Search Results - "Ivankov, Dmitry N"

Using AlphaFold to predict the impact of single mutations on protein stability and function by Pak, Marina A, Markhieva, Karina A, Novikova, Mariia S, Petrov, Dmitry S, Vorobyev, Ilya S, Maksimova, Ekaterina S, Kondrashov, Fyodor A, Ivankov, Dmitry N

“…AlphaFold changed the field of structural biology by achieving three-dimensional (3D) structure prediction from protein sequence at experimental quality. The…”
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An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape by 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 S, Filion, Guillaume J, Carey, Lucas B, Kondrashov, Fyodor A

“…Characterizing the fitness landscape, a representation of fitness for a large set of genotypes, is key to understanding how genetic information is interpreted…”
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Exact correspondence between walk in nucleotide and protein sequence spaces by Ivankov, Dmitry N

“…In the course of evolution, genes traverse the nucleotide sequence space, which translates to a trajectory of changes in the protein sequence in protein…”
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Analysis of the abundance and diversity of RNA secondary structure elements in RNA viruses using the RNAsselem Python package by Kazanov, Fedor M., Matveev, Evgenii V., Ponomarev, Gennady V., Ivankov, Dmitry N., Kazanov, Marat D.

“…Recent advancements in experimental and computational methods for RNA secondary structure detection have revealed the crucial role of RNA structural elements…”
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Solution of Levinthal's Paradox and a Physical Theory of Protein Folding Times by Ivankov, Dmitry N, Finkelstein, Alexei V

“…"How do proteins fold?" Researchers have been studying different aspects of this question for more than 50 years. The most conceptual aspect of the problem is…”
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Golden triangle for folding rates of globular proteins by Garbuzynskiy, Sergiy O., Ivankov, Dmitry N., Bogatyreva, Natalya S., Finkelstein, Alexei V.

“…The ability of protein chains to spontaneously form their spatial structures is a long-standing puzzle in molecular biology. Experimentally measured rates of…”
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In Silico Simulations Reveal Molecular Mechanism of Uranyl Ion Toxicity towards DNA-Binding Domain of PARP-1 Protein by Bulavko, Egor S., Pak, Marina A., Ivankov, Dmitry N.

“…The molecular toxicity of the uranyl ion (UO22+) in living cells is primarily determined by its high affinity to both native and potential metal-binding sites…”
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In-Frame Deletion of Dystrophin Exons 8-50 Results in DMD Phenotype by Egorova, Tatiana V, Galkin, Ivan I, Velyaev, Oleg A, Vassilieva, Svetlana G, Savchenko, Irina M, Loginov, Vyacheslav A, Dzhenkova, Marina A, Korshunova, Diana S, Kozlova, Olga S, Ivankov, Dmitry N, Polikarpova, Anna V

“…Mutations that prevent the production of proteins in the gene cause Duchenne muscular dystrophy. Most frequently, these are deletions leading to reading-frame…”
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Design of stable circular permutants of the GroEL chaperone apical domain by Melnik, Tatiana N, Majorina, Maria A, Vorobeva, Daria E, Nagibina, Galina S, Veselova, Victoria R, Glukhova, Ksenia A, Pak, Marina A, Ivankov, Dmitry N, Uversky, Vladimir N, Melnik, Bogdan S

“…Enhancing protein stability holds paramount significance in biotechnology, therapeutics, and the food industry. Circular permutations offer a distinctive…”
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Contact order revisited: Influence of protein size on the folding rate by Ivankov, Dmitry N., Garbuzynskiy, Sergiy O., Alm, Eric, Plaxco, Kevin W., Baker, David, Finkelstein, Alexei V.

“…Guided by the recent success of empirical model predicting the folding rates of small two‐state folding proteins from the relative contact order (CO) of their…”
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Machine Learning: How Much Does It Tell about Protein Folding Rates? by Corrales, Marc, Cuscó, Pol, Usmanova, Dinara R, Chen, Heng-Chang, Bogatyreva, Natalya S, Filion, Guillaume J, Ivankov, Dmitry N

“…The prediction of protein folding rates is a necessary step towards understanding the principles of protein folding. Due to the increasing amount of…”
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Prediction of Protein Folding Rates from the Amino Acid Sequence-Predicted Secondary Structure by Ivankov, Dmitry N., Finkelstein, Alexei V., Gelfand, I. M.

“…We present a method for predicting folding rates of proteins from their amino acid sequences only, or rather, from their chain lengths and their helicity…”
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Coupling between properties of the protein shape and the rate of protein folding by Ivankov, Dmitry N, Bogatyreva, Natalya S, Lobanov, Michail Yu, Galzitskaya, Oxana V

“…There are several important questions on the coupling between properties of the protein shape and the rate of protein folding. We have studied a series of…”
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QARIP: a web server for quantitative proteomic analysis of regulated intramembrane proteolysis by Ivankov, Dmitry N, Bogatyreva, Natalya S, Hönigschmid, Peter, Dislich, Bastian, Hogl, Sebastian, Kuhn, Peer-Hendrik, Frishman, Dmitrij, Lichtenthaler, Stefan F

“…Regulated intramembrane proteolysis (RIP) is a critical mechanism for intercellular communication and regulates the function of membrane proteins through…”
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Best templates outperform homology models in predicting the impact of mutations on protein stability by Pak, Marina A, Ivankov, Dmitry N

“…Prediction of protein stability change upon mutation (ΔΔG) is crucial for facilitating protein engineering and understanding of protein folding principles…”
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Unexpected diversity of signal peptides in prokaryotes by Payne, Samuel H, Bonissone, Stefano, Wu, Si, Brown, Roslyn N, Ivankov, Dmitry N, Frishman, Dmitrij, Pasa-Tolić, Ljiljana, Smith, Richard D, Pevzner, Pavel A

“…Signal peptides are a cornerstone mechanism for cellular protein localization, yet until now experimental determination of signal peptides has come from only a…”
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Local fitness landscape of the green fluorescent protein by Sarkisyan, Karen S., Bolotin, Dmitry A., Meer, Margarita V., Usmanova, Dinara R., Mishin, Alexander S., Sharonov, George V., Ivankov, Dmitry N., Bozhanova, Nina G., Baranov, Mikhail S., Soylemez, Onuralp, Bogatyreva, Natalya S., Vlasov, Peter K., Egorov, Evgeny S., Logacheva, Maria D., Kondrashov, Alexey S., Chudakov, Dmitry M., Putintseva, Ekaterina V., Mamedov, Ilgar Z., Tawfik, Dan S., Lukyanov, Konstantin A., Kondrashov, Fyodor A.

“…Comprehensive genotype–phenotype mapping of the green fluorescent protein shows that the local fitness peak is narrow, shaped by a high prevalence of epistatic…”
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Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation by 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, Ivankov, Dmitry N

“…Abstract Motivation Computational prediction of the effect of mutations on protein stability is used by researchers in many fields. The utility of the…”
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A structural perspective of compensatory evolution by Ivankov, Dmitry N, Finkelstein, Alexei V, Kondrashov, Fyodor A

“…The study of molecular evolution is important because it reveals how protein functions emerge and evolve. Recently, several types of studies indicated that…”
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Protein folding problem: enigma, paradox, solution by Finkelstein, Alexei V., Bogatyreva, Natalya S., Ivankov, Dmitry N., Garbuzynskiy, Sergiy O.

“…   The ability of protein chains to spontaneously form their three-dimensional structures is a long-standing mystery in molecular biology. The most conceptual…”
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