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1cpn-model

1CPN Coarse-grained model of chromatin

add-missing-residues-to-pdb-files

Add missing residue to pdb files

af2_conformations

A series of scripts that facilitate the prediction of protein structures in multiple conformations using AlphaFold2

af2complex

Predicting direct protein-protein interactions with AlphaFold deep learning neural network models.

alphafold_pytorch

An implementation of the DeepMind's AlphaFold based on PyTorch for research

ambergen

deprecated, see smdgen for steered molecular dynamics with namd and amber

antibodydesignlegacy

antibodyinterfaceprediction

software used in paper "Antibody interface prediction with 3D Zernike descriptors and SVM"

antigen-predict

Code for T cell receptor cross-reactive antigen prediction

asap

ASAP is a package that can quickly analyze and visualize datasets of crystal or molecular structures.

atomicfrustratometer_results

Results for atomic frustratometer manuscript.

attentive-neural-protein-structure-prediction

Prediction of protein tertiary structure via the “translation” of amino acid sequences into internal torsional angles.

attnpacker

Code and Pre-Trained Models for "AttnPacker: An end-to-end deep learning method for protein side-chain packing"

awsem

awsem-suite

Combined model for structure prediction using the AWSEM framework

awsemmd

Associated memory, Water mediated, Structure and Energy Model (AWSEM) protein simulation code

awsemmd_script

beta-barrel-oligomerization

Code for the Vik Nanda lab's study of beta barrels, focusing on prediction of oligomerization

betaserpentine

car_pipeline

cluspro-tools

Provides tools for analyzing ClusPro protein docking results

collepardolab_chromatin_model

Source code for "Nucleosome plasticity is a critical element of chromatin liquid–liquid phase separation and multivalent nucleosome interactions".

contact_map_prediciton_papers

A collection of all existing contact map prediciton papers.

conv_arithmetic

A technical report on convolution arithmetic in the context of deep learning

corerefine

This script generates a Resfile that allows better core packing of a protein.

cornell-cs5785-applied-ml

Teaching materials for the applied machine learning course at Cornell Tech

cs-video-courses

List of Computer Science courses with video lectures.

cs236

csga-pilc-wt-matlab

cu-tsp

Implementation of Accurate Protein Structure Prediction by Embeddings and Deep Learning Representations