An open library for the analysis of molecular dynamics trajectories

• UpdatedMar 12, 2025
• Python

Calculate Root-mean-square deviation (RMSD) of two molecules, using rotation, in xyz or pdb format

• UpdatedJan 13, 2025
• Python

📐 Symmetry-corrected RMSD in Python

• UpdatedNov 18, 2024
• Python

Preforms De novo protein design using machine learning and PyRosetta to generate a novel protein structure

• UpdatedMar 7, 2025
• Python

register 3D point clouds using rotation, translation, and scale transformations.

• UpdatedFeb 7, 2025
• Python

header-only C++ library for registering 3D point clouds using rotation, translation, and scale transformations

• UpdatedFeb 18, 2025
• C++

VMD plugin to calculate and visualize clusters of conformations for a trajectory

• UpdatedOct 24, 2018
• Tcl

Python script that receives a molecular dynamics or Monte Carlo trajectory and performs agglomerative clustering to classify similar structures.

• UpdatedFeb 4, 2025
• Python

PCA and normal mode analysis of proteins

• UpdatedMay 16, 2024
• C++

Molecular Crystal Simulation Library (mcse) is an open-source Python package for manipulating and analyzing molecular crystal structures

• UpdatedMay 30, 2022
• Python

Tool to calculate the root mean square deviation between molecular structures

• UpdatedJul 25, 2022
• Fortran

利用xvg生成的csv文件进行画图的脚本

• UpdatedMay 11, 2021
• Python

aligns arbitrarily ordered isomers

• UpdatedDec 28, 2019
• Python

Command line recipes for the working chemoinformatician

• UpdatedApr 6, 2022

A protein fragments picker

• UpdatedSep 26, 2019
• OCaml

MODE-TASK plugin for PyMOL

• UpdatedApr 28, 2023
• C++

Pairwise structural comparison of .xyz, a fork of aRMSD to work without PyInstaller in Linux. Note the project «aRMSD-minimalWindowsSupport», too.

• UpdatedAug 17, 2022
• Python

Calculate and apply the optimal transformation matrix that minimizes the RMSD (root mean squared deviation) between two paired sets of points.

• UpdatedMar 13, 2019
• JavaScript

VMD plugin for rmsd calculation and fitting of molecular structures

• UpdatedJun 5, 2014
• Tcl

📐 Implementation of the c-RMSD and d-RMSD algorithms

• UpdatedApr 23, 2021
• Jupyter Notebook