Trudeau, S.J., Hwang, H., Mathur, D., Begum, K., Petrey, D., Murray, D. and Honig, B. (2023) PrePCI: A Structure- and Chemical Similarity-Informed Database of Predicted Protein Compound Interactions. Protein Science e4594.

Petrey, D., Zhao, H., Trudeau, S., Murray, D. and Honig, B. (2023) PrePPI: A Structure Informed Proteome-Wide Database of Protein-Protein Interactions. J. of Mol. Biol. 435:168052. 

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.

Murray, D., Petrey, D. and Honig, B. (2021) Integrating 3D Structural Information into Systems Biology. J. Biol. Chem. 296:100562

Lasso, G., Honig, B. and Shapira, S. (2021) A Sweep of Earth’s Virome Reveals Host-Guided Viral Protein Structural Mimicry and Points to Determinants of Human Disease. Cell Systems. 12:82-91. Featured article.

Broyde, J., Simpson, D.R., Murray, D., Paull, E.O., Chu, B. W., Tagore, S., Jones, S.J., Griffin, A.T., Giorgi, F.M., Lachmann, A., Jackson, P., Sweet-Cordero, E.A., Honig, B. and Calfiano, A. (2021) Oncoprotein-specific molecular interaction maps (SigMaps) for cancer network analyses. Nature Biotech. 39:215-224.

Honig, B. and Shapiro, L. (2020) Adhesion Protein Structure, Molecular Affinities, and Principles of Cell-Cell Recognition. Cell 181:520-535.

Sergeeva, A.P., Katsamba, P.S., Cosmanescu, F., Brewer, J.J., Ahlsen, G., Mannepalli, S., Shapiro, L. and Honig B. (2020) DIP/Dpr Interactions and the Evolutionary Design of Specificity in Protein Families. Nature Comm. 11:2125.

Lasso, G., Mayer, S.V., Winkelmann, E.R., Chu, T., Elliot, O., Patino-Galindo, J.A., Park, K., Rabadan, R., Honig, B. and Shapira, S. (2019) A Structure Informed Atlas of Human-Virus Interactions. Cell 178:1526-1541.

• Highlight - Singh, A., (2019) Human-Virus Interactome Atlas. Nature Methods 16:1081.

Brasch, J., Goodman, K.M., Noble, A.J., Rapp, M., Mannepalli, S., Bahna, F., Dandey, V.P., Bepler, T., Berger, B., Maniatis, T., Potter, C.S., Carragher, B., Honig, B. and Shapiro, L. (2019) Visualization of Clustered Protocadherin Neuronal Self-Recognition Complexes. Nature 569:280-283.

Rubinstein, R., Thu, C.A., Goodman,K.M., Wolcott, H.N., Bahna, F., Mannepalli, S., Ahlsen, G., Chevee, M., Halim, A., Clausen, H., Maniatis, T., Shapiro, L. and Honig, B. (2015) Molecular Logic of Neuronal Self-recognition Through Protocadherin Domain Interactions. Cell 163:629-642.

Zhang, Q.C., Petrey, D., Deng, L., Qiang, L., Shi, Y., Thu, C.A., Bisikirska, B., Lefebvre, C., Accili, D., Hunter, T., Maniatis, T., Califano, A. and Honig, B. (2012) Structure-based Prediction of Protein-protein Interactions on a Genome-wide Scale. Nature 490:556 - 560.

Slattery, M., Riley, T., Liu, P., Abe, N., Gomez-Alcala, P., Dror, I., Zhou, T., Rohs, R., Honig, B., Bussemaker, H.J. and Mann, R.S. (2011) Cofactor Binding Evokes Latent Differences in DNA Binding Specificity Between Hox Proteins. Cell 147:1270-1282.

• Highlight - Ansari, A. and Peterson-Kaufman, K.J. (2011) A Partner Evokes Latent Differences Between Hox Proteins. Cell 147:1220.
• Highlight - Stower, H. (2011) Gene Regulation: Resolving Transcription Factor Binding. Nature Rev. Genet. 13:71.

Rohs, R., West, S.M., Sosinsky, A., Liu, P., Mann, R.S. and Honig, B. (2009) The Role of DNA Shape in Protein-DNA Recognition. Nature 461:1248-1253.

• Highlight - Tullis, T. (2009) Structural Biology: DNA Binding Shapes Up. Nature 461:1225-1226.
• Highlight - HHMI Chronicle In Brief. (2010) Double Helix, Revised. HHMI Bulletin. Feb:40-41.