326 citations · 3k across the 112 of their papers we have counts for
113 papers
Evaluating the roughness of structure-property relationships using pretrained molecular representations
David E. Graff, Edward O. Pyzer-Knapp, Kirk E. Jordan +2
Quantitative structure-property relationships (QSPRs) aid in understanding molecular properties as a function of molecular structure. When the correlation between structure and pro…
Evolutionary Dynamics of a Lattice Dimer: a Toy Model for Stability vs. Affinity Trade-offs in Proteins
Emanuele Loffredo, Elisabetta Vesconi, Rostam Razban +4
Understanding how a stressor applied on a biological system shapes its evolution is key to achieving targeted evolutionary control. Here we present a toy model of two interacting l…
Mapping the space of photoswitchable ligands and photodruggable proteins with computational modeling
Simon Axelrod, Eugene Shakhnovich, Rafael Gómez-Bombarelli
Light-activated drugs are a promising way to localize biological activity and minimize side effects. However, their development is complicated by the numerous photophysical and bio…
Thermal half-lives of azobenzene derivatives: virtual screening based on intersystem crossing using a machine learning potential
Simon Axelrod, Eugene Shakhnovich, Rafael Gomez-Bombarelli
Molecular photoswitches are the foundation of light-activated drugs. A key photoswitch is azobenzene, which exhibits trans-cis isomerism in response to light. The thermal half-life…
Systematic conformation-to-phenotype mapping via limited deep-sequencing of proteins
Eugene Serebryany, Victor Y. Zhao, Kibum Park +4
Non-native conformations drive protein misfolding diseases, complicate bioengineering efforts, and fuel molecular evolution. No current experimental technique is well-suited for el…
Excited state, non-adiabatic dynamics of large photoswitchable molecules using a chemically transferable machine learning potential
Simon Axelrod, Eugene Shakhnovich, Rafael Gómez-Bombarelli
Light-induced chemical processes are ubiquitous in nature and have widespread technological applications. For example, photoisomerization can allow a drug with a photo-switchable s…