Andrei N. Lupas

This paper simulates protein evolution using programmable fitness objectives derived from modern protein models, showing that combined objectives improve evolutionary realism and molecular plausibility.

This paper expands the known ligand space of Cereblon by identifying new chemically distinct ligands that bind through non-canonical mechanisms.

The paper investigates conformational diversity in poly-HAMP arrays and shows that axial helix rotation may be a conserved mechanism for signal transduction across different HAMP-containing systems.

TREAD improves repeat annotation by using protein embeddings instead of sequence profiles, outperforming HMMER in low-data and high-divergence scenarios.

The paper identifies a unique cysteine motif in DPY-6 that facilitates dimerization and is involved in cuticle formation in nematodes.

The paper introduces MONDE·T, a database and webserver for non-canonical amino acids in the PDB, providing structural analysis and visualization tools.

This study characterizes HLp, a bacterial histone that forms tetramers and wraps ~60 base pairs of DNA, revealing a new mode of histone-DNA interaction in bacteria.

This study investigates the DNA-binding properties of bacterial histone HBb in Bdellovibrio bacteriovorus, revealing its ability to bend DNA in a sequence-independent manner, similar to archaeal and eukaryotic histones.

The paper introduces pLM-Repeat, a tool using protein language model embeddings to detect repetitive sequences, achieving comparable sensitivity to HHrepID with faster performance.

The paper shows that β-propellers in major lineages are formed by amplification of single blades, with recent amplification events producing nearly identical blades.

This paper evaluates CASP14 models for molecular replacement using a new metric, reLLG, which is independent of diffraction data and shows AlphaFold2 models outperform others.

The paper analyzes the evolutionary relationships of VCBS-like β-propellers, showing they form a distinct supercluster with integrins and tachylectins, separate from WD40 and Asp-Box β-propellers.