Author

Arup Mondal

University of FloridaORCID 0000-0002-8970-3380Unclaimed 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· 3 Approach:statistical model· 3 Research Focus:benchmarking· 2 Assay:structural biology· 2 Research Focus:chromatin & epigenetic regulation· 1 Research Focus:database / resource· 1 Approach:experimental assay· 1 Organism:mouse· 1

Frequent Co-Authors

Alberto PéreziD· 4 shared Gaetano Thomas MontelioneiD· 2 shared Adam LiwoiD· 1 shared Aleksandras GutmanasiD· 1 shared Benjamin BardiauxiD· 1 shared Bhumika SinghiD· 1 shared Binod L. Perera· 1 shared Brian O. SmithiD· 1 shared

Activity by Year

2024-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 37 mutual co-author links

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4 shared papersBiophysics

Alberto PérezORCID

Mutual co-authors in cluster

Author profile →

4 papers

Recent·Most cited

The NMR Exchange Format (NEF): Specification and Applications

Eliza Płoskoń, Kumaran Baskaran, Roberto Tejero, Charles D. Schwieters, Benjamin Bardiaux, Peter Güntert, Rasmus H. Fogh, Aleksandras Gutmanas, Edward J. Brooksbank, Masashi Yokochi, David Scott Wishart, Jonathan R. Wedell, Wim Vranken, Daniel Thompson, Gary S. Thompson, , Geerten W. Vuister

The paper introduces NEF, a standard for NMR data exchange, and demonstrates its application in structure determination, metabolomics, and ligand screening.

bioRxiv · Apr 24, 2026 · PreprintBiochemistry

Loop Plasticity Drives Paralog-Specific Recognition in BET ET Domains

Guadalupe ÁLVAREZ, Elizabeth Sebastian, Arup Mondal, Monica J. Roth, Gaetano Thomas Montelione, Alberto Pérez

The paper investigates how sequence variations in BET ET domains influence paralog-specific peptide recognition through loop dynamics and conformational changes.

Journal of Chemical Information and Modeling · Apr 15, 2026Peer-reviewedBiophysics

MELD-Adapt: On-the-Fly Belief Updating in Integrative Molecular Dynamics

Bhumika Singh, Arup Mondal, Kari Gaalswyk, Justin L. MacCallum, Alberto Pérez

MELD-Adapt dynamically evaluates data reliability to improve structure prediction accuracy by adjusting initial beliefs and identifying reliable data fractions.

Journal of Chemical Theory and Computation · Oct 2, 2024Peer-reviewedBiophysics

Protein Retrieval via Integrative Molecular Ensembles (PRIME) through extended similarity indices

Lexin Chen, Arup Mondal, Alberto Pérez, Ramón Alain Miranda‐Quintana

PRIME improves identification of native-like protein structures from MD simulations by using extended similarity indices, achieving lower RMSD than traditional centroid-based methods.

Journal of Chemical Theory and Computation · Jul 9, 2024Peer-reviewedBiophysics