/tools

MDAnalysisMolSSIWorkshop-Intermediate2Day provides materials for a workshop on using MDAnalysis, a Python library for analyzing molecular dynamics simulations. The repository includes tutorials on loading, manipulating, and analyzing molecular simulation data, making it a valuable resource for those working in computational chemistry.

MD_ResearchTechniques is an educational resource designed for teaching computational chemistry techniques, specifically focusing on molecular dynamics simulations. It includes lectures, practical exercises, and materials for students to gain hands-on experience in using GROMACS and VMD software.

This repository provides educational materials for the 2025 CCPBioSim Training Week, focusing on parameterizing small molecules and conducting molecular dynamics simulations for protein-ligand complexes. It includes Jupyter Notebooks that guide users through practical applications in molecular modeling.

This repository provides an introduction to small molecule drug design using structure-based techniques and interactive Jupyter notebooks. It covers ligand-based analysis, generative design with REINVENT4, and docking to analyze interactions with the Zika virus protease.

The AdKGromacsTutorial repository offers a comprehensive guide for performing molecular dynamics simulations of the adenylate kinase enzyme using Gromacs. It includes steps for system setup, energy minimization, equilibration, and trajectory visualization, making it a valuable resource for researchers in molecular dynamics.

This repository contains resources and tutorials related to Cheminformatics, aimed at helping users understand and apply various molecular modeling techniques. It includes Jupyter notebooks and utilities that facilitate molecular property prediction and design.

Opemm_Tutorial provides tutorials for learning how to simulate molecular dynamics using OpenMM. It includes specific examples for protein and protein-ligand simulations, making it a useful resource for those interested in molecular simulations.

The ncaa_tutorial repository provides demos for generating non-canonical amino acid parameters and rotamers using the Rosetta software. It aims to assist in the design and modeling of proteins by offering tutorials on this specialized topic.

This repository contains a multipage Streamlit app that serves as a cheatsheet for cheminformatics, utilizing rdKit for various molecular tasks. It likely provides users with interactive tools for exploring molecular properties and cheminformatics concepts.

HyMD-tutorial offers a collection of Jupyter Notebook examples demonstrating the use of HylleraasMD for simulating various molecular systems, including monoatomic particles, polymers, and peptides. It covers different types of interactions, such as bonded, field, and electrostatic interactions, making it a useful resource for molecular dynamics studies.

The TBBLab repository provides a collection of resources and tutorials for bioinformatics and computational biology, focusing on molecular dynamics, docking, and cheminformatics. It serves as a guide for researchers and students in the field, offering insights into various molecular analysis techniques.

MDAnalysisWorkshop-Intermediate1Day contains materials for a workshop that teaches participants how to manipulate and analyze molecular dynamics simulations using the MDAnalysis library. The workshop includes lectures and tutorials on various analysis tools and techniques relevant to molecular simulations.

Gromacs-Tutorials provides tutorials and necessary files for running simulations using GROMACS, a widely used software for molecular dynamics. The tutorials cover topics such as colloidal forces and dielectric screening, which are relevant to molecular simulations.

The AlphaFold_Workshop repository provides a tutorial for predicting protein folding structures using ColabFold, which is based on AlphaFold2. It aims to enhance understanding of protein folding prediction and allows users to predict structures based on amino acid sequences.

This repository contains files and instructions for simulating PEGylated proteins using the Martini coarse-grained force-field. It focuses on molecular dynamics simulations to study the interactions between proteins and PEG polymers, providing insights into their behavior at a molecular level.

This repository contains a script designed to automate the execution of the 'Lysozyme in Water' tutorial using GROMACS with multiple force fields. It facilitates molecular dynamics simulations by allowing users to easily run simulations with different parameters and force fields.

MDAnalysisWorkshop-Intro1Day contains materials for a workshop that teaches participants how to use MDAnalysis for analyzing molecular dynamics simulations. The workshop covers basics, system manipulation, distance calculations, and analysis tools, making it a practical resource for those interested in molecular simulations.

Tutorial4JiaHong is a comprehensive guide for performing molecular dynamics simulations, covering theoretical foundations, practical applications using GROMACS and LAMMPS, and integration with Python scripting. It aims to educate users on simulating molecular interactions, particularly with proteins.

This repository offers a tutorial on conducting molecular dynamics simulations of proteins using the GROMACS software with an all-atom OPLS force field. It guides users through the setup and execution of a 20 ns simulation, along with basic analysis techniques for the resulting data.

GroPoB is a tutorial that guides users through the process of building polymer electrolyte systems and setting up molecular dynamics simulations to calculate the glass transition temperature. It utilizes the Generalized Amber Force Field (GAFF) parameters and includes steps for parameterizing monomers and generating initial configurations for simulations.

The Nequip Tutorial provides guidance on using the NequIP framework, which focuses on machine learning applications in molecular dynamics and property prediction. It serves as an educational resource for users interested in applying these techniques to molecular systems.

The RDKitTutorial repository offers a series of educational notebooks designed to teach MSc Drug Design students how to use RDKit for cheminformatics applications. It covers topics such as molecular similarity and substructure searching, which are essential for molecular property prediction and drug discovery.

The AFDB_notebooks repository contains Jupyter notebooks that facilitate querying, accessing, and analyzing protein structures from the AlphaFold Protein Structure Database. It includes various methods for interacting with the database, making it a useful resource for researchers in structural biology.

EDSAI_CADD_intro provides example notebooks for an EDSAI course, focusing on molecular representations and machine learning techniques applicable to drug discovery and cheminformatics. It includes topics such as similarity search and machine learning models for molecular data.