Author

Karim Malekzadeh

University of HoustonORCID 0009-0004-8185-4995Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Approach:deep learning· 2 Approach:statistical model· 2 Research Focus:benchmarking· 1 Assay:cryo-EM· 1 Research Focus:differential expression· 1 Research Focus:gene regulatory network inference· 1 Assay:multiome· 1 Research Focus:protein folding & dynamics· 1

Frequent Co-Authors

Gül H. ZerzeiD· 2 shared Ambuj SrivastavaiD· 1 shared Anika JainiD· 1 shared Anouka Saha· 1 shared Arne ElofssoniD· 1 shared Ayush GuptaiD· 1 shared Chandran NithiniD· 1 shared Daisuke KiharaiD· 1 shared

Activity by Year

2025-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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2 shared papersBiophysics

Gül H. ZerzeORCID

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2 papers

Recent·Most cited

BiophysicsProteins Structure Function and BioinformaticsPeer-reviewedNov 8, 2025

Blind Prediction of Complex Water and Ion Ensembles Around RNA in CASP16

Rachael C. Kretsch, Elisa Posani, Eugene F. Baulin…·Rhiju Das

This paper evaluates blind predictions of dynamic water and ion ensembles around RNA using cryo-EM densities from CASP16, finding that molecular dynamics approaches perform best.

5 citations

cryo-EMdeep learning

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BiophysicsJournal of Chemical Information and ModelingPeer-reviewedMar 29, 2025

Optimizing On-the-Fly Probability Enhanced Sampling for Complex RNA Systems: Sampling Free Energy Surfaces of an H-Type Pseudoknot

Karim Malekzadeh, Gül H. Zerze

This study optimizes the MM-OPES method to sample the free energy surface of an H-type RNA pseudoknot, identifying effective CVs and temperature ranges for accurate FES prediction.

7 citations

multiomedeep learning

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