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Alex MacKerell

@alexmackerell.bsky.social

Computational chemistry and biophysics. Empirical force fields, CADD, RNA, carbohydrates, and methods developments including SILCS (site identification by ligand competitive saturation, See SilcsBio LLC) and enhanced-sampling GCMC. And I surf....

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Alex MacKerell @alexmackerell.bsky.social · 22/05/2026

Nice. That reminds of a photo I took of the Boston skyline from Marblehead MA back around 1990. It was one of those chance moments when the sky, land, and sea all came together. I was using Ektachrome 400 ASA so the image is rather grainy.

Photo of the Boston skyline taken from Marblehead, MA. There is a wave breaking in the foreground.

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Alex MacKerell @alexmackerell.bsky.social · 29/06/2025

Take a look. The perspective includes examples of how MD simulations and the SILCS technology can be used to facilitate antibody-drug conjugate (ADC) development including regions of the mAb that have potential interactions with the drug warhead.

Images of the Fab and Fc regions of the NIST monoclonal antibody showing the site identification by ligand competitive saturation (SILCS) FragMaps along with where the drug conjugate warhead can bind as predicted by the SILCS and how those regions correspond with residues predicted by MD simulations to interact with the warhead.

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Alex MacKerell @alexmackerell.bsky.social · 15/04/2025

Nice to get a JCIM cover! Check out the SILCS-based method for dissociation pathway identification, 10.1021/acs.jcim.4c01814, and the SILCS-Kinetics physics/ML method for rapid estimation (really fast...) of small molecule koff values was just accepted in JCTC. @silcsbio

Representative images on a journal cover of the different types of molecular movement pathways.

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Alex MacKerell @alexmackerell.bsky.social · 30/12/2024

SILCS-Water allows for inclusion of explicit waters during ligand docking offering improved binding affinities and poses for select systems in a computationally efficient approach. SilcsBio is hosting seminar on January 7, 2025. Please join us! events.teams.microsoft.com/event/713bec...

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Alex MacKerell @alexmackerell.bsky.social · 14/12/2024

Hey, haven't posted for a while but trying to transition over from the "ex"... We've recently published a few papers on the polarizable Drude FF as follows. doi.org/10.1063/5.02... doi.org/10.1021/acs.... doi.org/10.1021/acs.... doi.org/10.1021/acs....

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