Easy to get started with molecular dynamics simulation.
☆65Jun 11, 2025Updated 9 months ago
Alternatives and similar repositories for AutoMD
Users that are interested in AutoMD are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Scripts for virtual screening, cross docking and protein relax using Schrödinegr and Rosetta☆85Apr 11, 2025Updated 11 months ago
- Incorporation of conformational space profile into molecular representation learning, and its application to drug discovery, including vi…☆67Jul 20, 2025Updated 8 months ago
- A Motif-Based PPI Searching Pipeline for PPI Mining and Protein Design☆22Feb 11, 2025Updated last year
- Download pdb/protein structures using Uniprot id; This script will download related PDB files, extract chains(Optional), remove duplicate…☆46Jul 24, 2024Updated last year
- Tutorial on the setup and simulation of a membrane protein with AMBER Lipid21 and PACKMOL-Memgen☆74Aug 11, 2023Updated 2 years ago
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- 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
- Efficient Sampling of PROTAC-Induced Ternary Complexes☆12Jun 3, 2025Updated 9 months ago
- 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
- Tutorial to build AMBER compatable protein+lipid systems☆16Apr 19, 2017Updated 8 years ago
- ☆71Jul 19, 2023Updated 2 years ago
- ☆101Feb 24, 2025Updated last year
- EXPRORER: Rational cosolvents set construction method for cosolvent molecular dynamics (CMD) with large-scale computation☆11Jul 28, 2022Updated 3 years ago
- A Tool to process and visualize the results of molecular dynamics simulations(GROMACS).☆103Feb 18, 2026Updated last month
- This script is designed for evaluating the binding affinity between a protein target and a small molecule, by calculating the binding fre…☆14May 1, 2023Updated 2 years ago
- DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- A collection of virtual screening benchmarking☆12Sep 16, 2023Updated 2 years ago
- The Vini in silico model of cancer☆12Mar 7, 2026Updated 3 weeks ago
- A Python package to calculate, visualize and analyze correlation maps of proteins.☆44Mar 14, 2026Updated 2 weeks ago
- An Integrative Drug Repurposing Pipeline using KNIME and Programmatic Data Access: A case study on COVID-19 Data☆15Sep 29, 2020Updated 5 years ago
- implicit or explicit water model based docking with Autodock vina engine. supporting pharmacophore /position constrained docking☆73Feb 9, 2026Updated last month
- Neural relational inference for molecular dynamics simulations☆59May 30, 2023Updated 2 years ago
- Fraction of Common Contacts Clustering Algorithm for Protein Structures☆27Aug 12, 2021Updated 4 years ago
- Fully automated high-throughput MD pipeline☆90Mar 11, 2026Updated 2 weeks ago
- pymol implementation of WaterDock with Akshay Sridhar (@akshay-sridhar) and refactoring work by Patrick McCubbin (@mccubbinp)☆11Mar 25, 2024Updated 2 years ago
- 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.
- gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.☆300Dec 8, 2025Updated 3 months ago
- DeepDelta is a pairwise deep learning approach based on Chemprop that processes two molecules simultaneously and learns to predict proper…☆50Mar 11, 2024Updated 2 years ago
- Package for storage and analysis of virtual screenings run with AutoDock-GPU and AutoDock Vina☆60Mar 16, 2026Updated 2 weeks ago
- ☆28Feb 27, 2026Updated last month
- InteractionDrawer is a JavaScript library for the drawing of highly interactive 2D ligand interaction diagrams.☆26Oct 16, 2023Updated 2 years ago
- ☆16Oct 28, 2024Updated last year
- An automatic workflow to perform MM/GB(PB)SA calculations from force field building, and structure optimization to free energy calculatio…☆135Jan 13, 2026Updated 2 months ago
- Clustering of SES virtual probes for pocket generation and ranking via Isolation Forest☆14Mar 22, 2023Updated 3 years ago
- Protein-ligand structure prediction☆239Jul 31, 2025Updated 7 months ago
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- Tools to add restraints to FEP runs. Includes a workflow to determine reference structures and restraint widths from plain MD simulations…☆11Mar 12, 2026Updated 2 weeks ago
- For the purpose of post progressing of MD carried by gromacs☆23Jul 2, 2025Updated 8 months ago
- UQ4DD: Uncertainty Quantification for Drug Discovery☆17Aug 4, 2025Updated 7 months ago
- A potential solution to the early-stage small molecule hit identification☆15Jan 27, 2026Updated 2 months ago
- This reposatory includes all scripts necessary to calculate the GRAil-based DEscriptor (GRADE) and the eXtended GRAil-based DEscriptor (X…☆13Jan 23, 2025Updated last year
- BINANA (BINding ANAlyzer) analyzes the geometries of predicted ligand poses to identify molecular interactions that contribute to binding…☆24Jun 30, 2025Updated 9 months ago
- Optimization of binding affinities in chemical space for drug discovery☆36Jan 31, 2023Updated 3 years ago