Author

Aakash Saha

University of California, RiversideORCID 0000-0003-0776-9771Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Biochemistry· 1 Biophysics· 1 Systems Biology· 1

Signature Assays, Organisms & Methods

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Organism:E. coli· 2 Research Focus:protein folding & dynamics· 2 Approach:statistical model· 2 Approach:biophysical modeling· 1 Assay:CRISPR screen· 1 Approach:deep learning· 1 Assay:DNA methylation· 1 Approach:experimental assay· 1

Frequent Co-Authors

Giulia PalermoiD· 2 shared A. Naravane· 1 shared Alexa L KnightiD· 1 shared Anthony NewmaniD· 1 shared Barry H. HonigiD· 1 shared Caroline VeleziD· 1 shared Charlotte S Dresser· 1 shared David Ward TayloriD· 1 shared

Activity by Year

2025-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 17 mutual co-author links

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2 shared papersBiophysics

Giulia PalermoORCID

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3 papers

Recent·Most cited

BiophysicsNature CommunicationsPeer-reviewedOct 9, 2026

A Cryptic Binding Pocket Regulates the Metal-Dependent Activity of Cas9

Mohd Ahsan, Alexa L Knight, Aakash Saha…·Giulia Palermo

This study identifies a cryptic divalent metal binding pocket that regulates Cas9's metal-dependent activity through conformational activation and catalytic efficiency.

3 citations

mechanistic / dynamical modelexperimental assay

𝕏 PostBluesky

Systems BiologyNature CommunicationsPeer-reviewedApr 11, 2026

Combining structural modeling and deep learning to calculate the E. coli protein interactome and functional networks

Haiqing Zhao, Caroline Velez, A. Naravane…·Barry H. Honig

The paper integrates three computational methods to predict E. coli protein-protein interactions and functional networks, identifying over 20K high-confidence interactions.

3 citations

E. coliprotein structure

𝕏 PostBluesky

BiochemistryNucleic Acids ResearchPeer-reviewedSep 23, 2025

CRISPR-Cas12a REC2 - NUC interactions drive target-strand cleavage and constrain trans cleavage.

Anthony Newman, Aakash Saha, Lora M. Starrs…·Gaétan Burgio

This study investigates differences in cis and trans cleavage efficiency among Cas12a orthologues and identifies REC2-NUC interactions as key determinants of their function.

14 citationstop 4%

E. colihuman

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