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structural biology, molecular modeling, protein design, artificial intelligence

Biography

My interests lie at the intersection of computational structural biology and artificial intelligence.

At the university, I decided that science is more important to me than taking classes, so I devoted most of my time and energy to research. From 2018 to 2021 I worked in the Virtual Structural Biology Group to study cardiovascular diseases. There I learned molecular modeling and structural biology of proteins and nucleic acids. In 2020 I decided to expand my horizons to Alzheimer's disease and started to investigate the effect of ions on the aggregation of amyloid fibrils in the Strodel lab at Forschungszentrum Jülich IBI-7. Since 2021, I joined Victor Greiff’s lab in Oslo, where I am working on antibody developability and modeling benchmarking projects on computational structural immunology and antibody design. At the same time, I started to work with Shuguang Zhang at the Laboratory of Molecular Architecture at MIT, where I am investigating water-soluble membrane proteins using various bioinformatician methods. Later that year I became a member of Sergey Ovchinnikov's lab at Harvard, where I am studying AlphaFold2 in the contest of protein de novo design. Aiming to open my own drug design startup in the future, I joined Biosim.AI in 2022 to boost my industrial skills. There I learned how biotech companies combined MD, AI, and quantum chemistry to accelerate the drug design process.

Activities

Employment (2)

University of Oslo: Oslo, NO

2024-07-12 to 2027-07-11 | PhD Research Fellow (Department of Immunology)
Employment
Source: Self-asserted source
Eva Smorodina

University of Oslo: Oslo, NO

2022-07-05 to 2024-07-11 | Research Assistant (Department of Immunology)
Employment
Source: Self-asserted source
Eva Smorodina

Education and qualifications (1)

University of Oxford: Oxford, Oxfordshire, GB

(Doctoral Training Centre (MPLS); New College)
Education
Source: check_circle
ORCID Integration at the University of Oxford

Works (19)

Computational engineering of water-soluble human potassium ion channels through QTY transformation

Scientific Reports
2024-11-15 | Journal article
Contributors: Eva Smorodina; Fei Tao; Rui Qing; Steve Yang; Shuguang Zhang
Source: check_circle
Crossref

Assessing AF2’s ability to predict structural ensembles of proteins

Structure
2024-09 | Journal article
Part of ISSN: 0969-2126
Contributors: Jakob R. Riccabona; Fabian C. Spoendlin; Anna-Lena M. Fischer; Johannes R. Loeffler; Patrick K. Quoika; Timothy P. Jenkins; James A. Ferguson; Eva Smorodina; Andreas H. Laustsen; Victor Greiff et al.
Source: Self-asserted source
Eva Smorodina

Biophysical cartography of the native and human-engineered antibody landscapes quantifies the plasticity of antibody developability

Communications Biology
2024-07-31 | Journal article
Contributors: Habib Bashour; Eva Smorodina; Matteo Pariset; Jahn Zhong; Rahmad Akbar; Maria Chernigovskaya; Khang Lê Quý; Igor Snapkow; Puneet Rawat; Konrad Krawczyk et al.
Source: check_circle
Crossref

Structural bioinformatics studies of glutamate transporters and their AlphaFold2 predicted water-soluble QTY variants and uncovering the natural mutations of L->Q, I->T, F->Y and Q->L, T->I and Y->F

PLOS ONE
2024-04-10 | Journal article
Contributors: Alper Karagöl; Andreia Cristina Karklin Mortensen; Taner Karagöl; Eva Smorodina; Shuguang Zhang
Source: check_circle
Crossref

Structural bioinformatics studies of six human ABC transporters and their AlphaFold2-predicted water-soluble QTY variants

QRB Discovery
2024-01-19 | Journal article
Part of ISSN: 2633-2892
Contributors: Emily Pan; Fei Tao; Eva Smorodina; Shuguang Zhang
Source: Self-asserted source
Eva Smorodina
grade
Preferred source (of 2)‎

Effects of ion type and concentration on the structure and aggregation of the amyloid peptide Aβ16−22$$ {\boldsymbol{\beta}}_{16-22} $$

Proteins: Structure, Function, and Bioinformatics
2023-11-14 | Journal article
Contributors: Eva Smorodina; Batuhan Kav; Hebah Fatafta; Birgit Strodel
Source: check_circle
Crossref

Biophysical cartography of the native and human-engineered antibody landscapes quantifies the plasticity of antibody developability

2023-10-30 | Preprint
Contributors: Habib Bashour; Eva Smorodina; Matteo Pariset; Jahn Zhong; Rahmad Akbar; Maria Chernigovskaya; Khang Lê Quý; Igor Snapkov; Puneet Rawat; Konrad Krawczyk et al.
Source: check_circle
Crossref

Scalable biomimetic sensing system with membrane receptor dual-monolayer probe and graphene transistor arrays

Science Advances
2023-07-21 | Journal article
Contributors: Rui Qing; Mantian Xue; Jiayuan Zhao; Lidong Wu; Andreas Breitwieser; Eva Smorodina; Thomas Schubert; Giovanni Azzellino; David Jin; Jing Kong et al.
Source: check_circle
Crossref

Toward real-world automated antibody design with combinatorial Bayesian optimization

Cell Reports Methods
2023-01 | Journal article
Part of ISSN: 2667-2375
Contributors: Asif Khan; Alexander I. Cowen-Rivers; Antoine Grosnit; Derrick-Goh-Xin Deik; Philippe A. Robert; Victor Greiff; Eva Smorodina; Puneet Rawat; Rahmad Akbar; Kamil Dreczkowski et al.
Source: Self-asserted source
Eva Smorodina

AntBO: Towards Real-World Automated Antibody Design with Combinatorial Bayesian Optimisation

2022 | Preprint
Contributors: Asif Khan; Alexander I. Cowen-Rivers; Antoine Grosnit; Derrick-Goh-Xin Deik; Philippe A. Robert; Victor Greiff; Eva Smorodina; Puneet Rawat; Kamil Dreczkowski; Rahmad Akbar et al.
Source: Self-asserted source
Eva Smorodina

Comparing 2 crystal structures and 12 AlphaFold2-predicted human membrane glucose transporters and their water-soluble glutamine, threonine and tyrosine variants

QRB Discovery
2022 | Journal article
Contributors: Eva Smorodina; Fei Tao; Rui Qing; David Jin; Steve Yang; Shuguang Zhang
Source: check_circle
Crossref

Progress and challenges for the machine learning-based design of fit-for-purpose monoclonal antibodies

mAbs
2022-12-31 | Journal article
Contributors: Rahmad Akbar; Habib Bashour; Puneet Rawat; Philippe A. Robert; Eva Smorodina; Tudor-Stefan Cotet; Karine Flem-Karlsen; Robert Frank; Brij Bhushan Mehta; Mai Ha Vu et al.
Source: check_circle
Crossref

Unconstrained generation of synthetic antibody–antigen structures to guide machine learning methodology for antibody specificity prediction

Nature Computational Science
2022-12-19 | Journal article
Contributors: Philippe A. Robert; Rahmad Akbar; Robert Frank; Milena Pavlović; Michael Widrich; Igor Snapkov; Andrei Slabodkin; Maria Chernigovskaya; Lonneke Scheffer; Eva Smorodina et al.
Source: check_circle
Crossref

Structural informatic study of determined and AlphaFold2 predicted molecular structures of 13 human solute carrier transporters and their water-soluble QTY variants

Scientific Reports
2022-11-22 | Journal article
Contributors: Eva Smorodina; Igor Diankin; Fei Tao; Rui Qing; Steve Yang; Shuguang Zhang
Source: check_circle
Crossref

Development of a High-Affinity Antibody against the Tumor-Specific and Hyperactive 611-p95HER2 Isoform

Cancers
2022-10-05 | Journal article
Contributors: Esmaeil Dorraji; Elin Borgen; Dario Segura-Peña; Puneet Rawat; Eva Smorodina; Claire Dunn; Victor Greiff; Nikolina Sekulić; Hege Russnes; Jon Amund Kyte
Source: check_circle
Crossref
grade
Preferred source (of 2)‎

Protein Design: From the Aspect of Water Solubility and Stability

Chemical Reviews
2022-09-28 | Journal article
Part of ISSN: 0009-2665
Part of ISSN: 1520-6890
Contributors: Rui Qing; Shilei Hao; Eva Smorodina; David Jin; Arthur Zalevsky; Shuguang Zhang
Source: Self-asserted source
Eva Smorodina

Study of determined and AlphaFold2 predicted molecular structures of 13 human solute carrier transporters and their water-soluble QTY variants

2022-08-23 | Preprint
Contributors: Eva Smorodina; Igor Diankin; Fei Tao; Rui Qing; Steve Yang; Shuguang Zhang
Source: Self-asserted source
Eva Smorodina

Comparing Native Crystal Structures and AlphaFold2 Predicted Water-Soluble G Protein-Coupled Receptor QTY Variants

Life
2021-11 | Journal article | Author
Contributors: Michael A. Skuhersky; Fei Tao; Rui Qing; Eva Smorodina; David Jin; Shuguang Zhang
Source: check_circle
Multidisciplinary Digital Publishing Institute
grade
Preferred source (of 2)‎

Unconstrained generation of synthetic antibody-antigen structures to guide machine learning methodology for real-world antibody specificity prediction

2021-07-08 | Preprint
Contributors: Philippe A. Robert; Rahmad Akbar; Robert Frank; Milena Pavlović; Michael Widrich; Igor Snapkov; Andrei Slabodkin; Maria Chernigovskaya; Lonneke Scheffer; Eva Smorodina et al.
Source: check_circle
Crossref

Peer review (3 reviews for 2 publications/grants)

Review activity for Cell systems. (2)
Review activity for PloS one. (1)