Dr. Anastasia Bakulina

Structural bioinformatician, protein designer

Research Expertise

molecular biology
bioinformatics

About

I have more than 20 years of experience as a freelancing biologist. I were involved in projects related to molecular biology, virology, human genetics, human aging and longevity, developing of scientific software, protein design. If you have a brilliant idea for a biotech startup I can explain why it would fail. If you are already in this, I can help as a problem solver.

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Publications

The properties of Bacillus cereus hemolysin II pores depend on environmental conditions
Biochimica et Biophysica Acta (BBA) - Biomembranes
2007
Extracellular Phosphorylation of Collagen XVII by Ecto-Casein Kinase 2 Inhibits Ectodomain Shedding
Journal of Biological Chemistry
2007
Model structure of the immunodominant surface antigen of Eimeria tenella identified as a target for sporozoite-neutralizing monoclonal antibody
Parasitology Research
2009
The N Termini of a-Subunit Isoforms Are Involved in Signaling between Vacuolar H+-ATPase (V-ATPase) and Cytohesin-2*
Journal of Biological Chemistry
2013
Specific motifs of the V-ATPase a2-subunit isoform interact with catalytic and regulatory domains of ARNO
Biochimica et Biophysica Acta (BBA) - Bioenergetics
2010
Broadly Neutralizing Antibodies against HIV-1 As a Novel Aspect of the Immune Response
Acta Naturae
2015
Cationic Polymers for the Delivery of the Ebola DNA Vaccine Encoding Artificial T-Cell Immunogen
Vaccines
2020
Selection of Peptide Mimics of HIV-1 Epitope Recognized by Neutralizing Antibody VRC01
PLOS ONE
2015
In silico design of influenza a virus artificial epitope-based T-cell antigens and the evaluation of their immunogenicity in mice
Journal of Biomolecular Structure and Dynamics
2020
A Novel Approach to the Development of Anticarcinogenic Vaccines
Acta Naturae
2010
HIV-1 Gag Matrix Protein Fragments and Polyacid Conjugates Designed for the HIV Inhibition
Antiviral Research
2009
Design and Visualization of DNA/RNA Nanostructures from Branched Oligonucleotides Using Blender Software
Russian Journal of Bioorganic Chemistry
2019
Structural model of a2‐subunit N‐terminus and its binding interface for cytohesin‐2: Implication for regulation of V‐ATPase function
The FASEB Journal
2013
Purification and cytotoxic properties of Bacillus cereus hemolysin II
Protein Expression and Purification
2006
Template-Assisted Assembly of DNA Nanostructures from Branched Oligonucleotides
Russian Journal of Bioorganic Chemistry
2021
Unipro UGENE: a unified bioinformatics toolkit
Bioinformatics
2012
The role of CCR5 chemokine ligands and antibodies to CCR5 coreceptors in preventing HIV infection
Trends in Immunology
2002
BGRS\SB 2018 Committee
2018 11th International Multiconference Bioinformatics of Genome Regulation and Structure\Systems Biology (BGRS\SB)
2018
An interaction of Zika virus envelope fragments with serum antibodies derived from subjects after flavivirus infections
Russian Journal of Infection and Immunity
2020
Structural model of cytosolic N-terminus of a2-subunit isoform of V-ATPase: Identification and characterization of two binding interfaces for cytohesin-2
Biochimica et Biophysica Acta (BBA) - Bioenergetics
2014
V‐ATPase is a novel evolutionarily conserved cytohesin‐signaling receptor
The FASEB Journal
2013
Introduction of foreign peptides in surface loops of alkaline phosphatase
Molecular Biology
2012
Ligand‐induced conformational changes in cytochrome P450 3A4 detected by luminescence resonance energy transfer (LRET)
The FASEB Journal
2012
Peculiarities of interaction of monoclonal antibody B2 with polycyclic aromatic hydrocarbons and peptide-mimotope of benzo[a]pyrene
Molecular Biology
2010
Excess properties of Lennard-Jones binary mixtures from computer simulation and theory
Molecular Physics
2002
Harmonic analysis of Lennard-Jones FCC grain boundaries
Modelling and Simulation in Materials Science and Engineering
1998
Army Gas-Cooled Reactor Systems Program. Outline of operating and maintenance procedures for fuel element replacement equipment ML-1 Mobile Nuclear Power Plant
Unknown Venue
1963
Molecular dynamics simulation of a Lennard-Jones triatomic - time autocorrelation functions
Advances in Molecular Relaxation and Interaction Processes
1982
Template-Assisted Assembly of Hybrid DNA/RNA Nanostructures Using Branched Oligodeoxy- and Oligoribonucleotides
International Journal of Molecular Sciences
2023
Biochemical and technological properties of moose (<i>Alces alces</i>) recombinant chymosin
Vavilov Journal of Genetics and Breeding
2022
Amyloidogenicity as a driving force for the formation of functional oligomers
Journal of Structural Biology
2020
Characterization of the Altai Maral Chymosin Gene, Production of a Chymosin Recombinant Analog in the Prokaryotic Expression System, and Analysis of Its Several Biochemical Properties
Biochemistry (Moscow)
2020
The Structural and Immunological Properties of Chimeric Proteins Containing HIV-1 MPER Sites
Acta Naturae
2019
Structural model of a2-subunit N-terminus and its binding interface for Arf-GEF CTH2: Implication for regulation of V-ATPase, CTH2 function and rational drug design
Current Topics in Membranes
2019
Establishment of Constraints on Amyloid Formation Imposed by Steric Exclusion of Globular Domains
Journal of Molecular Biology
2018
Humoral immunity to influenza in an at-risk population and severe influenza cases in Russia in 2016–2017
Archives of Virology
2018
Classification of β-hairpin repeat proteins
Journal of Structural Biology
2018
New intronic splicing mutation in the LMNA gene causing progressive cardiac conduction defects and variable myopathy
Gene
2016
Induction of an antitumor response using dendritic cells transfected with DNA constructs encoding the HLA-A*02:01-restricted epitopes of tumor-associated antigens in culture of mononuclear cells of breast cancer patients
Immunologic Research
2015
Artificial polyepitope HIV-1 immunogen containing mimotope of 2F5 epitope
Protein & Peptide Letters
2016
WITHDRAWN: Tetravalent Bispecific Single-Chain Fv Antibodies for Lysis of Leukemia Cells by Autologous T Cells
Journal of Molecular Biology
2012
Interaction of Mesalasine (5-ASA) with Translational Initiation Factors eIF4 Partially Explains 5-ASA Anti-Inflammatory and Anti-Neoplastic Activities
Medicinal Chemistry
2011
FILTREST3D: discrimination of structural models using restraints from experimental data
Bioinformatics
2010
Prediction of antigenically active regions in the OmpF-like porin of Yersinia pseudotuberculosis
Doklady Biochemistry and Biophysics
2007

Education

Novosibirsk State University

M.S., Physics / June, 2003

Novosibirsk

Ph.D, Molecular Biology / October, 2010

Koltsovo

Experience

Новосибирский государственный университет

зав.лабораторией / July, 2015February, 2022

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