Konstantin I. Popov

PHENOMS: Open-Source Software for Rust-Accelerated Hydrogen-Bond Analysis in Molecular Dynamics Simulations

PHENOMS analyzes hydrogen-bond networks in molecular dynamics simulations using Rust-accelerated code, achieving significant speedup over Python-based tools and demonstrating its utility with HDX-MS data.

Open-Source DNA-Encoded Library Package for Design, Decoding, and Analysis: DELi

DELi is an open-source platform for DNA-encoded library design, decoding, and analysis, demonstrating its effectiveness through the identification of a BRD4 binder.

Expansion of DNA-Encoded Library Hits Using Generative Chemistry and Ultra-Large Compound Catalogs

This paper combines DNA-encoded libraries with generative AI to expand hit compounds, finding AI-selected hits show better drug-likeness and diversity than initial DEL hits.

Characterization of the KRas G12D-inhibitor interactions by HDX-MS and molecular dynamics simulations

The paper uses HDX-MS and MD simulations to analyze KRas G12D-inhibitor interactions, showing a correlation between binding affinity and structural changes.