Author

B. Honig

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Biophysics· 4 Biochemistry· 1 Microbiology· 1

Signature Assays, Organisms & Methods

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Assay:protein structure· 4 Approach:statistical model· 4 Research Focus:protein folding & dynamics· 3 Approach:deep learning· 2 Organism:Drosophila· 2 Approach:experimental assay· 2 Organism:human· 2 Organism:bacteria (other)· 1

Frequent Co-Authors

L. Shapiro· 5 shared P. S. Katsamba· 5 shared A. P. Sergeeva· 4 shared S. Mannepalli· 3 shared F. Bahna· 2 shared F. Cosmanescu· 2 shared G. Ahlsen· 2 shared J. M. Sampson· 2 shared

Activity by Year

2020-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 39 mutual co-author links

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5 shared papersBiophysics

L. Shapiro

Mutual co-authors in cluster

Author profile →

6 papers

Recent·Most cited

Cis inhibition of co-expressed DIPs and Dprs shapes neural development

N. C. Morano, D. S. Lopez, H. Meltzer, A. P. Sergeeva, P. S. Katsamba, K. D. Rostam, H. P. Gupta, J. E. Becker, B. Bornstein, F. Cosmanescu, O. Schuldiner, B. Honig, R. S. Mann, L. Shapiro

The paper shows that DIPs and Dprs interact in cis within the same cells, regulating trans interactions and influencing neural development in Drosophila.

PLOS Biology · Mar 3, 2025Peer-reviewedBiochemistry

Robust prediction of relative binding energies for protein-protein complex mutations using free energy perturbation calculations

J. M. Sampson, D. A. Cannon, J. Duan, A. P. Sergeeva, J. C. K. Epstein, P. S. Katsamba, S. M. Mannepalli, F. A. Bahna, H. Adihou, S. M. Gueret, R. Gopalakrishnan, S. Geschwindner, D. G. Rees, A. Sigurdardottir, T. Wilkinson, , L. Wang

The paper benchmarks free energy perturbation calculations for predicting mutation effects on protein-protein binding affinity and introduces an automated method to improve accuracy.

bioRxiv · Apr 22, 2024Biophysics

Free energy perturbation calculations of mutation effects on SARS-CoV-2 RBD::ACE2 binding affinity

A. P. Sergeeva, P. S. Katsamba, J. M. Sampson, F. Bahna, S. Mannepalli, N. C. Morano, L. Shapiro, R. A. Friesner, B. Honig

This study uses free energy perturbation calculations to assess how mutations in SARS-CoV-2 RBD affect binding affinity to ACE2, showing FEP's superior accuracy in identifying stabilizing mutations.

bioRxiv · Aug 1, 2022Biophysics

How clustered protocadherin binding specificity is tuned for neuronal self/non-self-recognition

K. M. Goodman, P. S. Katsamba, R. Rubinstein, G. Ahlsen, F. Bahna, S. Mannepalli, H. Dan, R. Sampogna, L. Shapiro, B. Honig

This study investigates cPcdh interactions, showing promiscuous cis dimers and precise trans homophilic interactions, supporting their role in neuronal self/non-self-recognition.

bioRxiv · Jul 22, 2021Biophysics

A sweep of earth's virome reveals host-guided viral protein structural mimicry; with implications for human disease

G. Lasso, B. Honig, S. Shapira

The paper identifies over 6 million instances of viral protein structural mimicry across diverse hosts, revealing host-guided strategies and implications for human disease.

bioRxiv · Jun 18, 2020Microbiology

DIP/Dpr interactions and the evolutionary design of specificity in protein families

A. P. Sergeeva, P. S. Katsamba, F. Cosmanescu, J. J. Brewer, G. Ahlsen, S. Mannepalli, L. Shapiro, B. Honig

The paper investigates how specificity in DIP/Dpr protein interactions is achieved through negative constraints, using computational and experimental methods.

bioRxiv · Jan 13, 2020Biophysics