Jaroslav Koča

NAChRDB: A Web Resource of Structure-Function Annotations to Unravel the Allostery of Nicotinic Acetylcholine Receptors

NAChRDB provides a web resource with curated residue-level functional annotations and 3D visualization for neuromuscular nAChRs to aid in understanding their allosteric mechanisms.

Uncovering of Cytochrome P450 Anatomy by SecStrAnnotator

The paper analyzes the secondary structure anatomy of cytochrome P450 proteins using a workflow that identifies equivalent SSE groups and their properties.

The evolutionary advantage of toxin production among cyanobacteria, the oldest known organisms on Earth

The paper analyzes biosynthetic gene clusters in cyanobacteria to show that bioactivity of toxins drove their evolutionary diversity and survival strategies.

Charge-perturbation dynamics - a new avenue towards in silico protein folding

This paper introduces charge-perturbation dynamics (CPD), a molecular dynamics approach that accelerates protein folding simulations by perturbing atomic charges, achieving faster folding of medium-length peptides compared to classical MD.