List of works - Alexey Aleksandrov

300-Fold Increase in Production of the Zn2+-Dependent Dechlorinase TrzN in Soluble Form via Apoenzyme Stabilization

scientific article

A Molecular Mechanics Model for Flavins

scientific article published on 31 August 2019

A hybrid elastic band string algorithm for studies of enzymatic reactions

scientific article published on 10 May 2012

A molecular mechanics model for imatinib and imatinib:kinase binding

scientific article published in May 2010

Additive CHARMM force field for naturally occurring modified ribonucleotides

scientific article published on 3 February 2016

Additive CHARMM36 Force Field for Nonstandard Amino Acids

scientific article published on 19 May 2021

Advances and challenges in drug design against tuberculosis: application of in silico approaches

scientific article published on 26 November 2018

Alchemical free energy simulations for biological complexes: powerful but temperamental....

scientific article published on March 2010

Aminoacetylation Reaction Catalyzed by Leucyl-tRNA Synthetase Operates via a Self-Assisted Mechanism Using a Conserved Residue and the Aminoacyl Substrate

scientific article

An Overview of Electrostatic Free Energy Computations for Solutions and Proteins

Binding of tetracyclines to elongation factor Tu, the Tet repressor, and the ribosome: a molecular dynamics simulation study

scientific article published in December 2008

Combining the polarizable Drude force field with a continuum electrostatic Poisson-Boltzmann implicit solvation model

scientific article published on 08 May 2018

Computational modelling elucidates the mechanism of ciliary regulation in health and disease.

scientific article

Cyclization Reaction Catalyzed by Cyclodipeptide Synthases Relies on a Conserved Tyrosine Residue.

scientific article

Cyclodipeptide Synthases of the NYH Subfamily Recognize tRNA Using an α-Helix Enriched with Positive Residues

scientific article published on 17 December 2020

Efficient solvent boundary potential for hybrid potential simulations

scientific article published on 8 March 2011

Electrostatic free energies in translational GTPases: Classic allostery and the rest

scientific article

Identification of a second GTP-bound magnesium ion in archaeal initiation factor 2.

scientific article

Insights into molecular plasticity in protein complexes from Trm9-Trm112 tRNA modifying enzyme crystal structure

scientific article

Mechanism of activation of elongation factor Tu by ribosome: catalytic histidine activates GTP by protonation.

scientific article published on 17 July 2013

Molecular dynamics simulations of the 30S ribosomal subunit reveal a preferred tetracycline binding site

scientific article published in January 2008

Molecular dynamics simulations show that conformational selection governs the binding preferences of imatinib for several tyrosine kinases

scientific article published on 3 March 2010

Molecular mechanics models for tetracycline analogs

scientific article published in January 2009

Nonantibiotic properties of tetracyclines: structural basis for inhibition of secretory phospholipase A2

scientific article

Predicting the acid/base behavior of proteins: a constant-pH Monte Carlo approach with generalized born solvent

scientific article published in August 2010

Sampling the conformational energy landscape of a hyperthermophilic protein by engineering key substitutions

scientific article

Solvation and stabilization of palladium nanoparticles in phosphonium-based ionic liquids: a combined infrared spectroscopic and density functional theory study

scientific article published on 27 August 2014

Tet repressor induction by tetracycline: a molecular dynamics, continuum electrostatics, and crystallographic study

scientific article

Tetracycline-tet repressor binding specificity: insights from experiments and simulations

scientific article

The mechanism of citryl-coenzyme A formation catalyzed by citrate synthase

scientific article published on 22 April 2014

The structure of an E. coli tRNAfMet A1-U72 variant shows an unusual conformation of the A1-U72 base pair.

scientific article published on 31 January 2017

List of works by Alexey Aleksandrov

300-Fold Increase in Production of the Zn2+-Dependent Dechlorinase TrzN in Soluble Form via Apoenzyme Stabilization

A Molecular Mechanics Model for Flavins

A hybrid elastic band string algorithm for studies of enzymatic reactions

A molecular mechanics model for imatinib and imatinib:kinase binding

Additive CHARMM force field for naturally occurring modified ribonucleotides

Additive CHARMM36 Force Field for Nonstandard Amino Acids

Advances and challenges in drug design against tuberculosis: application of in silico approaches

Alchemical free energy simulations for biological complexes: powerful but temperamental....

Aminoacetylation Reaction Catalyzed by Leucyl-tRNA Synthetase Operates via a Self-Assisted Mechanism Using a Conserved Residue and the Aminoacyl Substrate

An Overview of Electrostatic Free Energy Computations for Solutions and Proteins

Binding of tetracyclines to elongation factor Tu, the Tet repressor, and the ribosome: a molecular dynamics simulation study

Combining the polarizable Drude force field with a continuum electrostatic Poisson-Boltzmann implicit solvation model

Computational modelling elucidates the mechanism of ciliary regulation in health and disease.

Cyclization Reaction Catalyzed by Cyclodipeptide Synthases Relies on a Conserved Tyrosine Residue.

Cyclodipeptide Synthases of the NYH Subfamily Recognize tRNA Using an α-Helix Enriched with Positive Residues

Efficient solvent boundary potential for hybrid potential simulations

Electrostatic free energies in translational GTPases: Classic allostery and the rest

Identification of a second GTP-bound magnesium ion in archaeal initiation factor 2.

Insights into molecular plasticity in protein complexes from Trm9-Trm112 tRNA modifying enzyme crystal structure

Mechanism of activation of elongation factor Tu by ribosome: catalytic histidine activates GTP by protonation.

Molecular dynamics simulations of the 30S ribosomal subunit reveal a preferred tetracycline binding site

Molecular dynamics simulations show that conformational selection governs the binding preferences of imatinib for several tyrosine kinases

Molecular mechanics models for tetracycline analogs

Nonantibiotic properties of tetracyclines: structural basis for inhibition of secretory phospholipase A2

Predicting the acid/base behavior of proteins: a constant-pH Monte Carlo approach with generalized born solvent

Sampling the conformational energy landscape of a hyperthermophilic protein by engineering key substitutions

Solvation and stabilization of palladium nanoparticles in phosphonium-based ionic liquids: a combined infrared spectroscopic and density functional theory study

Tet repressor induction by tetracycline: a molecular dynamics, continuum electrostatics, and crystallographic study

Tetracycline-tet repressor binding specificity: insights from experiments and simulations

The mechanism of citryl-coenzyme A formation catalyzed by citrate synthase

The structure of an E. coli tRNAfMet A1-U72 variant shows an unusual conformation of the A1-U72 base pair.