Browsing by Author "Ivankov, Dmitry N."

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  • A structural perspective of compensatory evolution
    Ivankov, Dmitry N.; Finkelstein, Alexei V.; Kondrashov, Fyodor A., 1979- (Elsevier, 2014)
    The study of molecular evolution is important because it reveals how protein functions emerge and evolve. Recently, several types of studies indicated that substitutions in molecular evolution occur in a compensatory manner, ...
  • An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape
    Pokusaeva, Victoria O.; Usmanova, Dinara R.; Putintseva, Ekaterina V.; Espinar, Lorena; Sarkisyan, Karen S.; Mishin, Alexander S.; Bogatyreva, Natalya S.; Ivankov, Dmitry N.; Akopyan, Arseniy V.; Avvakumov, Sergey Ya; Povolotskaya, Inna, 1986-; Filion, Guillaume; Carey, Lucas, 1980-; Kondrashov, Fyodor A., 1979- (Public Library of Science (PLoS), 2019)
    Characterizing the fitness landscape, a representation of fitness for a large set of genotypes, is key to understanding how genetic information is interpreted to create functional organisms. Here we determined the ...
  • Exact correspondence between walk in nucleotide and protein sequence spaces
    Ivankov, Dmitry N. (Public Library of Science (PLoS), 2017)
    In the course of evolution, genes traverse the nucleotide sequence space, which translates to a trajectory of changes in the protein sequence in protein sequence space. The correspondence between regions of the nucleotide ...
  • HypercubeME: two hundred million combinatorially complete datasets from a single experiment
    Esteban, Laura Avino; Lonishin, Lyubov R.; Bobrovskiy, Daniil; Leleytner, Gregory; Bogatyreva, Natalya S.; Kondrashov, Fyodor A., 1979-; Ivankov, Dmitry N. (Oxford University Press, 2020)
    Motivation: Epistasis, the context-dependence of the contribution of an amino acid substitution to fitness, is common in evolution. To detect epistasis, fitness must be measured for at least four genotypes: the reference ...
  • Machine learning: how much does it tell about protein folding rates?
    Corrales, Marc; Cuscó, Pol; Usmanova, Dinara R.; Chen, Heng-Chang; Bogatyreva, Natalya S.; Filion, Guillaume; Ivankov, Dmitry N. (Public Library of Science (PLoS), 2015)
    The prediction of protein folding rates is a necessary step towards understanding the principles of protein folding. Due to the increasing amount of experimental data, numerous protein folding models and predictors of ...
  • Rate of sequence divergence under constant selection
    Kondrashov, Alexey S.; Povolotskaya, Inna, 1986-; Ivankov, Dmitry N.; Kondrashov, Fyodor A., 1979- (BioMed Central, 2010)
    BACKGROUND: Divergence of two independently evolving sequences that originated from a common ancestor can be described by two parameters, the asymptotic level of divergence E and the rate r at which this level of divergence ...
  • Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation
    Usmanova, Dinara R.; Bogatyreva, Natalya S.; Ariño Bernad, Joan; Eremina, Aleksandra A.; Gorshkova, Anastasiya A.; Kanevskiy, German M.; Lonishin, Lyubov R.; Meister, Alexander V.; Yakupova, Alisa G.; Kondrashov, Fyodor A., 1979-; Ivankov, Dmitry N. (Oxford University Press, 2018)
    Motivation: Computational prediction of the effect of mutations on protein stability is used by researchers in many fields. The utility of the prediction methods is affected by their accuracy and bias. Bias, a systematic ...

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