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DOE OSTI · 1867785

OpenMDlr: parallel, open-source tools for general protein structure modeling and refinement from pairwise distances

Davidson, Russ·Woods, Jess·Effler, Chad·Thavappiragasam, Mathialakan·Mitchell, Julie·Parks, Jerry·Sedova, Ada
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Abstract

Easy-to-use, open-source, general-purpose programs for modeling a protein structure from inter-atomic distances are needed for modeling from experimental data and refinement of predicted protein structures. OpenMDlr is an open-source Python package for modeling protein structures from pairwise distances between any atoms, and optionally, dihedral angles. Finally, we provide a user-friendly input format for harnessing modern biomolecular force fields in an easy-to-install package that can efficiently make use of multiple compute cores.

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Davidson, Russ, Woods, Jess, Effler, Chad, Thavappiragasam, Mathialakan, Mitchell, Julie, Parks, Jerry, Sedova, Ada. 2022-05-05. OpenMDlr: parallel, open-source tools for general protein structure modeling and refinement from pairwise distances. https://doi.org/10.1093/bioinformatics%2Fbtac307

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