SubPEx (Sub-Pocket Explorer) is a tool to enhance ensemble (multiple-receptor/relaxed-complex) virtual screening. It uses weighted ensemble path sampling and molecular dynamics simulations to accelerate binding-pocket sampling.
☆18Jun 30, 2025Updated last year
Alternatives and similar repositories for subpex
Users that are interested in subpex are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆34Dec 10, 2023Updated 2 years ago
- pymol implementation of WaterDock with Akshay Sridhar (@akshay-sridhar) and refactoring work by Patrick McCubbin (@mccubbinp)☆11Mar 25, 2024Updated 2 years ago
- App for serotonergic targets☆12Jan 8, 2026Updated 6 months ago
- Clustering of SES virtual probes for pocket generation and ranking via Isolation Forest☆14Mar 22, 2023Updated 3 years ago
- FASTDock: A Pipeline for Allosteric Drug Discovery - example scripts and jupyter notebook☆19Jun 10, 2023Updated 3 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Multi-Level DBSCAN: A Hierarchical Density-Based Clustering Method for Analyzing Molecular Dynamics Trajectories☆13Dec 6, 2020Updated 5 years ago
- Optimization of binding affinities in chemical space for drug discovery☆36Jan 31, 2023Updated 3 years ago
- PocketMaster is a flexible and automated tool for analyzing, clustering, and visualizing protein binding sites. It allows you to quickly …☆19Feb 22, 2026Updated 4 months ago
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆20Updated this week
- Pocket dynamics analysis tool☆18Apr 24, 2026Updated 2 months ago
- Tutorial to build AMBER compatable protein+lipid systems☆16Apr 19, 2017Updated 9 years ago
- The BigBind protein-ligand binding dataset (and BayesBind benchmark)☆20Nov 14, 2024Updated last year
- ☆11Mar 28, 2024Updated 2 years ago
- Efficient Sampling of PROTAC-Induced Ternary Complexes☆19Jun 3, 2025Updated last year
- Serverless GPU API endpoints on Runpod - Get Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- Modelling protein conformational landscape with Alphafold☆61Aug 29, 2025Updated 10 months ago
- Tutorials and additional documentation for the WESTPA suite☆16Oct 20, 2025Updated 9 months ago
- A Motif-Based PPI Searching Pipeline for PPI Mining and Protein Design☆21Feb 11, 2025Updated last year
- AutoGrow4 is an open-source program for semi-automated computer-aided drug discovery. It uses a genetic algorithm to evolve predicted lig…☆58Oct 7, 2025Updated 9 months ago
- 好的CADD教程，资源总结☆26Apr 8, 2024Updated 2 years ago
- AdaptivePELE is a Python package aimed at enhancing the sampling of molecular simulations☆17Jul 1, 2026Updated 2 weeks ago
- ☆23Oct 2, 2024Updated last year
- A surface-based deep learning approach for the prediction of ligand binding sites on proteins☆46Apr 22, 2023Updated 3 years ago
- Pocket to Concavity is a tool for refinement of Protein-Ligand binding site shape from alpha-spheres☆16Oct 2, 2024Updated last year
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy (ABFE) and relative binding free energy (RB…☆226Mar 4, 2026Updated 4 months ago
- Automated Adaptive Absolute alchemical Free Energy calculator☆123May 1, 2026Updated 2 months ago
- Sire Molecular Simulations Framework☆98Jul 17, 2023Updated 3 years ago
- scripts to find PBD structures for cancer driver proteins☆31Feb 27, 2026Updated 4 months ago
- AI-augmented R-group exploration in medicinal chemistry☆20Sep 25, 2024Updated last year
- Source code and data of the paper entitled "iCYP-MFE: Identifying Human Cytochrome P450 Inhibitors using Multi-task Learning and Molecula…☆18Jun 27, 2023Updated 3 years ago
- A collection of cheminformatics scripts that use rdkit☆73Jul 1, 2022Updated 4 years ago
- ☆19Jun 27, 2024Updated 2 years ago
- Cloud GPU supported NAMD3-based binding free energy difference between two small molecules against the same protein target. This is prob…☆29Nov 2, 2025Updated 8 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.
- This script is designed for evaluating the binding affinity between a protein target and a small molecule, by calculating the binding fre…☆15May 1, 2023Updated 3 years ago
- Notebooks demonstrating how to do simple tasks related to free energy calculations.☆68Jul 7, 2026Updated last week
- 3D-MCTS: A general structure-based molecule generation method with MCTS.☆46Jun 26, 2024Updated 2 years ago
- Generate customized voxel representations of protein-ligand complexes using GPU.☆11Sep 8, 2025Updated 10 months ago
- ☆34Mar 19, 2023Updated 3 years ago
- ☆101Feb 24, 2025Updated last year
- The central entry point to the P2Rank project with links to the individual projects, including references to documentation, datasets, etc…☆14Feb 11, 2026Updated 5 months ago