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A bidirectional pipeline parallelism algorithm for computation-communication overlap in V3/R1 training.
The pDynamo molecular modeling and simulation program
The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy (ABFE) and relative binding free energy (RBFE) calculations on protein-ligand systems, compatible with …
Code and notebook for our paper "Assessing interaction recovery of predicted protein-ligand poses"
benchmarking AI-powered docking methods from the perspective of virtual screening
ORB forcefield models from Orbital Materials
Uni-FEP-Benchmarks is a benchmark dataset designed to systematically evaluate Uni-FEP.
Analysis of potential functions for covalent bonds for usage in molecular simulations
A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.
Inference code for scalable emulation of protein equilibrium ensembles with generative deep learning
CLI tool and python library that converts the output of popular command-line tools, file-types, and common strings to JSON, YAML, or Dictionaries. This allows piping of output to tools like jq and …
For advanced physics-driven combined with neural network enhancement force field.
Official repository for the Deep Docking protocol
The simplest, fastest repository for training/finetuning medium-sized GPTs.
Cosine acceleration for viscosity calculation
Workflow to clean up and fix structural problems in protein-ligand binding datasets
Boltzmann-ranked alternative protein conformations from reduced-MSA AlphaFold2
A Python framework for high performance GPU simulation and graphics
An interoperable Python framework for biomolecular simulation.
easyPARM is a computational tool developed to simplify the derivation of force field parameters for metal-containing molecular systems and to enable charge restraints on specific atoms.
Quantum chemistry program executor and IO standardizer (QCSchema).
BackPACK - a backpropagation package built on top of PyTorch which efficiently computes quantities other than the gradient.
A Knowledge Graph of Common Chemical Names to their Molecular Definition
Official implementation of Stochastic Taylor Derivative Estimator (STDE) NeurIPS2024
Implement minimal boilerplate CLIs derived from type hints and parse from command line, config files and environment variables
Official implementation of MatterGen -- a generative model for inorganic materials design across the periodic table that can be fine-tuned to steer the generation towards a wide range of property c…