Author

D. L. Lynch

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· 2 Biochemistry· 1

Signature Assays, Organisms & Methods

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Assay:structural biology· 3 Research Focus:protein folding & dynamics· 2 Approach:experimental assay· 1 Research Focus:host-pathogen & immune response· 1 Organism:human· 1 Approach:machine learning (classical)· 1 Approach:mechanistic / dynamical model· 1 Organism:virus· 1

Frequent Co-Authors

A. Acharya· 2 shared A. Pavlova· 2 shared C. Chipot· 2 shared J. C. Gumbart· 2 shared J. M. Parks· 2 shared Y. T. Pang· 2 shared A. A. Golosov· 1 shared A. Kovalevsky· 1 shared

Activity by Year

2020-2024 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 36 mutual co-author links

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2 shared papersBiophysics

A. Acharya

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3 papers

Recent·Most cited

Substrate recognition mechanism of the endoplasmic reticulum-associated ubiquitin ligase Doa10

K. Wu, S. Itskanov, D. L. Lynch, Y. Chen, A. Turner, J. Gumbart, E. Park

This study defines the substrate recognition mechanism of Doa10 using structural and functional analyses in yeast, revealing a lateral tunnel and fence-like domains that facilitate substrate access.

bioRxiv · Jan 9, 2024 · PreprintBiochemistry

Critical interactions for SARS-CoV-2 spike protein binding to ACE2 identified by machine learning

A. Pavlova, Z. Zhang, A. Acharya, D. L. Lynch, Y. T. Pang, Z. Mou, J. M. Parks, C. Chipot, J. C. Gumbart

This study identifies critical residues for SARS-CoV-2 spike protein binding to ACE2 using machine learning and free energy calculations, showing how specific mutations affect binding affinity.

bioRxiv · Mar 19, 2021Biophysics

Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease

A. Pavlova, D. L. Lynch, I. Daidone, L. Zanetti-Polzi, M. D. Smith, C. Chipot, D. W. Kneller, A. Kovalevsky, L. Coates, A. A. Golosov, C. J. Dickson, C. Velez-Vega, J. S. Duca, J. V. Vermaas, Y. T. Pang, , J. C. Gumbart

This study uses molecular dynamics simulations to investigate how inhibitor binding affects the protonation states of histidines in SARS-CoV-2 main protease, showing their impact on structural stability and inhibitor binding.

bioRxiv · Sep 7, 2020Biophysics