NeuralMD for Protein-ligand Binding Simulation, Nature Communicaitons 2025 https://www.nature.com/articles/s41467-025-67808-z
☆47Nov 4, 2025Updated 5 months ago
Alternatives and similar repositories for NeuralMD
Users that are interested in NeuralMD are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- ☆12May 3, 2025Updated 11 months ago
- Official repo for paper "AlphaFold-Multimer accurately captures interactions and dynamics of intrinsically disordered protein regions"☆17Dec 8, 2024Updated last year
- Code of "Instruction Multi-Constraint Molecular Generation Using a Teacher-Student Large Language Model"☆14Jul 8, 2025Updated 9 months ago
- PackDock: a Diffusion Based Side Chain Packing Model for Flexible Protein-Ligand Docking☆57Mar 30, 2026Updated 2 weeks ago
- Apo2Mol: 3D Molecule Generation via Dynamic Pocket-Aware Diffusion Models☆33Dec 23, 2025Updated 3 months ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- A bare metal Python library for building and manipulating protein molecular structures☆19Updated this week
- ☆15Jan 27, 2025Updated last year
- [ICLR 2025] Hotspot-Driven Peptide Design via Multi-Fragment Autoregressive Extension☆19May 5, 2025Updated 11 months ago
- Synthetic Accessibility via Fragment Assembly Generation☆23Updated this week
- This repository houses all the scripts and notebooks utilized for generating, analyzing, and validating the mdCATH dataset. Some user ex…☆58Dec 16, 2025Updated 3 months ago
- Implementation of NeurIPS24 paper "Generalized Protein Pocket Generation with Prior-Informed Flow Matching"☆19May 15, 2025Updated 10 months ago
- ☆20Aug 5, 2025Updated 8 months ago
- Serializing molecule 3D structures☆14Nov 27, 2024Updated last year
- This Code is for Fragment-wise 3D Structure-based Molecular Generation with Reliable Geometry☆34Mar 24, 2025Updated last year
- Wordpress hosting with auto-scaling - Free Trial • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- [ICML 2024] Code for Pairwise Alignment Improves Graph Domain Adaptation (Pair-Align)☆14Jun 15, 2024Updated last year
- protein backbone refinement☆15Sep 12, 2024Updated last year
- Code for the paper "OneProt: Towards Multi-Modal Protein Foundation Models"☆21Oct 31, 2025Updated 5 months ago
- Code fo ICLR2025 paper "A Simple yet Effective DDG Predictor is An Unsupervised Antibody Optimizer and Explainer"☆22Jul 18, 2025Updated 8 months ago
- A framework for training energy-based diffusion models for sampling and energy estimation.☆95Nov 21, 2025Updated 4 months ago
- [ICLR 2025 Spotlight] Boltzmann-Aligned Inverse Folding Model as a Predictor of Mutational Effects on Protein-Protein Interactions☆44Mar 10, 2025Updated last year
- Diffusion model based protein-ligand flexible docking method☆118Oct 30, 2024Updated last year
- [ICLR 2024 Spotlight] The official repo for the paper "De novo Protein Design using Geometric Vector Field Networks".☆31Aug 23, 2024Updated last year
- Protein function prediction using protein structures and deep graph neural networks.☆21Jan 24, 2025Updated last year
- 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.
- ☆29Oct 7, 2024Updated last year
- Baseline model for PPB-Affinity benchmark data☆37May 21, 2025Updated 10 months ago
- A tutorials suite for BioSimSpace.☆36Oct 22, 2025Updated 5 months ago
- [PNAS 2025] Code of "Manifold-Constrained Nucleus-Level Denoising Diffusion Model for Structure-Based Drug Design".☆35Jan 18, 2026Updated 2 months ago
- Access to data for workshops and extended tests of MDAnalysis.☆19Apr 3, 2026Updated last week
- Layer Integrated Toolkit and Engine for Simulations of Photo-induced Phenomena☆10May 23, 2024Updated last year
- Predicting mutational effects on protein binding from folding energy. ICML 2025.☆41Aug 4, 2025Updated 8 months ago
- Codebase of paper "Structure Language Models for Protein Conformation Generation" (ICLR'25)☆76Feb 24, 2025Updated last year
- ☆18Aug 28, 2025Updated 7 months ago
- Wordpress hosting with auto-scaling - Free Trial • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Research repository to the publication: Navigating the Design Space of Equivariant Diffusion-Based Generative Models for De Novo 3D Molec…☆14Apr 2, 2024Updated 2 years ago
- ☆22Feb 25, 2025Updated last year
- Conformational sampling for highly flexible proteins☆15Jan 31, 2025Updated last year
- ☆15Jan 31, 2026Updated 2 months ago
- DualBind is a 3D structure-based deep learning model with a dual-loss framework for accurate and fast protein-ligand binding affinity pre…☆18Oct 21, 2025Updated 5 months ago
- The gmx_rrcs script is designed to calculate the residues-residues contact scores (rrcs) from a trajectory file generated by GROMACS.☆18Jun 16, 2025Updated 9 months ago
- Implementation of AGDIFF: Attention-Enhanced Diffusion for Molecular Geometry Prediction☆16Jun 19, 2025Updated 9 months ago