Search Results - "S̆vedas, Vytas"

Prospects of Using Biocatalysis for the Synthesis and Modification of Polymers by Nikulin, Maksim, Švedas, Vytas

“…Trends in the dynamically developing application of biocatalysis for the synthesis and modification of polymers over the past 5 years are considered, with an…”
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Conformational transitions induced by NADH binding promote reduction half-reaction in 2-hydroxybiphenyl-3-monooxygenase catalytic cycle by Kopylov, Kirill, Kirilin, Evgeny, Švedas, Vytas

“…2-Hydroxybiphenyl-3-monoxygenase from Pseudomonas azelaica is an effective catalyst of the regiospecific conversions of various aromatic compounds. A…”
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Yosshi: a web-server for disulfide engineering by bioinformatic analysis of diverse protein families by Suplatov, Dmitry, Timonina, Daria, Sharapova, Yana, Švedas, Vytas

“…Disulfide bonds play a significant role in protein stability, function or regulation but are poorly conserved among evolutionarily related proteins. The Yosshi…”
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Tyrosyl-DNA Phosphodiesterase 1 Inhibitors: Usnic Acid Enamines Enhance the Cytotoxic Effect of Camptothecin by Zakharenko, Alexandra, Luzina, Olga, Koval, Olga, Nilov, Dmitry, Gushchina, Irina, Dyrkheeva, Nadezhda, Švedas, Vytas, Salakhutdinov, Nariman, Lavrik, Olga

“…Tyrosyl-DNA phosphodiesterase 1 (TDP1) is a repair enzyme for stalled DNA-topoisomerase 1 (Top1) cleavage complexes and other 3′-end DNA lesions. TDP1 is a…”
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Robust enzyme design: Bioinformatic tools for improved protein stability by Suplatov, Dmitry, Voevodin, Vladimir, Švedas, Vytas

“…The ability of proteins and enzymes to maintain a functionally active conformation under adverse environmental conditions is an important feature of…”
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Bifunctional Inhibitors of Influenza Virus Neuraminidase: Molecular Design of a Sulfonamide Linker by Evteev, Sergei, Nilov, Dmitry, Polenova, Aleksandra, Švedas, Vytas

“…The growing resistance of the influenza virus to widely used competitive neuraminidase inhibitors occupying the active site of the enzyme requires the…”
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Neuraminidase A from Streptococcus pneumoniae has a modular organization of catalytic and lectin domains separated by a flexible linker by Sharapova, Yana, Suplatov, Dmitry, Švedas, Vytas

“…Neuraminidase A (NanA) of the pathogen Streptococcus pneumoniae cleaves receptors of the human respiratory epithelial surface during bacterial colonization…”
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vsFilt: A Tool to Improve Virtual Screening by Structural Filtration of Docking Poses by Gushchina, Irina V, Polenova, Aleksandra M, Suplatov, Dmitry A, Švedas, Vytas K, Nilov, Dmitry K

“…The ability of ligands to form crucial interactions with a protein target, characteristic for the substrate and/or inhibitors, could be considered a structural…”
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Zebra2: advanced and easy-to-use web-server for bioinformatic analysis of subfamily-specific and conserved positions in diverse protein superfamilies by Suplatov, Dmitry, Sharapova, Yana, Geraseva, Elizaveta, Švedas, Vytas

“…Abstract Zebra2 is a highly automated web-tool to search for subfamily-specific and conserved positions (i.e. the determinants of functional diversity as well…”
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Mustguseal and Sister Web-Methods: A Practical Guide to Bioinformatic Analysis of Protein Superfamilies by Suplatov, Dmitry, Sharapova, Yana, Švedas, Vytas

“…Bioinformatic analysis of functionally diverse superfamilies can help to study the structure-function relationship in proteins, but represents a methodological…”
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Computational design of a pH stable enzyme: understanding molecular mechanism of penicillin acylase's adaptation to alkaline conditions by Suplatov, Dmitry, Panin, Nikolay, Kirilin, Evgeny, Shcherbakova, Tatyana, Kudryavtsev, Pavel, Svedas, Vytas

“…Protein stability provides advantageous development of novel properties and can be crucial in affording tolerance to mutations that introduce functionally…”
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Mechanism of PARP1 Elongation Reaction Revealed by Molecular Modeling by Pushkarev, Sergey V., Kirilin, Evgeny M., Švedas, Vytas K., Nilov, Dmitry K.

“…Poly(ADP-ribose) polymerase 1 (PARP1) plays a major role in the DNA damage repair and transcriptional regulation, and is targeted by a number of clinical…”
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Modeling the Structure of Human tRNA-Guanine Transglycosylase in Complex with 7-Methylguanine and Revealing the Factors that Determine the Enzyme Interaction with Inhibitors by Pushkarev, Sergey V., Vinnik, Valeriia A., Shapovalova, Irina V., Švedas, Vytas K., Nilov, Dmitry K.

“…tRNA-guanine transglycosylase, an enzyme catalyzing replacement of guanine with queuine in human tRNA and participating in the translation mechanism, is…”
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Preparative Biocatalytic Synthesis of α-Ketoglutaramate by Nikulin, Maksim, Drobot, Viktor, Švedas, Vytas, Krasnikov, Boris F

“…α-Ketoglutaramate (KGM) is an underexamined metabolite of L-glutamine in the metabolic pathway of glutaminase II of α-ketoglutarate formation. Presumably, KGM…”
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parMATT: parallel multiple alignment of protein 3D-structures with translations and twists for distributed-memory systems by Shegay, Maksim V, Suplatov, Dmitry A, Popova, Nina N, Švedas, Vytas K, Voevodin, Vladimir V

“…Abstract Motivation Accurate structural alignment of proteins is crucial at studying structure-function relationship in evolutionarily distant homologues…”
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Preparative Biocatalytic Synthesis of α-Ketomethylselenobutyrate—A Putative Agent for Cancer Therapy by Nikulin, Maksim V, Drobot, Viktor V, Shurubor, Yevgeniya I, Švedas, Vytas K, Krasnikov, Boris F

“…Biomedical studies of the role of organic selenium compounds indicate that the amino acid derivative of L-selenomethionine, α-ketomethylselenobutyrate (KMSB),…”
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Mustguseal: a server for multiple structure-guided sequence alignment of protein families by Suplatov, Dmitry A, Kopylov, Kirill E, Popova, Nina N, Voevodin, Vladimir V, Švedas, Vytas K

“…Abstract Motivation Comparative analysis of homologous proteins in a functionally diverse superfamily is a valuable tool at studying structure-function…”
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Guidelines for reporting of biocatalytic reactions by Gardossi, Lucia, Poulsen, Poul B, Ballesteros, Antonio, Hult, Karl, Švedas, Vytas K, Vasić-Rački, Đurđa, Carrea, Giacomo, Magnusson, Anders, Schmid, Andreas, Wohlgemuth, Roland, Halling, Peter J

“…Enzymes and whole cells are being increasingly applied in research and industry, but the adoption of biocatalysis relies strongly on useful scientific…”
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Bioinformatic analysis of the fold type I PLP‐dependent enzymes reveals determinants of reaction specificity in l‐threonine aldolase from Aeromonas jandaei by Fesko, Kateryna, Suplatov, Dmitry, Švedas, Vytas

“…Understanding the role of specific amino acid residues in the molecular mechanism of a protein's function is one of the most challenging problems in modern…”
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A New Approach for Studying Poly(ADP-Ribose) Polymerase Inhibitors Using Permeabilized Adherent Cells by Shram, Stanislav I., Shcherbakova, Tatyana A., Abramova, Tatyana V., Smirnovskaya, Maria S., Balandina, Anastasia I., Kulikov, Andrey V., Švedas, Vytas K., Silnikov, Vladimir N., Myasoedov, Nikolay F., Nilov, Dmitry K.

“…Poly(ADP-ribose) polymerase (PARP) inhibitors have been proposed as pharmacological agents in the treatment of various diseases. Recently, factors and…”
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