Honig, Barry

The role of DNA shape in protein–DNA recognition

Rohs, R., West, S. M., Sosinsky, A., Liu, P., Mann, R. S., & Honig, B. (2009) · Nature

DNA and Nucleic Acid ChemistryDiffusion and Search Dynamics

Cited by 1,096

Structure-based prediction of protein–protein interactions on a genome-wide scale

Zhang, Q. C., Petrey, D., Deng, L., Qiang, L., Shi, Y., Thu, C. A., Bisikirska, B., Lefebvre, C., Accili, D., Hunter, T., et al. (2012) · Nature

Bioinformatics and Genomic NetworksProtein Structure and Dynamics

Cited by 723

An external point-charge model for bacteriorhodopsin to account for its purple color

Nakanishi, K., Balogh-Nair, V., Arnaboldi, M., Tsujimoto, K., & Honig, B. (1980) · Journal of the American Chemical Society

Photoreceptor and optogenetics researchPhotochemistry and Electron Transfer Studies

Cited by 327

Protein interface conservation across structure space

Zhang, Q. C., Petrey, D., Norel, R., & Honig, B. H. (2010) · Proceedings of the National Academy of Sciences

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 156

A structure-informed atlas of human-virus interactions

Lasso, G., Mayer, S. V., Winkelmann, E. R., Chu, T., Elliot, O., Patino-Galindo, J. A., Park, K., Rabadan, R., Honig, B., & Shapira, S. D. (2019) · Cell

Bioinformatics and Genomic Networksvaccines and immunoinformatics approaches

Cited by 133

Visualization of clustered protocadherin neuronal self-recognition complexes

Brasch, J., Goodman, K. M., Noble, A. J., Rapp, M., Mannepalli, S., Bahna, F., Dandey, V. P., Bepler, T., Berger, B., Maniatis, T., et al. (2019) · Nature

Axon Guidance and Neuronal SignalingNeuroscience and Neuropharmacology Research

Cited by 99

Free energy perturbation calculation of relative binding free energy between broadly neutralizing antibodies and the gp120 glycoprotein of HIV-1

Clark, A. J., Gindin, T., Zhang, B., Wang, L., Abel, R., Murret, C. S., Xu, F., Bao, A., Lu, N. J., Zhou, T., et al. (2017) · Journal of Molecular Biology

Protein Structure and DynamicsComputational Drug Discovery Methods

Cited by 96

Neuron-subtype-specific expression, interaction affinities, and specificity determinants of DIP/Dpr cell recognition proteins

Cosmanescu, F., Katsamba, P. S., Sergeeva, A. P., Ahlsen, G., Patel, S. D., Brewer, J. J., Tan, L., Xu, S., Xiao, Q., Nagarkar-Jaiswal, S., et al. (2018) · Neuron

Axon Guidance and Neuronal SignalingNeurobiology and Insect Physiology Research

Cited by 78

PrePPI: A structure informed proteome-wide database of protein-protein interactions

Petrey, D., Zhao, H., Trudeau, S., Murray, D., & Honig, B. (2023) · Journal of Molecular Biology

Bioinformatics and Genomic NetworksProtein Structure and Dynamics

Cited by 49

Lipids Regulate Lck Protein Activity through Their Interactions with the Lck Src Homology 2 Domain

Sheng, R., Jung, D.-J., Silkov, A., Kim, H., Singaram, I., Wang, Z.-G., Xin, Y., Kim, E., Park, M.-J., Thiagarajan-Rosenkranz, P., et al. (2016) · Journal of Biological Chemistry

Lipid Membrane Structure and BehaviorProtein Kinase Regulation and GTPase Signaling

Cited by 43

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

Sergeeva, A. P., Katsamba, P. S., Cosmanescu, F., Brewer, J. J., Ahlsen, G., Mannepalli, S., Shapiro, L., & Honig, B. (2020) · Nature Communications

Protein Structure and DynamicsAxon Guidance and Neuronal Signaling

Cited by 38

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

Sergeeva, A. P., Katsamba, P. S., Liao, J., Sampson, J. M., Bahna, F., Mannepalli, S., Morano, N. C., Shapiro, L., Friesner, R. A., & Honig, B. (2023) · Journal of Molecular Biology

SARS-CoV-2 and COVID-19 ResearchProtein Structure and Dynamics

Cited by 27

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

Sampson, J. M., Cannon, D. A., Duan, J., Epstein, J. C. K., Sergeeva, A. P., Katsamba, P. S., Mannepalli, S. M., Bahna, F. A., Adihou, H., Guéret, S. M., et al. (2024) · Journal of Molecular Biology

Protein Structure and DynamicsComputational Drug Discovery Methods

Cited by 24

PrePCI: A structure- and chemical similarity-informed database of predicted protein compound interactions

Trudeau, S. J., Hwang, H., Mathur, D., Begum, K., Petrey, D., Murray, D., & Honig, B. (2022) · Protein Science

Computational Drug Discovery MethodsProtein Interaction Studies and Fluorescence Analysis

Cited by 16

PrePCI : A structure‐ and chemical similarity‐informed database of predicted protein compound interactions

Trudeau, S. J., Hwang, H., Mathur, D., Begum, K., Petrey, D., Murray, D., & Honig, B. (2023) · Protein Science

Computational Drug Discovery MethodsProtein Interaction Studies and Fluorescence Analysis

Cited by 16