Author

R. I. Dima

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Biophysics· 5 Bioengineering· 1

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Research Focus:protein folding & dynamics· 3 Approach:deep learning· 2 Approach:experimental assay· 2 Approach:mechanistic / dynamical model· 2 Assay:protein structure· 2 Approach:statistical model· 2 Research Focus:clustering· 1 Research Focus:drug response / drug discovery· 1

Frequent Co-Authors

R. A. Varikoti· 4 shared M. S. Kelly· 3 shared S. Mullen· 3 shared A. C. Macke· 2 shared G. Stan· 2 shared M. Damre· 2 shared A. Dayananda· 1 shared A. Javidi· 1 shared

Activity by Year

2019-2024 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 26 mutual co-author links

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4 shared papersBiophysics

R. A. Varikoti

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Author profile →

6 papers

Recent·Most cited

Machine Learning Approaches in Label-Free Small Extracellular Vesicles Analysis with Surface-Enhanced Raman Scattering (SERS) for Cancer Diagnostics

D. Vang, M. Kelly, M. Sharma, M. Sheokand, L. Esfandiari, R. I. Dima, P. Strobbia

This paper demonstrates a proof-of-concept model using machine learning and SERS to predict cancer from small extracellular vesicles, with explainable AI for interpretability.

bioRxiv · Feb 19, 2024 · PreprintBioengineering

Searching for Structure: Characterizing the Protein Conformational Landscape with Clustering-based Algorithms

A. C. Macke, J. E. Stump, M. S. Kelly, J. Rowley, V. Herath, S. Mullen, R. I. Dima

This paper introduces StELa, a clustering method that identifies protein conformational minima more effectively than existing methods like GROMOS and CATS.

bioRxiv · Sep 13, 2023Biophysics

Microtubule severing enzymes oligomerization and allostery: a tale of two domains

A. C. Macke, M. S. Kelly, R. A. Varikoti, D. Groves, C. Forbes, S. Mullen, R. I. Dima

The paper investigates the oligomerization and allostery of microtubule severing enzymes, showing that oligomer stability depends on binding partners and the type of severing protein.

bioRxiv · Jul 26, 2022Biophysics

Exploring the effect of mechanical anisotropy of protein structures in the unfoldase mechanism of AAA+ molecular machines

R. A. Varikoti, H. Y. Y. Fonseka, M. S. Kelly, A. Javidi, M. Damre, S. Mullen, J. L. Nugent, C. M. Gonzales, G. Stan, R. I. Dima

This study investigates how mechanical anisotropy in protein structures influences the unfolding mechanisms of AAA+ molecular machines like spastin and ClpY.

bioRxiv · Apr 6, 2022Biophysics

Factors Underlying Asymmetric Dynamics of Disaggregase and Microtubule Severing AAA+ Machines

M. Damre, A. Dayananda, R. A. Varikoti, G. Stan, R. I. Dima

This study uses molecular dynamics simulations to analyze the asymmetric dynamics of AAA+ disaggregase and microtubule-severing proteins, revealing differences in inter-protomer coupling and substrate processing mechanisms.

bioRxiv · Nov 25, 2020Biophysics

Molecular Investigations into the Unfoldase Action of Severing Enzymes on Microtubules

R. A. Varikoti, A. Macke, V. Speck, J. L. Ross, R. I. Dima

The paper uses molecular simulations to test a model of microtubule severing by unfolding enzymes, finding that enzyme concentration and placement affect cooperative removal of protofilament fragments.

bioRxiv · Dec 11, 2019Biophysics