Stars
Tool to predict water molecules placement and energy in ligand binding sites
Software for analyzing multiple protein-protein interaction docking solutions, calculating contact regions using mdtraj, and visualizing in useful ways via nglview.
Package to perform minimum-distance distribution analyses of complex solute-solvent interactions
📽️ Game-changing scripts for molecular visualization — produce Hollywood-quality visuals with scientific accuracy and cinematic impact
Library for computing dynamic non-covalent contact networks in proteins throughout MD Simulation
A collection of Jupyter notebooks and tools for analyzing water behavior and protein-ligand interactions from molecular dynamics (MD) simulations. Includes scripts for water residence time, density…
The algorithm to track crystallographic water sites in MD simulations
Supporting files for "Unraveling the Bürgi-Dunitz Angle with Precision: The Power of a Two-Dimensional Energy Decomposition Analysis"
A tool for modeling different kinase conformations with various ligand binding poses.
Automated Docking Tool with Autodock Vina
This script automates the calculation of Root Mean Square Fluctuations (RMSF) for the C-alpha (CA) atoms of specified systems using VMD (Visual Molecular Dynamics). It is designed for systems with …
Matplotlib tutorial for beginner
Python, MDAnalysis script to calculate the RMSD between atom selections and a reference structure
Manual de utilização do Supercomputador Santos Dumont II
Search for catalytic triades in enzymes based on genetic algorithms
Autonomous enzyme design system that combines agentic literature search with AlphaGo-style exploration to discover novel enzyme scaffolds around conserved catalytic triads.
Detect catalytic triads in serine protease PDB files based on geometry
PyRod - Tracing water molecules in molecular dynamics simulations
Solvent network analysis. Hop is a python package based on MDAnalysis to analyze solvation dynamics.
Public/backup repository of the GROMACS molecular simulation toolkit. Please do not mine the metadata blindly; we use https://gitlab.com/gromacs/gromacs for code review and issue tracking.
Shell script to automate setup of multiple identical MD simulations
Comandos úteis e outras informações necessárias para execução de scripts no supercomputador SDumont