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  • Computing the Dynamic Supramolecular Structural Proteome 

    Nussinov, Ruth; Papin, Jason A.; Vakser, Ilya A. (Public Library of Science, 2017-01-19)
  • Crosstalk and the evolvability of intracellular communication 

    Rowland, Michael A.; Greenbaum, Joseph M.; Deeds, Eric J. (Nature Research, 2017-07-10)
    Metazoan signalling networks are complex, with extensive crosstalk between pathways. It is unclear what pressures drove the evolution of this architecture. We explore the hypothesis that crosstalk allows different cell ...
  • Fundamental trade-offs between information flow in single cells and cellular populations 

    Suderman, Ryan; Bachman, John A.; Smith, Adam; Sorger, Peter K.; Deeds, Eric J. (National Academy of Sciences, 2017-05)
    Signal transduction networks allow eukaryotic cells to make decisions based on information about intracellular state and the environment. Biochemical noise significantly diminishes the fidelity of signaling: networks ...
  • Lineage space and the propensity of bacterial cells to undergo growth transitions 

    Bandyopadhyay, Arnab; Wang, Huijing; Ray, J. Christian J. (Public Library of Science, 2018-08-22)
    The molecular makeup of the offspring of a dividing cell gradually becomes phenotypically decorrelated from the parent cell by noise and regulatory mechanisms that amplify phenotypic heterogeneity. Such regulatory mechanisms ...
  • Natural language processing in text mining for structural modeling of protein complexes 

    Badal, Varsha D.; Kundrotas, Petras J.; Vakser, Ilya A. (BioMed Central, 2018-03-05)
    BACKGROUND: Structural modeling of protein-protein interactions produces a large number of putative configurations of the protein complexes. Identification of the near-native models among them is a serious challenge. ...
  • Structure Fluctuations and Conformational Changes in Protein Binding 

    Ruvinsky, Anatoly M.; Kirys, Tatsiana; Tuzikov, Alexander V.; Vakser, Ilya A. (World Scientific Publishing, 2012-04)
    Structure fluctuations and conformational changes accompany all biological processes involving macromolecules. The paper presents a classification of protein residues based on the normalized equilibrium fluctuations of the ...
  • Side-Chain Conformational Changes upon Protein-Protein Association 

    Ruvinsky, Anatoly M.; Kirys, Tatsiana; Tuzikov, Alexander V.; Vakser, Ilya A. (Elsevier, 2011-02-25)
    Conformational changes upon protein-protein association are the key element of the binding mechanism. The study presents a systematic large-scale analysis of such conformational changes in the side chains. The results ...
  • Maturation of the proteasome core particle induces an affinity switch that controls regulatory particle association 

    Wani, Prashant S.; Rowland, Michael A.; Ondracek, Alex; Deeds, Eric J.; Roelofs, Jeroen (Nature Publishing Group, 2015-03-16)
    Proteasome assembly is a complex process, requiring 66 subunits distributed over several subcomplexes to associate in a coordinated fashion. Ten proteasome-specific chaperones have been identified that assist in this ...
  • Transmembrane Helix Assembly by Window Exchange Umbrella Sampling 

    Park, Soohyung; Kim, Taehoon; Im, Wonpil (American Physical Society, 2012-03-08)
    A method of window exchange umbrella sampling molecular dynamics simulation is employed for transmembrane helix assembly. An analytical expression for the average acceptance probability between neighboring windows is derived ...
  • Template-Based Modeling of Protein-RNA Interactions 

    Zheng, Jinfang; Kundrotas, Petras J.; Vakser, Ilya A.; Liu, Shiyong (Public Library of Science, 2016-09-23)
    Protein-RNA complexes formed by specific recognition between RNA and RNA-binding proteins play an important role in biological processes. More than a thousand of such proteins in human are curated and many novel RNA-binding ...