Published in Nature Communications, 2024
Characterizing protein dynamics in the crystalline state Read more
Recommended citation: Klyshko E, Kim JS-H, McGough L, Valeeva V, Lee E, Ranganathan R, Rauscher S (2024) "Functional protein dynamics in a crystal." Nature Communications 15(1):3244 /files/efx.pdf
Published in BMC Bioinformatics, 2023
A computer vision tool to detect baker yeast colonies Read more
Recommended citation: Christopher J Nunn, Eugene Klyshko, Sid Goyal (2023). "petiteFinder: An automated computer vision tool to compute Petite colony frequencies in bakers yeast." BMC Bioinformatics 24, 50. /files/pf.pdf
Published in Biophysical Journal, 2022
Computational method to track ordered water in simulations Read more
Recommended citation: E Klyshko, JSH Kim, S Rauscher (2022). "LAWS: Local Alignment for Water Sites — tracking ordered water in simulations." Biophysical Journal. 122 (14), 2871-2883 /files/laws.pdf
Published in Computational and Structural Biotechnology Journal, 2022
The paper describing a computational model of microtubule dynamics Read more
Recommended citation: Evgenii Kliuchnikov, Eugene Klyshko, Maria S. Kelly, Artem Zhmurov, Ruxandra I. Dima, Kenneth A. Marx, Valeri Barsegov (2022). "Microtubule assembly and disassembly dynamics model: Exploring dynamic instability and identifying features of Microtubules’ Growth, Catastrophe, Shortening, and Rescue." Computational and Structural Biotechnology Journal. 20(1). /files/maddy.pdf
Published in PLoS computational biology, 2021
Graph convolutional network to spead up de novo protein design Read more
Recommended citation: Jack B Maguire, Daniele Grattarola, Vikram Khipple Mulligan, Eugene Klyshko, Hans Melo (2021). "XENet: Using a new graph convolution to accelerate the timeline for protein design on quantum computers." PLoS computational biology. 9 (17). /files/xenet.pdf