Clusttraj: A Solvent-Informed Clustering Tool for Molecular Modeling.

ABSTRACT: Clustering techniques are consolidated as a powerful strategy for analyzing the extensive data generated from molecular modeling. In particular, some tools have been developed to cluster configurations from classical simulations with a standard focus on individual units, ranging from small molecules to complex proteins. Since the standard approach includes computing the root mean square deviation (RMSD) of atomic positions, accounting for the permutation between atoms is crucial for optimizing the clustering procedure in the presence of identical molecules. To address this issue, we present the clusttraj program, a solvent-informed clustering package that fixes inflated RMSD values by finding the optimal pairing between configurations. The program combines reordering schemes with the Kabsc

SUBMITTER: Ribeiro RB 

PROVIDER: S-EPMC12288011 | biostudies-literature | 2025 Jul

REPOSITORIES: biostudies-literature