Vol. 9 No. 2 (2022): Special Issue on Supercomputing in Computational Biology and Molecular Modeling of Living Systems

Call For Papers: https://superfri.org/index.php/superfri/special-issue-vol9-no2-2022

Invited Editors:

Dr. Alexander Nemukhin (Faculty of Chemistry, Lomonosov Moscow State University, Moscow, Russia)
Dr. Konstantin Shaitan (Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia)
Dr. Vytas Švedas (Faculty of Bioengineering and Bioinformatics, Research Computing Center, Lomonosov Moscow State University, Moscow, Russia)

DOI: https://doi.org/10.14529/jsfi2202

Published: 2022-11-07

View or download the full issue:

Articles

Computational Characterization of N-acetylaspartylglutamate Synthetase: From the Protein Primary Sequence to Plausible Catalytic Mechanism

Igor V. Polyakov, Artem E. Kniga, Alexander V. Nemukhin

4-13

DOI: https://doi.org/10.14529/jsfi220201
- PDF
Predicting the Activity of Boronate Inhibitors Against Metallo-β-lactamase Enzymes

Elena O. Levina, Maria G. Khrenova, Vladimir G. Tsirelson

14-32

DOI: https://doi.org/10.14529/jsfi220202
- PDF
Predicting Binding Free Energies for DPS Protein-DNA Complexes and Crystals Using Molecular Dynamics

Eduard V. Tereshkin, Ksenia B. Tereshkina, Yurii F. Krupyanskii

33-45

DOI: https://doi.org/10.14529/jsfi220203
- PDF
Computational Modeling of the Interaction of Molecular Oxygen with the Flavin-dependent Enzyme RutA

Igor V. Polyakov, Tatiana M. Domratcheva, Anna M. Kulakova, Alexander V. Nemukhin, Bella L. Grigorenko

46-55

DOI: https://doi.org/10.14529/jsfi220204
- PDF
Analysis of Ion Atmosphere Around Nucleosomes Using Supercomputer MD Simulations

Nikita A. Kosarim, Grigoriy A. Armeev, Mikhail P. Kirpichnikov, Alexey K. Shaytan

56-67

DOI: https://doi.org/10.14529/jsfi220205
- PDF
Molecular Modeling of Penicillin Acylase Binding with a Penicillin Nucleus by High Performance Computing: Can Enzyme or its Mutants Possess β-lactamase Activity?

Evgeny M. Kirilin, Anna A. Bochkova, Nikolay V. Panin, Igor V. Pochinok, Vytas Švedas

68-78

DOI: https://doi.org/10.14529/jsfi220206
- PDF
Search for Ligands Complementary to the 430-cavity of Influenza Virus Neuraminidase by Virtual Screening

Dmitry K. Nilov, Michaela Schmidtke, Vadim A. Makarov, Vytas K. Švedas

79-83

DOI: https://doi.org/10.14529/jsfi220207
- PDF

Vol. 9 No. 2 (2022): Special Issue on Supercomputing in Computational Biology and Molecular Modeling of Living Systems

Articles

Computational Characterization of N-acetylaspartylglutamate Synthetase: From the Protein Primary Sequence to Plausible Catalytic Mechanism

Predicting the Activity of Boronate Inhibitors Against Metallo-β-lactamase Enzymes

Predicting Binding Free Energies for DPS Protein-DNA Complexes and Crystals Using Molecular Dynamics

Computational Modeling of the Interaction of Molecular Oxygen with the Flavin-dependent Enzyme RutA

Analysis of Ion Atmosphere Around Nucleosomes Using Supercomputer MD Simulations

Molecular Modeling of Penicillin Acylase Binding with a Penicillin Nucleus by High Performance Computing: Can Enzyme or its Mutants Possess β-lactamase Activity?

Search for Ligands Complementary to the 430-cavity of Influenza Virus Neuraminidase by Virtual Screening

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