Author

Aiden R. Kolodziej

Massachusetts Institute of TechnologyORCID 0000-0003-0745-1157Unclaimed ORCID profile · follow to get notified of new preprints

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Biophysics· 1

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Research Focus:benchmarking· 1 Approach:deep learning· 1 Approach:graph neural network· 1 Research Focus:protein design· 1 Assay:protein structure· 1 Research Focus:protein structure prediction· 1

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S. Mazdak AbulnagaiD· 1 shared Sergey OvchinnikoviD· 1 shared

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2025-2025 · peak 1/yr

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1 shared paperBiophysics

S. Mazdak AbulnagaORCID

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BiophysicsbioRxivPreprintNov 18, 2025

CIRPIN: Learning Circular Permutation-Invariant Representations to Uncover Putative Protein Homologs

Aiden R. Kolodziej, S. Mazdak Abulnaga, Sergey Ovchinnikov

CIRPIN identifies protein homologs related by circular permutation using a permutation-invariant graph neural network, uncovering thousands of novel pairs and revealing natural PDZ domain permutations.

DOI 10.1101/2025.11.18.689110

protein structuredeep learning

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