Publications by authors named "Yury Vorobjev"

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An effective molecular blocker of ion channel of M2 protein as anti-influenza a drug.
Yury N Vorobjev

J Biomol Struct Dyn· April 2021

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Role of Ionizing Amino Acid Residues in the Process of DNA Binding by Human AP Endonuclease 1 and in Its Catalysis.
Irina V Alekseeva, Artemiy S Bakman, Yury N Vorobjev, Olga S Fedorova, Nikita A Kuznetsov

J Phys Chem B· November 2019

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Outline of an experimental design aimed to detect a protein A mirror image in solution.
Osvaldo A Martin, Yury Vorobjev, Harold A Scheraga, Jorge A Vila

PeerJ Phys Chem· October 2019

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The Role of Active-Site Residues Phe98, His239, and Arg243 in DNA Binding and in the Catalysis of Human Uracil-DNA Glycosylase SMUG1.
Danila A Iakovlev, Irina V Alekseeva, Yury N Vorobjev, Nikita A Kuznetsov, Olga S Fedorova

Molecules· August 2019

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Roles of Active-Site Amino Acid Residues in Specific Recognition of DNA Lesions by Human 8-Oxoguanine-DNA Glycosylase (OGG1).
Timofey E Tyugashev, Yury N Vorobjev, Alexandra A Kuznetsova, Maria V Lukina, Nikita A Kuznetsov

J Phys Chem B· June 2019

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A comprehensive analysis of the computed tautomer fractions of the imidazole ring of histidines in Loligo vulgaris.
Yury N Vorobjev, Harold A Scheraga, Jorge A Vila

J Biomol Struct Dyn· September 2018

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Coupled molecular dynamics and continuum electrostatic method to compute the ionization pKa's of proteins as a function of pH. Test on a large set of proteins.
Yury N Vorobjev, Harold A Scheraga, Jorge A Vila

J Biomol Struct Dyn· February 2018

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Evaluation of the Gibbs Free Energy Changes and Melting Temperatures of DNA/DNA Duplexes Using Hybridization Enthalpy Calculated by Molecular Dynamics Simulation.
Alexander A Lomzov, Yury N Vorobjev, Dmitrii V Pyshnyi

J Phys Chem B· December 2015

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MDTRA: a molecular dynamics trajectory analyzer with a graphical user interface.
Alexander V Popov, Yury N Vorobjev, Dmitry O Zharkov

J Comput Chem· February 2013

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Potential of mean force of water-proton bath and molecular dynamic simulation of proteins at constant pH.
Yury N Vorobjev

J Comput Chem· March 2012

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Advances in implicit models of water solvent to compute conformational free energy and molecular dynamics of proteins at constant pH.
Yury N Vorobjev

Adv Protein Chem Struct Biol· February 2012

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Conformational dynamics of abasic DNA upon interactions with AP endonuclease 1 revealed by stopped-flow fluorescence analysis.
Lyubov Yu Kanazhevskaya, Vladimir V Koval, Yury N Vorobjev, Olga S Fedorova

Biochemistry· February 2012

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Assessing the fractions of tautomeric forms of the imidazole ring of histidine in proteins as a function of pH.
Jorge A Vila, Yelena A Arnautova, Yury Vorobjev, Harold A Scheraga

Proc Natl Acad Sci U S A· April 2011

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Blind docking method combining search of low-resolution binding sites with ligand pose refinement by molecular dynamics-based global optimization.
Yury N Vorobjev

J Comput Chem· April 2010

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Identifying native-like protein structures with scoring functions based on all-atom ECEPP force fields, implicit solvent models and structure relaxation.
Yelena A Arnautova, Yury N Vorobjev, Jorge A Vila, Harold A Scheraga

Proteins· October 2009

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Arrangement of 3'-terminus of tRNA on the human ribosome as revealed from cross-linking data.
Konstantin Bulygin, Alain Favre, Soria Baouz-Drahy, Codjo Hountondji, Yury Vorobjev

Biochimie· July 2009

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FAMBE-pH: a fast and accurate method to compute the total solvation free energies of proteins.
Yury N Vorobjev, Jorge A Vila, Harold A Scheraga

J Phys Chem B· September 2008

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Coupling between conformation and proton binding in proteins.
Jorge A Vila, Daniel R Ripoll, Yelena A Arnautova, Yury N Vorobjev, Harold A Scheraga

Proteins· October 2005

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Free energies of protein decoys provide insight into determinants of protein stability.
Yury N Vorobjev, Jan Hermans

Protein Sci· April 2002

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