Alina Sergeeva


Associate Research Scientist

Alina Sergeeva is an associate research scientist in the Honig Lab. She joined the Honig Lab in 2012 as a postdoctoral research scientist. Prior to this, Alina was involved in fundamental research aimed at predicting structure and rationalizing stability and chemical bonding of various chemical species, from clusters and multiply charged anions to organometallic complexes and solid state materials. A desire to understand the behavior of molecules and chemical reactions at the molecular level brought Alina into quantum chemistry. Having figured how to deal with single molecules by applying ab initio methods, she has been learning to use methods from biophysics and bioinformatics to study the structure and function of proteins. In particular, Alina is currently investigating how biological specificity is encoded on structures of various cell adhesion molecules.

Education History

PhD, Utah State University 
Theoretical and Computational Chemistry

BS, Peoples Friendship University of Russia


The following is a list of selected publications. Visit Alina's website for a full list.

Sergeeva, A.P. , Katsamba, P.S., Liao, J., Sampson, J.M., Bahna, F., Mannepalli, S., Morano, N.C., Shapiro, L., Friesner, R.A. and Honig, B. (2023) Free Energy Perturbation Calculations of Mutation Effects on SARS-CoV-2 RBD::ACE2 Binding Affinity. J. Mol. Biol. 435:168187.

Xu, S., Sergeeva, A.P. , Katsamba, P.S., Mannepalli, S., Bimela, J., Zipursky, S.L., Shapiro, L, Honig, B. and Zinn, Kai. (2022) Affinity Requirements for Control of Synaptic Targeting and Neuronal Cell Survival by Heterophilic IgSF Cell Adhesion Molecules. Cell Reports 39:110618.

Troyanovsky, R.B., Sergeeva, A.P., Indra, I., Chen, C.-S., Kato, R., Shapiro, L., Honig, B. and Troyanovsky, S.M. (2021) Sorting Of Cadherin-Catenin-Associated Proteins Into Individual Clusters. Proc. Natl. Acad. of Sci. 118:e2105550118.

Sergeeva AP,  Katsamba PS, Cosmanescu F, Brewer JJ, Ahlsen G, Mannepalli S,  Shapiro L, Honig B. DIP/Dpr interactions and the evolutionary design of specificity in protein families. Nat. Commun. 2020 11:2125.

Sergeeva AP, Popov IA, Piazza ZA, Li WL, Romanescu C, Wang LS, Boldyrev AI. Understanding boron through size-selected clusters: structure, chemical bonding, and fluxionality. Acc Chem Res. 2014 Apr 15;47(4):1349-58.

Sergeeva AP, Piazza ZA, Romanescu C, Li WL, Boldyrev AI, Wang LS. B22- and B23-: all-boron analogues of anthracene and phenanthrene. J Am Chem Soc. 2012 Oct 31;134(43):18065-73.

Zhang J, Sergeeva AP, Sparta M, Alexandrova AN. B13+: a photodriven molecular Wankel engine. Angew Chem Int Ed Engl. 2012 Aug 20;51(34):8512-5.

Sergeeva AP, Boldyrev AI. δ-Bonding in the [Pd44-C9H9)(μ4-C8H8)]+ sandwich complex. Phys Chem Chem Phys. 2010 Oct 14;12(38):12050-4.

Sergeeva AP, Boldyrev AI. Flattening a puckered pentasilacyclopentadienide ring by suppression of the pseudo Jahn-Teller effect. Organometallics. 2010;29(17):3951-3954.

Huang W, Sergeeva AP, Zhai HJ, Averkiev BB, Wang LS, Boldyrev AI. A concentric planar doubly π-aromatic B19- cluster. Nat Chem. 2010 Mar;2(3):202-6.