Publications by authors named "Darya Stepanenko"

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Modeling Protein-Protein and Protein-Ligand Interactions by the ClusPro Team in CASP16.
Ryota Ashizawa, Sergei Kotelnikov, Omeir Khan, Stan Xiaogang Li, Ernest Glukhov, Darya Stepanenko

Proteins· October 2025

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MHC-Fine: Fine-tuned AlphaFold for precise MHC-peptide complex prediction.
Ernest Glukhov, Dmytro Kalitin, Darya Stepanenko, Yimin Zhu, Thu Nguyen

Biophys J· September 2024

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Assessing pH-Dependent Conformational Changes in the Fusion Peptide Proximal Region of the SARS-CoV-2 Spike Glycoprotein.
Darya Stepanenko, Yuzhang Wang, Carlos Simmerling

Viruses· July 2024

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MHC-Fine: Fine-tuned AlphaFold for Precise MHC-Peptide Complex Prediction.
Ernest Glukhov, Dmytro Kalitin, Darya Stepanenko, Yimin Zhu, Thu Nguyen

bioRxiv· December 2023

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SpikeScape: A Tool for Analyzing Structural Diversity in Experimental Structures of the SARS-CoV-2 Spike Glycoprotein.
Darya Stepanenko, Stephanie Budhan, Carlos Simmerling

J Chem Inf Model· February 2023

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Search and Localization Dynamics of the CRISPR-Cas9 System.
Qiao Lu, Deepak Bhat, Darya Stepanenko, Simone Pigolotti

Phys Rev Lett· November 2021

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Free Energy Landscapes from SARS-CoV-2 Spike Glycoprotein Simulations Suggest that RBD Opening Can Be Modulated via Interactions in an Allosteric Pocket.
Lucy Fallon, Kellon A A Belfon, Lauren Raguette, Yuzhang Wang, Darya Stepanenko

J Am Chem Soc· August 2021

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