Binding Sites

Xu, B., G. He, B. G. Weiner, P. Ronceray, Y. Meir, M. C. Jonikas, and N. S. Wingreen. (2020) 2020. “Rigidity Enhances a Magic-Number Effect in Polymer Phase Separation”. Nat Commun 11: 1561.

Reference Link
Kulkarni, Rahul, Kerwyn Casey Huang, Morten Kloster, and Ned Wingreen. (2004) 2004. “Pattern Formation Within Escherichia Coli: Diffusion, Membrane Attachment, and Self-Interaction of MinD Molecules.”. Phys Rev Lett 93 (22): 228103. doi:10.1103/PhysRevLett.93.228103.

Reference Link
Endres, Robert, Thomas Schulthess, and Ned Wingreen. (2004) 2004. “Toward an Atomistic Model for Predicting Transcription-Factor Binding Sites.”. Proteins 57 (2): 262-8. doi:10.1002/prot.20199.

Reference Link
Endres, Robert, and Ned Wingreen. (2006) 2006. “Weight Matrices for Protein-DNA Binding Sites from a Single Co-Crystal Structure.”. Phys Rev E Stat Nonlin Soft Matter Phys 73 (6 Pt 1): 061921. doi:10.1103/PhysRevE.73.061921.

Reference Link
Skoge, Monica, Robert Endres, and Ned Wingreen. (2006) 2006. “Receptor-Receptor Coupling in Bacterial Chemotaxis: Evidence for Strongly Coupled Clusters.”. Biophys J 90 (12): 4317-26. doi:10.1529/biophysj.105.079905.

Reference Link
Pompeani, Audra, Joseph Irgon, Michael Berger, Martha Bulyk, Ned Wingreen, and Bonnie Bassler. (2008) 2008. “The Vibrio Harveyi Master Quorum-Sensing Regulator, LuxR, a TetR-Type Protein Is Both an Activator and a Repressor: DNA Recognition and Binding Specificity at Target Promoters.”. Mol Microbiol 70 (1): 76-88. doi:10.1111/j.1365-2958.2008.06389.x.

Reference Link
Ndifon, Wilfred, Ned Wingreen, and Simon Levin. (2009) 2009. “Differential Neutralization Efficiency of Hemagglutinin Epitopes, Antibody Interference, and the Design of Influenza Vaccines.”. Proc Natl Acad Sci U S A 106 (21): 8701-6. doi:10.1073/pnas.0903427106.

Reference Link
Ng, Wai-Leung, Yunzhou Wei, Lark Perez, Jianping Cong, Tao Long, Matthew Koch, Martin Semmelhack, Ned Wingreen, and Bonnie Bassler. (2010) 2010. “Probing Bacterial Transmembrane Histidine Kinase Receptor-Ligand Interactions With Natural and Synthetic Molecules.”. Proc Natl Acad Sci U S A 107 (12): 5575-80. doi:10.1073/pnas.1001392107.

Reference Link
Broedersz, Chase, Xindan Wang, Yigal Meir, Joseph Loparo, David Rudner, and Ned Wingreen. (2014) 2014. “Condensation and Localization of the Partitioning Protein ParB on the Bacterial Chromosome.”. Proc Natl Acad Sci U S A 111 (24): 8809-14. doi:10.1073/pnas.1402529111.

Reference Link