A Generalised workflow for obtaining protein and peptide molecular structures, docking the peptide into the protein and running a molecular dynamic simulation over a large number of trajectories.
☆14Jan 1, 2025Updated last year
Alternatives and similar repositories for MD-Simulation
Users that are interested in MD-Simulation are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- ☆12Jan 15, 2016Updated 10 years ago
- Predicting the effect of mutations on protein stability and protein-protein interaction affinity.☆10Mar 29, 2021Updated 5 years ago
- ATTRACT program suite for macromolecular docking (protein-protein, protein-nucleic acid, protein-peptide)☆20Mar 13, 2026Updated 7 months ago
- ☆11Aug 19, 2024Updated 2 years ago
- A collection of molecular modelling tools for UCSF Chimera☆18Mar 26, 2019Updated 7 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- Nextflow pipeline to do protein design tasks at the end of 2025.☆12Sep 29, 2026Updated last month
- Automated construction of protein chimeras and their analysis.☆15Sep 29, 2023Updated 3 years ago
- Protein preparation for MD, made faster and easier !☆15Dec 18, 2023Updated 2 years ago
- Biobb_amber is a BioBB category for AMBER MD package.☆15Oct 6, 2026Updated 3 weeks ago
- MD-ligand-receptor is a bioinformatics pipeline written in Python for analyzing non-covalent ligand-receptor interactions in 3D structure…☆12Jun 18, 2023Updated 3 years ago
- Associated code/pipeline for the publication "AI-assisted protein design to rapidly convert antibody sequences to intrabodies targeting d…☆18Feb 18, 2025Updated last year
- Model-based clustering package for mixed data☆13May 21, 2026Updated 5 months ago
- Transfer-Learning based Sugarcane Leaf Disease Detection Using DenseNet201 Architecture☆10Nov 30, 2023Updated 2 years ago
- Non Metric Space ( Approximate ) Library in R☆12Feb 2, 2023Updated 3 years ago
- 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.
- Fast computation of Distance Correlation and Distance Covariance in R☆10Sep 27, 2023Updated 3 years ago
- Deep learning architectures for protein secondary structure prediction (version 2)☆11Mar 24, 2023Updated 3 years ago
- Gromacs_py is a python library allowing a simplified use of the gromacs MD simulation software. Gromacs_py can build topologie based on a…☆53Jul 5, 2022Updated 4 years ago
- Docking viewer plug-in for PyMOL☆11Oct 7, 2024Updated 2 years ago
- Connect your UART/I2C/1-Wire sensor directly in the browser!☆14Oct 9, 2026Updated 3 weeks ago
- Code to perform scaffold hopping and virtual screening using WHALES descriptors.☆33Jan 12, 2021Updated 5 years ago
- Prediction of reaction free energies with machine learning☆10Sep 28, 2021Updated 5 years ago
- ☆11Nov 19, 2021Updated 4 years ago
- Gromacs molecular dynamics simulation analysis scripts☆10Apr 5, 2022Updated 4 years ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Copernicus☆18Oct 27, 2017Updated 9 years ago
- Various tutorials about MD setup and analysis, protein-ligand docking, machine learning and lots of other interesting things.☆35Jan 2, 2021Updated 5 years ago
- Data and analysis scripts for understanding molecular entropies, including conformer flexibility☆13Mar 29, 2021Updated 5 years ago
- Code for "De novo molecular design with chemical language models"☆13Nov 10, 2021Updated 4 years ago
- pains filter using rdktit☆11Mar 17, 2015Updated 11 years ago
- A docker image containing changes applied to the ETKDG conformer generator workflow, with example scripts.☆13Jun 15, 2019Updated 7 years ago
- Perform probe-guided blind docking with FTMap and DOCK6☆10Apr 25, 2023Updated 3 years ago
- A simple BLOSUM module for python3☆18Nov 21, 2025Updated 11 months ago
- easyPARM is a computational tool developed to simplify the derivation of force field parameters for metal-containing molecular systems an…☆48May 21, 2026Updated 5 months 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.
- A repository for the development of data analysis tools for replica exchange molecular dynamics (REMD) simulations☆14Feb 20, 2023Updated 3 years ago
- Peptide Virtual Screening Pipeline☆14Jul 3, 2019Updated 7 years ago
- Elaborate Tutorial for Teaching Molecular Dynamics directed to university students in their graduate program. The course is designed to b…☆45Sep 11, 2025Updated last year
- Notebooks and files from the paper De novo Design and Bioactivity Prediction of SARS-CoV-2 Main Protease Inhibitors using Recurrent Neura…☆14Jan 13, 2023Updated 3 years ago
- A library for solving POMDPs☆11Apr 15, 2025Updated last year
- ChEMBL Database used to create Lipinski Descriptors (ADME Pharmokinetic Profile) to use in a Random Forest Regression Model☆16Nov 8, 2020Updated 5 years ago
- An open-source automated peptide synthesizer based on Arduino and Python☆15Dec 19, 2025Updated 10 months ago