Sridhar's repositories
openmmtools
A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.
alphaflow
AlphaFold Meets Flow Matching for Generating Protein Ensembles
alphafold
Open source code for AlphaFold.
antiberta
Public repository describing training and testing of AntiBERTa.
antiref
AntiRef: reference clusters of human antibody sequences
DeepAb
Deep learning models and structure realization scripts for the DeepAb antibody structure prediction method.
equiformer-pytorch
Implementation of the Equiformer, SE3/E3 equivariant attention network that reaches new SOTA, and adopted for use by EquiFold for protein folding
Icolos
Icolos: A workflow manager for structure based post-processing of de novo generated small molecules
IgFold
Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies
ImmuneBuilder
Predict the structure of immune receptor proteins
infretis
A python library for replica exchange transition interface sampling with infinite swaps
Machine-learning-for-proteins
Listing of papers about machine learning for proteins.
molearn
protein conformational spaces meet machine learning
open-data-registry
A registry of publicly available datasets on AWS
openfold
Trainable PyTorch reproduction of AlphaFold 2
openmm
OpenMM is a toolkit for molecular simulation using high performance GPU code.
perses
Experiments with expanded ensembles to explore chemical space
ProDAR
Implementation of Protein Dynamically Activated Residues (ProDAR) for dyamics-informed protein function prediction/annotation
ProteinMPNN
Code for the ProteinMPNN paper
RoseTTAFold2NA
RoseTTAFold2 protein/nucleic acid complex prediction
se3-transformer-pytorch
Implementation of SE3-Transformers for Equivariant Self-Attention, in Pytorch. This specific repository is geared towards integration with eventual Alphafold2 replication.
weblogo
WebLogo 3: Sequence Logos redrawn