Modeling the Solvation Sites in Rare-Gas Matrices with the Simulated Annealing Monte Carlo Technique. - Alexander A. Moskovsky; Alexander V. Nemukhin (J. Chem. Inf. Comput. Sci., 1999)

Flexible effective fragment QM/MM method: Validation through the challenging tests. - Alexander V. Nemukhin; Bella L. Grigorenko; Igor A. Topol; Stanley K. Burt (J. Comput. Chem., 2003)

Quantum chemical modeling of the reduction of cis-diammineplatinum(IV) tetrachloride [Pt(NH3)2Cl4] by methyl thiolate anion. - Ia. I. Dobrogorskaia-Méreau; Alexander V. Nemukhin (J. Comput. Chem., 2005)

Mechanism of proteolysis in matrix metalloproteinase-2 revealed by QM/MM modeling. - Tatiana Vasilevskaya; Maria G. Khrenova; Alexander V. Nemukhin; Walter Thiel (J. Comput. Chem., 2015)

Multi-Scale Supercomputing of Large Molecular Aggregates: A Case Study of the Light-Harvesting Photosynthetic Center. - Alexander V. Nemukhin; Igor V. Polyakov; Alexander A. Moskovsky (Supercomput. Front. Innov., 2015)

Methodological aspects of QM/MM calculations: A case study on matrix metalloproteinase-2. - Tatiana Vasilevskaya; Maria G. Khrenova; Alexander V. Nemukhin; Walter Thiel (J. Comput. Chem., 2016)

Role of Protein Dimeric Interface in Allosteric Inhibition of N-Acetyl-Aspartate Hydrolysis by Human Aspartoacylase. - Ekaterina D. Kots; Sofya V. Lushchekina; Sergey D. Varfolomeev; Alexander V. Nemukhin (J. Chem. Inf. Model., 2017)

Benchmarking Quantum Chemistry Methods in Calculations of Electronic Excitations. - Bella L. Grigorenko; Vladimir A. Mironov; Igor V. Polyakov; Alexander V. Nemukhin (Supercomput. Front. Innov., 2018)

Allosteric Control of N-Acetyl-Aspartate Hydrolysis by the Y231C and F295S Mutants of Human Aspartoacylase. - Ekaterina D. Kots; Maria G. Khrenova; Alexander V. Nemukhin (J. Chem. Inf. Model., 2019)

Dipole Moment Variation Clears Up Electronic Excitations in the π-Stacked Complexes of Fluorescent Protein Chromophores. - Maria G. Khrenova; Fedor D. Mulashkin; Egor S. Bulavko; Tatiana M. Zakharova; Alexander V. Nemukhin (J. Chem. Inf. Model., 2020)

Computational Characterization of the Substrate Activation in the Active Site of SARS-CoV-2 Main Protease. - Maria G. Khrenova; Vladimir G. Tsirelson; Alexander V. Nemukhin (Supercomput. Front. Innov., 2020)

Computational Modeling of the SARS-CoV-2 Main Protease Inhibition by the Covalent Binding of Prospective Drug Molecules. - Alexander V. Nemukhin; Bella L. Grigorenko; Igor V. Polyakov; Sofya V. Lushchekina (Supercomput. Front. Innov., 2020)

Light-Induced Change of Arginine Conformation Modulates the Rate of Adenosine Triphosphate to Cyclic Adenosine Monophosphate Conversion in the Optogenetic System Containing Photoactivated Adenylyl Cyclase. - Maria G. Khrenova; Anna M. Kulakova; Alexander V. Nemukhin (J. Chem. Inf. Model., 2021)

Modeling Spectral Tuning in Red Fluorescent Proteins Using the Dipole Moment Variation upon Excitation. - Maria G. Khrenova; Fedor D. Mulashkin; Alexander V. Nemukhin (J. Chem. Inf. Model., 2021)