Tutorial on the setup and simulation of a membrane protein with AMBER Lipid21 and PACKMOL-Memgen
☆76Aug 11, 2023Updated 2 years ago
Alternatives and similar repositories for AMBER-Membrane_protein_tutorial
Users that are interested in AMBER-Membrane_protein_tutorial are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Tutorial to build AMBER compatable protein+lipid systems☆16Apr 19, 2017Updated 9 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 6 months ago
- Generate Ramachandran plots for single PDB structure and as heatmap for MD trajectory☆11Apr 6, 2022Updated 4 years ago
- Tutorials on doing AMBER based Metadynamics and Gaussian Accelerated MD (GaMD)☆12Dec 1, 2025Updated 5 months ago
- Easy to get started with molecular dynamics simulation.☆66Apr 18, 2026Updated 2 weeks ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆34Dec 10, 2023Updated 2 years ago
- SubPEx (Sub-Pocket Explorer) is a tool to enhance ensemble (multiple-receptor/relaxed-complex) virtual screening. It uses weighted ensemb…☆18Jun 30, 2025Updated 10 months ago
- 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
- implicit or explicit water model based docking with Autodock vina engine. supporting pharmacophore /position constrained docking☆73Feb 9, 2026Updated 2 months ago
- Scripts for virtual screening, cross docking and protein relax using Schrödinegr and Rosetta☆85Apr 11, 2025Updated last year
- For the purpose of post progressing of MD carried by gromacs☆23Jul 2, 2025Updated 10 months ago
- Neural relational inference for molecular dynamics simulations☆59May 30, 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
- FEP-SPell-ABFE: An Open Source Alchemical Absolute Binding Free Energy Calculation Workflow for Drug Discovery☆85Jan 8, 2025Updated last year
- 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.
- Repo for the publication titled: "Key Interaction Networks: Identifying Evolutionarily Conserved Non-Covalent Interaction Networks Across…☆18Nov 14, 2023Updated 2 years ago
- An open tool implementing some recommended practices for analyzing alchemical free energy calculations☆137May 24, 2024Updated last year
- Notebooks demonstrating how to do simple tasks related to free energy calculations.☆65Updated this week
- PROTACable is an end-to-end in-silico design toolkit for novel PROTACs☆29Jun 3, 2024Updated last year
- This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.☆64Dec 17, 2025Updated 4 months ago
- The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy (ABFE) and relative binding free energy (RB…☆222Mar 4, 2026Updated 2 months ago
- A collection of small scripts and utilities that would otherwise float around in other repositories☆15Apr 4, 2025Updated last year
- ☆41Nov 2, 2024Updated last year
- A tool for setting up free energy simulations.☆37Oct 20, 2022Updated 3 years 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.
- ☆18Jul 29, 2025Updated 9 months ago
- A Motif-Based PPI Searching Pipeline for PPI Mining and Protein Design☆22Feb 11, 2025Updated last year
- OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method☆161Apr 9, 2026Updated 3 weeks ago
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆41Updated this week
- ☆101Feb 24, 2025Updated last year
- Clustering of SES virtual probes for pocket generation and ranking via Isolation Forest☆14Mar 22, 2023Updated 3 years ago
- Predict allosteric pockets on proteins☆15Mar 28, 2022Updated 4 years ago
- A tutorial for Streamlined Alchemical Free Energy Perturbations with NAMD☆15Apr 3, 2026Updated last month
- CosolvKit is a versatile tool for cosolvent MD preparation and analysis☆31Apr 4, 2026Updated last month
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calcula…☆98Jul 16, 2025Updated 9 months ago
- This is a short tutorial showing how to use both VMD and MDAnalysis to analyse a molecular dynamics simulation of a membrane protein.☆28Oct 1, 2020Updated 5 years ago
- Examples of applications of pymbar to various problems in simulation and experiment☆23Jan 16, 2015Updated 11 years ago
- Fragment Linker Prediction Using Deep Encoder-Decoder Network for PROTAC Drug Design☆12Oct 2, 2023Updated 2 years ago
- Incorporation of conformational space profile into molecular representation learning, and its application to drug discovery, including vi…☆69Jul 20, 2025Updated 9 months ago
- Random Acceleration Molecular Dynamics in GROMACS☆44Jul 19, 2024Updated last year
- A Tool to process and visualize the results of molecular dynamics simulations(GROMACS).☆106Updated this week