GLYCO-2: a Tool to Quantify Glycan Shielding of Glycosylated Proteins with Improved Data Processing and Computation Speed.

ABSTRACT:

Motivation

Glycans bound to glycoproteins mediate immune response, including antibody recognition and immune evasion. Previously, we developed an in silico tool GLYCO (GLYcan COverage) to quantify the glycan shielding of a protein surface, applying it to various studies. However, GLYCO lacks sufficient computational efficiency when analyzing larger datasets.

Results

Here we introduce GLYCO-2 which improves the computational speed by ~4-fold compared to GLYCO by adopting a new analytical cylinder method with k-d trees. GLYCO-2 can calculate glycan shielding from a single coordinate file or from multiple frames derived from molecular dynamics simulations accounting for the inherent flexibility of oligosaccharides. We applied GLYCO-2 to quantify glycan shielding o

SUBMITTER: Reveiz M 

PROVIDER: S-EPMC12190171 | biostudies-literature | 2025 Feb

REPOSITORIES: biostudies-literature