A Motif-Based PPI Searching Pipeline for PPI Mining and Protein Design
☆22Feb 11, 2025Updated last year
Alternatives and similar repositories for PPI-Miner
Users that are interested in PPI-Miner are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- FASTDock: A Pipeline for Allosteric Drug Discovery - example scripts and jupyter notebook☆19Jun 10, 2023Updated 2 years ago
- Easy to get started with molecular dynamics simulation.☆65Jun 11, 2025Updated 9 months ago
- This script can clean up the disordered region in the AlphaFold DB structures to adapt it to the molecular docking, extract the sequence …☆15Apr 20, 2023Updated 2 years ago
- Incorporation of conformational space profile into molecular representation learning, and its application to drug discovery, including vi…☆67Jul 20, 2025Updated 8 months ago
- Scripts for virtual screening, cross docking and protein relax using Schrödinegr and Rosetta☆85Apr 11, 2025Updated 11 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.
- SubPEx (Sub-Pocket Explorer) is a tool to enhance ensemble (multiple-receptor/relaxed-complex) virtual screening. It uses weighted ensemb…☆18Jun 30, 2025Updated 9 months ago
- implicit or explicit water model based docking with Autodock vina engine. supporting pharmacophore /position constrained docking☆73Feb 9, 2026Updated last month
- EViS: an Enhanced Virtual Screening Approach based on Pocket Ligand Similarity☆14Dec 7, 2021Updated 4 years ago
- De novo design of small molecule binding sites into proteins☆12Apr 14, 2021Updated 4 years ago
- Neural relational inference for molecular dynamics simulations☆59May 30, 2023Updated 2 years ago
- ☆62Mar 14, 2023Updated 3 years ago
- ☆11Mar 28, 2024Updated 2 years ago
- Fraction of Common Contacts Clustering Algorithm for Protein Structures☆27Aug 12, 2021Updated 4 years ago
- ☆28Jan 2, 2026Updated 2 months ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- EnzyDock: Protein–Ligand Docking of Multiple Reactive States along a Reaction Coordinate in Enzymes☆18Sep 5, 2024Updated last year
- The central entry point to the P2Rank project with links to the individual projects, including references to documentation, datasets, etc…☆13Feb 11, 2026Updated last month
- pymol implementation of WaterDock with Akshay Sridhar (@akshay-sridhar) and refactoring work by Patrick McCubbin (@mccubbinp)☆11Mar 25, 2024Updated 2 years ago
- scripts to find PBD structures for cancer driver proteins☆31Feb 27, 2026Updated last month
- Download pdb/protein structures using Uniprot id; This script will download related PDB files, extract chains(Optional), remove duplicate…☆46Jul 24, 2024Updated last year
- 3D-MCTS: A general structure-based molecule generation method with MCTS.☆45Jun 26, 2024Updated last year
- Package for reading, analysis and visualization of metadynamics HILLS☆39Nov 28, 2023Updated 2 years ago
- ☆31Mar 11, 2023Updated 3 years ago
- fragbuilder is a tool to create, setup and analyze QM calculations on peptides.☆15Oct 31, 2014Updated 11 years ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting with the flexibility to host WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Cloudways by DigitalOcean.
- Source code for fitting thermodynamic models (MoCHI), downstream analyses and to reproduce all figures in the following publication: Mapp…☆22Jul 20, 2023Updated 2 years ago
- Integrative modeling of PROTAC-mediated ternary complex☆29May 4, 2022Updated 3 years ago
- Input files and binding free energy values from our benchmark with QuantumBind-RBFE☆16Apr 16, 2025Updated 11 months ago
- My first ever repository, some notebooks useful, others sucks. Topics include file format conversion with obabel, docking with Auto Dock,…☆26Oct 22, 2025Updated 5 months ago
- ☆21Oct 2, 2024Updated last year
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆34Dec 10, 2023Updated 2 years ago
- Tutorial on the setup and simulation of a membrane protein with AMBER Lipid21 and PACKMOL-Memgen☆74Aug 11, 2023Updated 2 years ago
- ☆28Updated this week
- Protein interaction calculator☆13Feb 11, 2025Updated last year
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click and start building anything your business needs.
- This repository contains code for the paper: "Tertiary motifs as building blocks for the design of protein-binding peptides"☆21Jan 15, 2024Updated 2 years ago
- ☆32Sep 23, 2023Updated 2 years ago
- ☆13Jul 11, 2023Updated 2 years ago
- ☆20Jul 3, 2024Updated last year
- Multi-Level DBSCAN: A Hierarchical Density-Based Clustering Method for Analyzing Molecular Dynamics Trajectories☆13Dec 6, 2020Updated 5 years ago
- Method for drug repurposing from knowledge graphs and literature☆36Aug 28, 2020Updated 5 years ago
- Pocket dynamics analysis tool☆18May 8, 2025Updated 10 months ago