Yury Vorobjev : rechercher sur Z-Library

Yury N. Vorobjev, Juan Carlos Almagro, Jan Hermans

Année:

1997

Langue:

english

Fichier:

PDF, 236 KB

english, 1997

Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model

Journal:

Proteins: Structure, Function, and Bioinformatics

Année:

1998

Langue:

english

Fichier:

PDF, 179 KB

english, 1998

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

Yury N. Vorobjev

Journal:

Année:

2010

Langue:

english

Fichier:

PDF, 399 KB

english, 2010

Potential of mean force of water–proton bath and molecular dynamic simulation of proteins at constant pH

Yury N. Vorobjev

Journal:

Mikhail Karasev, Yuri Vorobjev

Année:

2012

Langue:

english

Fichier:

PDF, 1.40 MB

english, 2012

Integral Representations over Isotropic Submanifolds and Equations of Zero Curvature

Journal:

Advances in Mathematics

Année:

1998

Langue:

english

Fichier:

PDF, 656 KB

english, 1998

ES/IS: Estimation of conformational free energy by combining dynamics simulations with explicit solvent with an implicit solvent continuum model

Yury N. Vorobjev, Jan Hermans

Journal:

Biophysical Chemistry

Année:

1999

Langue:

english

Fichier:

PDF, 161 KB

english, 1999

Free energies of protein decoys provide insight into determinants of protein stability

Yury N. Vorobjev, Jan Hermans

Journal:

Protein Science

Année:

2002

Langue:

english

Fichier:

PDF, 33 KB

english, 2002

Coupling between conformation and proton binding in proteins

Jorge A. Vila, Daniel R. Ripoll, Yelena A. Arnautova, Yury N. Vorobjev, Harold A. Scheraga

Journal:

Proteins: Structure, Function, and Bioinformatics

Année:

2005

Langue:

english

Fichier:

PDF, 471 KB

english, 2005

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

Journal:

Proteins: Structure, Function, and Bioinformatics

Année:

2009

Langue:

english

Fichier:

PDF, 478 KB

english, 2009

Free energies of protein decoys provide insight into determinants of protein stability

Yury N. Vorobjev, Jan Hermans

Journal:

Protein Science

Année:

2001

Langue:

english

Fichier:

PDF, 127 KB

english, 2001

Interaction of Yeast Importin α with the NLS of Prothymosin α Is Insufficient to Trigger Nuclear Uptake of Cargos

Vitaliy R. Shakulov, Ivan A. Vorobjev, Yuri P. Rubtsov, Nina V. Chichkova, Andrey B. Vartapetian

Journal:

Biochemical and Biophysical Research Communications

Année:

2000

Langue:

english

Fichier:

PDF, 153 KB

english, 2000

Coupling Between Folding and Ionization Equilibria: Effects of pH on the Conformational Preferences of Polypeptides

Daniel R. Ripoll, Yury N. Vorobjev, Adam Liwo, Jorge A. Vila, Harold A. Scheraga

Journal:

Journal of Molecular Biology

Année:

1996

Langue:

english

Fichier:

PDF, 1.16 MB

english, 1996

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, Aliya Ven'yaminova, Dmitri Graifer, Galina Karpova

Journal:

Biochimie

Année:

2008

Langue:

english

Fichier:

PDF, 986 KB

english, 2008

Mutational analysis of human prothymosin α reveals a bipartite nuclear localization signal

Yuri P. Rubtsov, Andrei S. Zolotukhin, Ivan A. Vorobjev, Nina V. Chichkova, Nickolay A. Pavlov, Elena M. Karger, Alexandra G. Evstafieva, Barbara K. Felber, Andrey B. Vartapetian

Journal:

FEBS Letters

Année:

1997

Langue:

english

Fichier:

PDF, 702 KB

english, 1997

[Advances in Protein Chemistry and Structural Biology] Computational chemistry methods in structural biology Volume 85 || Advances in Implicit Models of Water Solvent to Compute Conformational Free Energy and Molecular Dynamics of Proteins at Constant pH

Vorobjev, Yury N.

Année:

2011

Langue:

english

Fichier:

PDF, 719 KB

english, 2011

MDTRA: A molecular dynamics trajectory analyzer with a graphical user interface

Popov, Alexander V., Vorobjev, Yury N., Zharkov, Dmitry O.

Journal:

Vila, Jorge A., Ripoll, Daniel R., Villegas, Myriam E., Vorobjev, Yury N., Scheraga, Harold A.

Année:

2013

Langue:

english

Fichier:

PDF, 2.16 MB

english, 2013

Role of Hydrophobicity and Solvent-Mediated Charge-Charge Interactions in Stabilizing α-Helices

Journal:

Biophysical Journal

Année:

1998

Langue:

english

Fichier:

PDF, 554 KB

english, 1998

Conformational Dynamics of Abasic DNA upon Interactions with AP Endonuclease 1 Revealed by Stopped-Flow Fluorescence Analysis

Kanazhevskaya, Lyubov Yu., Koval, Vladimir V., Vorobjev, Yury N., Fedorova, Olga S.

Journal:

Biochemistry

Année:

2012

Langue:

english

Fichier:

PDF, 3.91 MB

english, 2012

FAMBE-pH: A Fast and Accurate Method to Compute the Total Solvation Free Energies of Proteins

Vorobjev, Yury N., Vila, Jorge A., Scheraga, Harold A.

Journal:

Kuznetsov, Nikita A., Koval, Vladimir V., Zharkov, Dmitry O., Vorobjev, Yuri N., Nevinsky, Georgy A., Douglas, Kenneth T., Fedorova, Olga S.

Année:

2008

Langue:

english

Fichier:

PDF, 665 KB

english, 2008

Pre-Steady-State Kinetic Study of Substrate Specificity of Escherichia coli Formamidopyrimidine−DNA Glycosylase †

Journal:

Biochemistry

Année:

2007

Langue:

english

Fichier:

PDF, 799 KB

english, 2007

Computation of the Structure-Dependent p K a Shifts in a Polypentapeptide of the Poly[ f v (IPGVG), f E (IPGEG)] Family

Vila, Jorge A., Ripoll, Daniel R., Vorobjev, Yury N., Scheraga, Harold A.

Journal:

Vorobjev, Yury N., Hermans, Jan

Année:

1998

Langue:

english

Fichier:

PDF, 42 KB

english, 1998

A Critical Analysis of Methods of Calculation of a Potential in Simulated Polar Liquids: Strong Arguments in Favor of “Molecule-Based” Summation and of Vacuum Boundary Conditions in Ewald Summation

Journal:

Medvedev, Kirill E, Alemasov, Nikolay A, Vorobjev, Yuri N, Boldyreva, Elena V, Kolchanov, Nikolay A, Afonnikov, Dmitry A

Année:

1999

Langue:

english

Fichier:

PDF, 103 KB

english, 1999

Molecular dynamics simulations of the Nip7 proteins from the marine deep- and shallow-water Pyrococcus species

Journal:

BMC Structural Biology

Année:

2014

Langue:

english

Fichier:

PDF, 1.93 MB

english, 2014

73 Molecular dynamics approach for DNA duplex thermal stability prediction

Lomzov, Alexander, Vorobjev, Yury, Pyshnyi, Dmitryi

Journal:

Popov, Alexander V., Vorobjev, Yuri N., Zharkov, Dmitry O.

Année:

2013

Langue:

english

Fichier:

PDF, 106 KB

english, 2013

109 Molecular dynamics done quick: efficient trajectory analysis software

Journal:

Vorobjev, Yury N., Scheraga, Harold A., Honig, Barry

Année:

2013

Langue:

english

Fichier:

PDF, 98 KB

english, 2013

Theoretical Modeling of Electrostatic Effects of Titratable Side Chain Groups on Protein Conformation in a Polar Ionic Solution. 2. pH-Induced Helix-Coil Transition of Poly(L-lysine) in Water and Methanol Ionic Solutions

Journal:

Journal of Physical Chemistry

Année:

1995

Langue:

english

Fichier:

PDF, 865 KB

english, 1995

Theoretical Modeling of Electrostatic Effects of Titratable Side-Chain Groups on Protein Conformation in a Polar Ionic Solution. 1. Potential of Mean Force between Charged Lysine Residues and Titration of Poly(L-lysine) in 95% Methanol Solution

Vorobjev, Yury N., Scheraga, Harold A., Hitz, Ben, Honig, Barry

Journal:

Journal of Physical Chemistry

Année:

1994

Langue:

english

Fichier:

PDF, 1.05 MB

english, 1994

Interaction of a biomolecule with mobile ions in aqueous solution: comparison of three fast approximate methods with the direct solution of the nonlinear Poisson-Boltzmann equation

Vorobjev, Yury N., Scheraga, Harold A.

Journal:

Journal of Physical Chemistry

Année:

1993

Langue:

english

Fichier:

PDF, 1.22 MB

english, 1993

55 MDTRA: unified approach to molecular dynamics data preparation and analysis

Popov, Alexander V., Vorobjev, Yuri N., Zharkov, Dmitry O.

Journal:

Jorge A. Vila, Yelena A. Arnautova, Yury Vorobjev and Harold A. Scheraga

Année:

2015

Langue:

english

Fichier:

PDF, 577 KB

english, 2015

Assessing the fractions of tautomeric forms of the imidazole ring of histidine in proteins as a function of pH

Journal:

Proceedings of the National Academy of Sciences

Année:

2011

Langue:

english

Fichier:

PDF, 1.30 MB

english, 2011

Evaluation of the Gibbs Free Energy Changes and Melting Temperatures of DNA/DNA Duplexes Using Hybridization Enthalpy Calculated by Molecular Dynamics Simulation

Lomzov, Alexander A., Vorobjev, Yury N., Pyshnyi, Dmitrii V.

Journal:

Miroshnikova, Anastasia D., Kuznetsova, Alexandra A., Vorobjev, Yuri N., Kuznetsov, Nikita A., Fedorova, Olga S.

Année:

2015

Langue:

english

Fichier:

PDF, 2.27 MB

english, 2015

Effects of mono- and divalent metal ions on DNA binding and catalysis of human apurinic/apyrimidinic endonuclease 1

Journal:

Molecular BioSystems

Année:

2016

Langue:

english

Fichier:

PDF, 4.32 MB

english, 2016

SPIE Proceedings [SPIE Material Science and Material Properties for Infrared Optoelectronics - Kiev, Ukraine (Monday 28 September 1998)] Fourth International Conference on Material Science and Material Properties for Infrared Optoelectronics - Spontaneous IR intersublevel emission from quantum dots conditioned by main interband lasing

Vorobjev, Leonid E., Firsov, D. A., Shalygin, V. A., Tulupenko, Victor N., Shernyakov, Yuri M., Egorov, A. Y., Zhukov, Alexey E., Kovsh, Alexey R., Kop'ev, Petr S., Kochnev, I. N., Ledentsov, Nikolai

Année:

1999

Langue:

english

Fichier:

PDF, 378 KB

english, 1999

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

Vorobjev, Yury N., Scheraga, Harold A., Vila, Jorge A.

Journal:

Alexander V. Popov,Anton V. Endutkin,Yuri N. Vorobjev…

Année:

2017

Langue:

english

Fichier:

PDF, 1.18 MB

english, 2017

Molecular dynamics simulation of the opposite-base preference and interactions in the active site of formamidopyrimidine-DNA glycosylase

Journal:

BMC Structural Biology

Année:

2018

Langue:

english

Fichier:

PDF, 2.56 MB

english, 2018

A comprehensive analysis of the computed tautomer fractions of the imidazole ring of histidines in Loligo vulgaris

Vorobjev, Yury N., Scheraga, Harold A., Vila, Jorge A.

Journal:

Kuznetsov, Nikita A., Kuznetsova, Alexandra A., Vorobjev, Yuri N., Krasnoperov, Lev N., Fedorova, Olga S., Leng, Fenfei

Année:

2017

Langue:

english

Fichier:

PDF, 2.04 MB

english, 2017

Thermodynamics of the DNA Damage Repair Steps of Human 8-Oxoguanine DNA Glycosylase

Journal:

PLoS ONE

Année:

2014

Langue:

english

Fichier:

PDF, 837 KB

english, 2014

Substrate specificity of human apurinic/apyrimidinic endonuclease APE1 in the nucleotide incision repair pathway

Kuznetsova, Alexandra A, Matveeva, Anna G, Milov, Alexander D, Vorobjev, Yuri N, Dzuba, Sergei A, Fedorova, Olga S, Kuznetsov, Nikita A

Journal:

Nucleic Acids Research

Année:

2018

Langue:

english

Fichier:

PDF, 1.81 MB

english, 2018

Roles of Active-Site Amino Acid Residues in Specific Recognition of DNA Lesions by Human 8-Oxoguanine-DNA Glycosylase (OGG1)

Tyugashev, Timofey E., Vorobjev, Yury N., Kuznetsova, Alexandra A., Lukina, Maria V., Kuznetsov, Nikita A., Fedorova, Olga S.

Journal:

Iakovlev, Danila A., Alekseeva, Irina V., Vorobjev, Yury N., Kuznetsov, Nikita A., Fedorova, Olga S.

Année:

2019

Langue:

english

Fichier:

PDF, 5.53 MB

english, 2019

The Role of Active-Site Residues Phe98, His239, and Arg243 in DNA Binding and in the Catalysis of Human Uracil–DNA Glycosylase SMUG1

Journal:

Molecules

Année:

2019

Langue:

english

Fichier:

PDF, 3.14 MB

english, 2019

The Role of Ionizing Amino Acid Residues in the Process of DNA Binding by Human AP Endonuclease 1 and in its Catalysis

Alekseeva, Irina V., Bakman, Artemiy S., Vorobjev, Yury N, Fedorova, Olga S., Kuznetsov, Nikita A.

Journal:

Alekseeva, Irina V., Bakman, Artemiy S., Vorobjev, Yury N, Fedorova, Olga S., Kuznetsov, Nikita A.

Année:

2019

Langue:

english

Fichier:

PDF, 2.35 MB

english, 2019

The Role of Ionizing Amino Acid Residues in the Process of DNA Binding by Human AP Endonuclease 1 and in its Catalysis

Journal:

Année:

2019

Fichier:

PDF, 2.35 MB

2019

An effective molecular blocker of ion channel of M2 protein as anti-influenza A drug

Vorobjev, Yury N.

Journal: