spyrmsd: symmetry-corrected RMSD calculations in Python
By Rocco Meli, Philip C. Biggin. 2020
99 citations recorded by the source corpus.
Root mean square displacement (RMSD) calculations play a fundamental role in the comparison of different conformers of the same ligand. This is particularly important in the evaluation of protein-ligand docking, where different ligand poses are generated by docking software and their quality is usually assessed by RMSD calculations. Unfortunately, many RMSD calculation tools do not take into account the symmetry of the molecule, remain difficult to integrate flawlessly in cheminformatics and machine learning pipelines—which are often written in Python—or are shipped within large code bases. Here we present a new open-source RMSD calculation tool written in Python, designed to be extremely lightweight and easy to integrate into existing software.
Subfields: Computational Theory and Mathematics, Materials Chemistry, Molecular Biology
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In Computational Theory and Mathematics
- Tommi S. Jaakkola
- Regina Barzilay
- Bowen Jing
- Gabriele Corso
- Hannes Stärk
- Wengong Jin
- José Miguel Hernández-Lobato
- Shitong Luo
In Materials Chemistry
- Tommi S. Jaakkola
- Regina Barzilay
- Gabriele Corso
- Bowen Jing
- Hannes Stärk
- Wengong Jin
- José Miguel Hernández-Lobato
- William L. Hamilton
In Molecular Biology
- Tommi S. Jaakkola
- Regina Barzilay
- Hannes Stärk
- Bowen Jing
- Gabriele Corso
- Shuya Nakata
- Shigenori Tanaka
- Yoshiharu Mori
Citations in the corpus
- DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking (2022, methodology): “To account for permutation symmetries in the ligand, we use the symmetry-corrected RMSD of sPyRMSD [24].”