de novo design of high affinity biological binders

Conditional Memory via Scalable Lookup: A New Axis of Sparsity for Large Language Models

RNA visualizing tool

ProCEDiS: a state-annotation-free framework to generate compact, diverse protein conformational ensembles via MSA recombination, AlphaFold2, and short MD.

Code for designing biased protein states

functions to plot text with <highlighted substrings> in matplotlib.

Semiautomated SAS data Analysis

Package for calculation of small angle scattering models using OpenCL.

GerNA-Bind: Geometric-enhanced RNA-ligand Binding Specificity Prediction with Deep Learning

Shrinking Proteins with Diffusion

Official repository of "ODesign: A World Model for Biomolecular Interaction Design"

UCBShift is a program for predicting chemical shifts for backbone atoms and β-carbon of a protein in solution. It utilizes a machine learning module that makes predictions from features extracted f…

Reduce - tool for adding and correcting hydrogens in PDB files

Profluent-E1 family of Protein Encoder Models

Official Repository for ProteinConformers: Benchmark Dataset for Simulating Protein Conformational Landscape Diversity and Plausibility

An open-source neural network for performing accurate ML/MM MD simulation with electrostatic embedding.

NequIP is a code for building E(3)-equivariant interatomic potentials

Efficient manipulation of protein structures in Python

PeptoneBench: evaluating protein ensembles across the order-disorder continuum

IDP-o: Intrinsically Disordered Protein Ensemble Generator

PyTorch implementation of MoCo: https://arxiv.org/abs/1911.05722

From cryo-EM density map to atomic structure

The code, training and test data for PLMDA-PPI, a mechanism-aware deep learning framework for protein-protein interaction prediction.