NeuralMD for Protein-ligand Binding Simulation, Nature Communicaitons 2025 https://www.nature.com/articles/s41467-025-67808-z
☆49Nov 4, 2025Updated 8 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:
- ☆24Dec 4, 2025Updated 7 months ago
- [PNAS 2025] Code of "Manifold-Constrained Nucleus-Level Denoising Diffusion Model for Structure-Based Drug Design".☆38Jul 17, 2026Updated last week
- ☆15Jun 25, 2026Updated last month
- ☆45Apr 24, 2026Updated 3 months ago
- ☆138Jul 14, 2026Updated last 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.
- Physics-Guided All-Atom Diffusion Model for Accurate Protein-Ligand Complex Prediction☆92Oct 6, 2025Updated 9 months ago
- DynamicGT: a dynamic-aware geometric transformer model to predict protein binding interfaces in flexible and disordered regions☆16Jun 18, 2026Updated last month
- ☆68Jul 7, 2026Updated 2 weeks ago
- ☆50Jun 15, 2026Updated last month
- ☆85May 18, 2026Updated 2 months ago
- code and source data for de novo design of Kemp elimination paper☆26Sep 18, 2025Updated 10 months ago
- A tutorial for Streamlined Alchemical Free Energy Perturbations with NAMD☆16Apr 3, 2026Updated 3 months ago
- ☆13May 24, 2026Updated 2 months ago
- Fully automated high-throughput MD pipeline☆104Updated 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.
- Code of "Instruction Multi-Constraint Molecular Generation Using a Teacher-Student Large Language Model"☆13Jul 8, 2025Updated last year
- Official repo for paper "AlphaFold-Multimer accurately captures interactions and dynamics of intrinsically disordered protein regions"☆17Dec 8, 2024Updated last year
- A framework for training energy-based diffusion models for sampling and energy estimation.☆108May 10, 2026Updated 2 months ago
- Knowledge-Guided Diffusion Model for 3D Ligand-Pharmacophore Mapping☆50Jun 5, 2026Updated last month
- ☆13Dec 29, 2022Updated 3 years ago
- Design scripts corresponding to "Computational design of sequence-specific DNA-binding proteins."☆21Oct 23, 2025Updated 9 months ago
- Fast protein backbone flexibility prediction model☆36Jan 4, 2026Updated 6 months ago
- TrajCast: Force-Free MD Through Autoregressive Equivariant Networks☆84Sep 23, 2025Updated 10 months ago
- PackDock: a Diffusion Based Side Chain Packing Model for Flexible Protein-Ligand Docking☆63Mar 30, 2026Updated 3 months ago
- End-to-end encrypted email - Proton Mail • AdSpecial offer: 40% Off Yearly / 80% Off First Month. All Proton services are open source and independently audited for security.
- CovDocker: Benchmarking Covalent Drug Design with Tasks, Datasets, and Solutions (KDD'25 research track accepted)☆17Aug 6, 2025Updated 11 months ago
- A universal structure-directed lead optimization☆76Jan 30, 2026Updated 5 months ago
- GatorAffinity: Boosting Protein-Ligand Binding Affinity Prediction with Large-Scale Synthetic Structural Data☆35Apr 10, 2026Updated 3 months ago
- Longxing Cao's Contact Molecular Surface without pyrosetta☆15May 24, 2026Updated 2 months ago
- ☆18Jan 15, 2026Updated 6 months ago
- Codebase for SigmaDock: Untwisting Molecular Docking with SE(3) Fragmented Diffusion☆94Apr 7, 2026Updated 3 months ago
- Diffusion model based protein-ligand flexible docking method☆118Oct 30, 2024Updated last year
- SurfDock is a Surface-Informed Diffusion Generative Model for Reliable and Accurate Protein-ligand Complex Prediction☆254Sep 29, 2025Updated 9 months ago
- This repository provides with custom code and analysis scripts to generate structural ensembles of intrinsically disordered proteins by u…☆24Oct 31, 2025Updated 8 months ago
- 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.
- 👑 A lightweight molecular dynamics pipeline for running protein simulations on portable hardware☆53Mar 23, 2026Updated 4 months ago
- Official implementation for BioKinema☆23Jun 26, 2026Updated 3 weeks ago
- Generative modeling of molecular dynamics trajectories☆222Mar 22, 2026Updated 4 months ago
- ☆12May 3, 2025Updated last year
- Baseline model for PPB-Affinity benchmark data☆43May 21, 2025Updated last year
- The codebase for EnzyGen2☆30Apr 20, 2026Updated 3 months ago
- Deconvolving mutation effects on protein stability and function with disentangled protein language models☆18May 15, 2026Updated 2 months ago