predicting splice site strengths.
Language:Python00
plmc
Inference of couplings in proteins and RNAs from sequence variation
Language:C00
ProteinMPNN
Code for the ProteinMPNN paper
Language:Jupyter Notebook00

jacknicoludis/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/
jacknicoludis/ProteinMPNN
Code for the ProteinMPNN paper
jacknicoludis/ColabDesign
Making Protein Design accessible to all via Google Colab!
jacknicoludis/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.
Language:Python
jacknicoludis/Pangolin
Pangolin is a deep-learning method for predicting splice site strengths.
jacknicoludis/openfold
Trainable PyTorch reproduction of AlphaFold 2
Language:Python
jacknicoludis/EVcouplings
Evolutionary couplings from protein and RNA sequence alignments
jacknicoludis/ChimeraX_MDTraj_Viewer
A ChimeraX trajectory loader based on the mdtraj package
Language:Python
jacknicoludis/scikit-learn
scikit-learn: machine learning in Python
jacknicoludis/plmc
Inference of couplings in proteins and RNAs from sequence variation
jacknicoludis/HIVClassifier
Insight Health Data Science project on predicting HIV infection state from microbiome data
Language:Jupyter Notebook1