Y. Vorobjev

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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

H. Scheraga, B. Honig, Y. Vorobjev, 1995 .

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

H. Scheraga, J. Vila, Y. Vorobjev, 2018, Journal of biomolecular structure & dynamics.

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

H. Scheraga, J. Vila, Y. Vorobjev, 2018, Journal of biomolecular structure & dynamics.

Assessing the histidine tautomer fractions in proteins. Test on diisopropylfluorophosphatase, a large all-β protein, from Loligo vulgaris

H. Scheraga, J. Vila, Y. Vorobjev, 2017 .

Coupling between conformation and proton binding in proteins

H. Scheraga, D. Ripoll, J. Vila, 2005, Proteins.

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

J. Hermans, Y. Vorobjev, Y N Vorobjev, 1999, Biophysical chemistry.

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

H. Scheraga, J. Vila, Y. A. Arnautova, 2011, Proceedings of the National Academy of Sciences.

Coupling between folding and ionization equilibria: effects of pH on the conformational preferences of polypeptides.

H A Scheraga, J A Vila, A. Liwo, 1996, Journal of molecular biology.

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

Jan Hermans, J. Hermans, J. C. Almagro, 1998, Proteins.

A fast adaptive multigrid boundary element method for macromolecular electrostatic computations in a solvent

H. Scheraga, Y. Vorobjev, 1997 .

Design of an Efficient Inhibitor for the Influenza A Virus M2 Ion Channel

Y. Vorobjev, Yu. N. Vorobjev, 2020, Molecular Biology.

Modeling of Electrostatic Effects in Macromolecules

Y. Vorobjev, 2018, Springer Series on Bio- and Neurosystems.

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

Y. Vorobjev, Yury N Vorobjev, 2011, Advances in protein chemistry and structural biology.

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

J. Hermans, Y. Vorobjev, Y N Vorobjev, 2001, Protein science : a publication of the Protein Society.

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

H. Scheraga, Y. Vorobjev, 1993 .

Identifying native‐like protein structures with scoring functions based on all‐atom ECEPP force fields, implicit solvent models and structure relaxation

H. Scheraga, J. Vila, Y. A. Arnautova, 2009, Proteins.

Outline of an experimental design aimed to detect a protein A mirror image in solution.

H. Scheraga, J. Vila, Y. Vorobjev, 2019, PeerJ physical chemistry.

Does protein A mirror image exist in solution? Outline of an experimental design aimed to detect it

H. Scheraga, J. Vila, Y. Vorobjev, 2018 .

Block‐units method for conformational calculations of large nucleic acid chains. I. Block‐units approximation of atomic structure and conformational energy of polynucleotides

Y. Vorobjev, Yu. N. Vorobjev, 1990 .

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

Y. Vorobjev, 2020, Journal of biomolecular structure & dynamics.

Polyproline II helical structure in protein unfolded states: Lysine peptides revisited

T. Creamer, Y. Vorobjev, J. Hermans, 2002, Protein science : a publication of the Protein Society.

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

D. Pyshnyi, Y. Vorobjev, A. Lomzov, 2015, The journal of physical chemistry. B.

Modeling context-dependent conformation parameters of DNA duplexes

Y. Vorobjev, D. Emel’yanov, 2006 .

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

J. Hermans, Y. Vorobjev, 2001, Protein science : a publication of the Protein Society.

PELDOR analysis of enzyme-induced structural changes in damaged DNA duplexes.

A. Milov, Y. Vorobjev, N. Isaev, 2011, Molecular bioSystems.

73 Molecular dynamics approach for DNA duplex thermal stability prediction

Y. Vorobjev, A. Lomzov, D. Pyshnyi, 2013 .

Arrangement of 3'-terminus of tRNA on the human ribosome as revealed from cross-linking data.

Y. Vorobjev, A. Favre, C. Hountondji, 2008, Biochimie.

Model of the structure of the eukaryotic ribosomal translation termination complex

Y. Vorobjev, L. Kisselev, 2007, Molecular Biology.

A fast adaptive multigrid boundary element method for macromolecular electrostatic computations in a solvent

Harold A. Scheraga, Yury N. Vorobjev, H. Scheraga, 1997, J. Comput. Chem..

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

I. V. Alekseeva, Y. Vorobjev, N. Kuznetsov, 2019, Molecules.

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

Yury N. Vorobjev, Y. Vorobjev, 2009, J. Comput. Chem..

Conformational dynamics of abasic DNA upon interactions with AP endonuclease 1 revealed by stopped-flow fluorescence analysis.

Y. Vorobjev, V. Koval, O. Fedorova, 2012, Biochemistry.

In Silico Modeling and Conformational Mobility of DNA Duplexes

Y. Vorobjev, Y. Vorobjev, 2003, Molecular Biology.

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

I. V. Alekseeva, Y. Vorobjev, N. Kuznetsov, 2019, The journal of physical chemistry. B.

Role of hydrophobicity and solvent-mediated charge-charge interactions in stabilizing alpha-helices.

H. Scheraga, D. Ripoll, J. Vila, 1998, Biophysical journal.

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

Y. Vorobjev, N. Kuznetsov, O. Fedorova, 2019, The journal of physical chemistry. B.

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

Yury N. Vorobjev, Alexander V. Popov, Dmitry O. Zharkov, 2013, J. Comput. Chem..

A combined iterative and boundary-element approach for solution of the nonlinear Poisson-Boltzmann equation

Harold A. Scheraga, H. Scheraga, J. A. Grant, 1992 .

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

Yury N. Vorobjev, Y. Vorobjev, 2012, J. Comput. Chem..

Block‐units method for conformational calculations of large nucleic acid chains. II. The two‐hierarchical approach and its application to conformational arrangement of the unusual TψC loop of rabbit tRNAval

Y. Vorobjev, 1990, Biopolymers.

FAMBE-pH: a fast and accurate method to compute the total solvation free energies of proteins.

Harold A. Scheraga, Jorge A. Vila, Yury N. Vorobjev, 2008, The journal of physical chemistry. B.

Design of Effective Molecular Blocker of E Protein Channel as Anti SARS-Cov-2 Virus Drug

Y. Vorobjev, 2021 .

Modeling of the positioning of eRF1 and the mRNA stop codon explains the proximity of the eRF1 C domain to the stop codon in the ribosomal complex

Y. Vorobjev, L. Kisselev, 2008, Molecular Biology.

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

Yury N. Vorobjev, Jan Hermans, J. Hermans, 1999 .

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

H. Scheraga, B. Honig, B. Hitz, 1994 .