spyrmsd: symmetry-corrected RMSD calculations in Python
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 usua...
| Main Authors: | , |
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| Formato: | Journal article |
| Idioma: | English |
| Publicado em: |
BioMed Central
2020
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| _version_ | 1826294860077858816 |
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| author | Meli, R Biggin, PC |
| author_facet | Meli, R Biggin, PC |
| author_sort | Meli, R |
| collection | OXFORD |
| description | 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. |
| first_indexed | 2024-03-07T03:52:11Z |
| format | Journal article |
| id | oxford-uuid:c1a78e32-a86a-43ad-b9fc-91ee54993867 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T03:52:11Z |
| publishDate | 2020 |
| publisher | BioMed Central |
| record_format | dspace |
| spelling | oxford-uuid:c1a78e32-a86a-43ad-b9fc-91ee549938672022-03-27T06:03:15Zspyrmsd: symmetry-corrected RMSD calculations in PythonJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:c1a78e32-a86a-43ad-b9fc-91ee54993867EnglishSymplectic ElementsBioMed Central2020Meli, RBiggin, PCRoot 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. |
| spellingShingle | Meli, R Biggin, PC spyrmsd: symmetry-corrected RMSD calculations in Python |
| title | spyrmsd: symmetry-corrected RMSD calculations in Python |
| title_full | spyrmsd: symmetry-corrected RMSD calculations in Python |
| title_fullStr | spyrmsd: symmetry-corrected RMSD calculations in Python |
| title_full_unstemmed | spyrmsd: symmetry-corrected RMSD calculations in Python |
| title_short | spyrmsd: symmetry-corrected RMSD calculations in Python |
| title_sort | spyrmsd symmetry corrected rmsd calculations in python |
| work_keys_str_mv | AT melir spyrmsdsymmetrycorrectedrmsdcalculationsinpython AT bigginpc spyrmsdsymmetrycorrectedrmsdcalculationsinpython |