LongHung-Pham

COATI

COATI: multi-modal contrastive pre-training for representing and traversing chemical space

PaddleHelix

Bio-Computing Platform Featuring Large-Scale Representation Learning and Multi-Task Deep Learning “螺旋桨”生物计算工具集

interface_overlay_coev

Create interface summary from pdb. Uses kmeans. Default distance between atoms considered is 5 Angstrom.

genomic-FM

Defined_Proteins

The DEFINED-PROTEINS software package allows users to: (i) derive descriptor of elementary functions of interest directly from protein structures; (ii) use derived descriptor in rational design and protein engineering of protein functions.

CBGBench

Official code repository of CBGBench: Fill in the Blank of Protein-Molecule Complex Binding Graph

Prop3D

A protein structure dataset that combines 3D atomic coordinates with biophysical and evolutionary properties for every atom in every "cleaned" domain structure in CATH.

arctic3d

Automatic Retrieval and ClusTering of Interfaces in Complexes from 3D structural information

bitbirch

BitBIRCH clustering algorithm

ChatMol

ChatGPT in PyMOL now!

plmc

Inference of couplings in proteins and RNAs from sequence variation

PheSAExamples

acegen-open

Language models for drug discovery using torchrl

GLOW_IVES

AlphaSpace2

Protein surface topographical mapping tool

science-paper-rf-machine-learned-scoring-2022

relative-interaction-frequencies

A repository to keep code for interaction frequency work going forwards.

quantum-torsions

GA-Best-Practices

TorsionNet

A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM

kallisto

Efficiently calculate 3D-features for quantitative structure-activity relationship approaches.

mamba-tabular

Mambular is a Python package that brings the power of Mamba architectures to tabular data, offering a suite of deep learning models for regression, classification, and distributional regression tasks. This includes models like Mambular, FT-Transformer, TabTransformer and tabular ResNets.

auroris

Curate datasets with ease.

EPISOL

The Expanded Package for IET Solvation

rismical

The reference interaction site model integrate calculator

mordred

a molecular descriptor calculator

ball

The Biochemical Algorithms Library

3D-RISM-AI

DL-PLBAP

Structure-based, deep-learning models for PLBAP

Voronoi

Voronoi entropy scripts