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  • 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 ...