The Multiscale Future of RNA Modeling

por Šulc, Petr
Publicado 2020

Understanding DNA interactions in crowded environments with a coarse-grained model

por Hong, Fan, Schreck, John S, Šulc, Petr
Publicado 2020

Phenotype Bias Determines How Natural RNA Structures Occupy the Morphospace of All Possible Shapes

por Dingle, Kamaludin, Ghaddar, Fatme, Šulc, Petr, Louis, Ard A
Publicado 2021

Design strategies for the self-assembly of polyhedral shells

por Pinto, Diogo E. P., Šulc, Petr, Sciortino, Francesco, Russo, John
Publicado 2023

OxDNA.org: a public webserver for coarse-grained simulations of DNA and RNA nanostructures

por Poppleton, Erik, Romero, Roger, Mallya, Aatmik, Rovigatti, Lorenzo, Šulc, Petr
Publicado 2021

Nanobase.org: a repository for DNA and RNA nanostructures

por Poppleton, Erik, Mallya, Aatmik, Dey, Swarup, Joseph, Joel, Šulc, Petr
Publicado 2021

Unified Nanotechnology Format: One Way to Store Them All

por Kuťák, David, Poppleton, Erik, Miao, Haichao, Šulc, Petr, Barišić, Ivan
Publicado 2021

Design, optimization and analysis of large DNA and RNA nanostructures through interactive visualization, editing and molecular simulation

por Poppleton, Erik, Bohlin, Joakim, Matthies, Michael, Sharma, Shuchi, Zhang, Fei, Šulc, Petr
Publicado 2020

DNA hybridization kinetics: zippering, internal displacement and sequence dependence

por Ouldridge, Thomas E., Šulc, Petr, Romano, Flavio, Doye, Jonathan P. K., Louis, Ard A.
Publicado 2013

The Heterogeneous Landscape and Early Evolution of Pathogen-Associated CpG Dinucleotides in SARS-CoV-2

por Di Gioacchino, Andrea, Šulc, Petr, Komarova, Anastassia V, Greenbaum, Benjamin D, Monasson, Rémi, Cocco, Simona
Publicado 2021

Desmocollin-1 is associated with pro-metastatic phenotype of luminal A breast cancer cells and is modulated by parthenolide

por Lapcik, Petr, Sulc, Petr, Janacova, Lucia, Jilkova, Katerina, Potesil, David, Bouchalova, Pavla, Müller, Petr, Bouchal, Pavel
Publicado 2023

Atomistic Picture of Opening–Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations

por Zhang, Zhengyue, Šponer, Jiří, Bussi, Giovanni, Mlýnský, Vojtěch, Šulc, Petr, Simmons, Chad R., Stephanopoulos, Nicholas, Krepl, Miroslav
Publicado 2023

A localized DNA finite-state machine with temporal resolution

por Liu, Lan, Hong, Fan, Liu, Hao, Zhou, Xu, Jiang, Shuoxing, Šulc, Petr, Jiang, Jian-Hui, Yan, Hao
Publicado 2022

DNA hairpins destabilize duplexes primarily by promoting melting rather than by inhibiting hybridization

por Schreck, John S., Ouldridge, Thomas E., Romano, Flavio, Šulc, Petr, Shaw, Liam P., Louis, Ard A., Doye, Jonathan P.K.
Publicado 2015

Generative and interpretable machine learning for aptamer design and analysis of in vitro sequence selection

por Di Gioacchino, Andrea, Procyk, Jonah, Molari, Marco, Schreck, John S., Zhou, Yu, Liu, Yan, Monasson, Rémi, Cocco, Simona, Šulc, Petr
Publicado 2022

On the biophysics and kinetics of toehold-mediated DNA strand displacement

por Srinivas, Niranjan, Ouldridge, Thomas E., Šulc, Petr, Schaeffer, Joseph M., Yurke, Bernard, Louis, Ard A., Doye, Jonathan P. K., Winfree, Erik
Publicado 2013

The influence of Holliday junction sequence and dynamics on DNA crystal self-assembly

por Simmons, Chad R., MacCulloch, Tara, Krepl, Miroslav, Matthies, Michael, Buchberger, Alex, Crawford, Ilyssa, Šponer, Jiří, Šulc, Petr, Stephanopoulos, Nicholas, Yan, Hao
Publicado 2022

Biomotors, viral assembly, and RNA nanobiotechnology: Current achievements and future directions

por Rolband, Lewis, Beasock, Damian, Wang, Yang, Shu, Yao-Gen, Dinman, Jonathan D., Schlick, Tamar, Zhou, Yaoqi, Kieft, Jeffrey S., Chen, Shi-Jie, Bussi, Giovanni, Oukhaled, Abdelghani, Gao, Xingfa, Šulc, Petr, Binzel, Daniel, Bhullar, Abhjeet S., Liang, Chenxi, Guo, Peixuan, Afonin, Kirill A.
Publicado 2022

Y RNAs are conserved endogenous RIG-I ligands across RNA virus infection and are targeted by HIV-1

por Vabret, Nicolas, Najburg, Valérie, Solovyov, Alexander, Gopal, Ramya, McClain, Christopher, Šulc, Petr, Balan, Sreekumar, Rahou, Yannis, Beauclair, Guillaume, Chazal, Maxime, Varet, Hugo, Legendre, Rachel, Sismeiro, Odile, Sanchez David, Raul Y., Chauveau, Lise, Jouvenet, Nolwenn, Markowitz, Martin, van der Werf, Sylvie, Schwartz, Olivier, Tangy, Frédéric, Bhardwaj, Nina, Greenbaum, Benjamin D., Komarova, Anastassia V.
Publicado 2022