End-to-end Reaction-Path Modeling from PDB Structures Using Machine-Learning Interatomic Potentials
☆37Oct 24, 2026Updated this week
Alternatives and similar repositories for pdb2reaction
Users that are interested in pdb2reaction are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Machine‑Learning / Molecular‑Mechanics (ML/MM) hybrid calculator and CLI toolset for Mechanistic Investigation of Enzymatic Reactions.☆25Updated this week
- UMA – Pysisyphus Interface☆13Oct 2, 2026Updated 3 weeks ago
- Collection of shallow wrappers around popular Neural Network potentials for use with the NNPot interface in the GROMACS molecular simulat…☆21May 8, 2026Updated 5 months ago
- Fast and Transferable MLIP Implicit Solvation☆19Oct 14, 2026Updated 2 weeks ago
- DyNoPy☆10Sep 5, 2024Updated 2 years ago
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- Fast, open RMSD_n crystal-packing similarity for molecular crystals (OXtalign)☆23Sep 18, 2026Updated last month
- OMNI-P2x: A universal neural network potential for excited states☆16Mar 19, 2026Updated 7 months ago
- ☆14Updated this week
- We provide a set of scripts to calculate native contacts from a MD. Native contacts are determined according to the overlap and rCSU appr…☆16Jul 2, 2024Updated 2 years ago
- ☆19Apr 13, 2026Updated 6 months ago
- ColabReaction☆22Dec 31, 2025Updated 9 months ago
- mdml: Deep Learning for Molecular Simulations☆55May 17, 2025Updated last year
- A Python implementation of the direct MaxFlux method for transition state search☆45Aug 16, 2026Updated 2 months ago
- Right into the Saddle: Stereochemistry-Aware Generation of Molecular Transition States☆25Aug 9, 2026Updated 2 months ago
- Bare Metal GPUs on DigitalOcean Gradient AI • AdPurpose-built for serious AI teams training foundational models, running large-scale inference, and pushing the boundaries of what's possible.
- ☆15Nov 18, 2025Updated 11 months ago
- PyMOL-wasm port's binary and html/javascript code☆58Aug 31, 2026Updated last month
- Efficient manipulation of protein structures in Python☆68Jun 16, 2026Updated 4 months ago
- Miniprotein and antibody design pipeline for ESMFold2☆47Sep 23, 2026Updated last month
- Automatic generation of LAMMPS data file for atomistic and coarse-grained simulations of molecular and polymeric materials with various t…☆28Sep 24, 2026Updated last month
- A Python package to assist with parameterization and construction of all-atomistic polymer simulations☆18Feb 11, 2025Updated last year
- ☆20Nov 10, 2021Updated 4 years ago
- ☆51Jul 17, 2026Updated 3 months ago
- Molecular dynamics simulation skills for AI agents☆17Updated this week
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Flexible solvation benchmark and analysis tool for evaluating (implicit) solvation models on the large and conformationally flexible mole…☆15Apr 2, 2026Updated 6 months ago
- An engine for electrostatic ML embedding for multiscale modelling.☆31Oct 6, 2026Updated 3 weeks ago
- ☆13Mar 9, 2026Updated 7 months ago
- An easy (and fast) API for popular 3D molecular datasets!☆50May 3, 2026Updated 5 months ago
- Code for "Applying Large Graph Neural Networks to Predict Transition Metal Complex Energies Using the tmQM_wB97MV Dataset"☆12Apr 9, 2024Updated 2 years ago
- Interface enabling use of ANI-style, and other NN-IPs in the Amber molecular dynamics software suite. Works with both Amber engines, sand…☆18Updated this week
- Simulating protein interactions with organometallic ligands using Universal Model of Atoms (UMA)☆15Apr 13, 2026Updated 6 months ago
- NAMD QM/MM Tutorial on Free Energy Profile of Reaction Mechanisms☆17Sep 14, 2018Updated 8 years ago
- protein folding app running on modal☆39May 30, 2026Updated 5 months ago
- Deploy open-source AI quickly and easily - Special Bonus Offer • AdRunpod Hub is built for open source. One-click deployment and autoscaling endpoints without provisioning your own infrastructure.
- Predicting water moelcule placements on protein surfaces using flow matching conditioned on learned protein structure embeddings.☆17Sep 17, 2026Updated last month
- Self-driving platform for protein engineering: ML agent + lab-automation environment (paper code).☆13Aug 17, 2026Updated 2 months ago
- A fast, programmable molecular viewer for research, scripting, and the web☆223Updated this week
- Machine-learning force-field (MLFF)–native molecular modeling platform☆78Oct 20, 2026Updated last week
- Deep Residual Learning for Molecular Force Fields☆13Aug 12, 2026Updated 2 months ago
- Free Parametrization for Small Molecules☆66Jun 30, 2026Updated 4 months ago
- Python program for modelling and simulating polymers.☆46Jul 6, 2026Updated 3 months ago