rmsd

利用xvg生成的csv文件进行画图的脚本

A program that compares a protein structure prediction to a solved structure and evaluates the prediction's accuracy using RMSD.

Kabsch algorithm for optimal 3D molecular coordinates alignment, rigid translation, and RMSD distance calculation

Superimpose a set of protein structures and report a RSMD matrix, in CSV and Mega-compatible formats, using Pymol as a module

F@H Data Analysis: Root-mean-square Deviation & Radius of Gyration Calculations

A measured benchmark of three docking scoring functions on 308 protein-ligand complexes, reporting pose accuracy and physical validity together, with the success rate recomputed after removing the crystal starting conformer and the ligand-centred search box.

Kabsch algorithm for optimal 3D molecular coordinates alignment, rigid translation, and RMSD distance calculation

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

Pairwise structural comparison of .xyz by a Kabsch test with adjustable weights. For versions prior to v1.0.0, note the project «aRMSD-minimalWindowsSupport», too.

Compute a moving root mean squared error (RMSE) incrementally, ignoring NaN values.

Clustering for molecular configurations

aligns arbitrarily ordered isomers

This repository contains Jupyter notebooks used to perform computational analysis of LAT1 (SLC7A5) cholesterol binding sites, as published in JCTC

Differentiable, gradient-safe Kabsch (SVD) and Horn (quaternion) point-cloud alignment across NumPy, PyTorch, JAX, TensorFlow, and MLX.

Command line recipes for the working chemoinformatician

Kabsch algorithm for optimally aligning two paired sets of points

Step-by-step GROMACS workflow for protein molecular dynamics simulations

Project for analysis of protein structures in .pdb file format. It calculates some structure parameters and can compare two structures by calculating the RMSD.

Superimpose a set of protein structures and report a RSMD matrix, in CSV and Mega-compatible formats.

Implementation of MDTraj in Rust