Multifaceted computational modeling in glycoscience

S Perez, O Makshakova - Chemical Reviews, 2022 - ACS Publications
Glycoscience assembles all the scientific disciplines involved in studying various molecules
and macromolecules containing carbohydrates and complex glycans. Such an ensemble …

Three-dimensional structures of carbohydrates and where to find them

SI Scherbinina, PV Toukach - International journal of molecular sciences, 2020 - mdpi.com
Analysis and systematization of accumulated data on carbohydrate structural diversity is a
subject of great interest for structural glycobiology. Despite being a challenging task …

Vina-Carb: improving glycosidic angles during carbohydrate docking

AK Nivedha, DF Thieker, S Makeneni… - Journal of chemical …, 2016 - ACS Publications
Molecular docking programs are primarily designed to align rigid, drug-like fragments into
the binding sites of macromolecules and frequently display poor performance when applied …

Solution NMR characterization of chemokine CXCL8/IL-8 monomer and dimer binding to glycosaminoglycans: structural plasticity mediates differential binding …

PRB Joseph, PD Mosier, UR Desai… - Biochemical …, 2015 - portlandpress.com
Chemokine CXCL8/interleukin-8 (IL-8) plays a crucial role in directing neutrophils and
oligodendrocytes to combat infection/injury and tumour cells in metastasis development …

Zero-Dimensional (Piperidinium)2MnBr4: Ring Puckering-Induced Isostructural Transition and Strong Electron–Phonon Coupling-Mediated Self-Trapped Exciton …

DP Panda, D Swain, A Sundaresan - Inorganic Chemistry, 2022 - ACS Publications
We report on the synthesis, structure, and photophysical properties of a lead-free organic–
inorganic hybrid halide,(Piperidinium) 2MnBr4 (PipMBr). It crystallizes in a monoclinic P 21/n …

GlycoTorch Vina: docking designed and tested for glycosaminoglycans

ED Boittier, JM Burns, NS Gandhi… - Journal of Chemical …, 2020 - ACS Publications
Glycosaminoglycans (GAGs) are a family of anionic carbohydrates that play an essential
role in the physiology and pathology of all eukaryotic life forms. Experimental determination …

[HTML][HTML] 3-O-Sulfation induces sequence-specific compact topologies in heparan sulfate that encode a dynamic sulfation code

SG Holmes, B Nagarajan, UR Desai - Computational and Structural …, 2022 - Elsevier
Heparan sulfate (HS) is arguably the most diverse linear biopolymer that is known to
modulate hundreds of proteins. Whereas the configurational and conformational diversity of …

Comparison of cellooligosaccharide conformations in complexes with proteins with energy maps for cellobiose

AD French, DW Montgomery, NT Prevost… - Carbohydrate …, 2021 - Elsevier
Shapes (conformations) of cellulose molecules are described by their glycosidic linkage
torsion angles ϕ and ψ. Although the torsions are known for cellulose in crystals, amorphous …

Carbohydrate structure: the rocky road to automation

J Agirre, GJ Davies, KS Wilson, KD Cowtan - Current Opinion in Structural …, 2017 - Elsevier
Highlights•New sugar dictionaries must have starting coordinates for a minimal-energy
conformer.•The current way of forcing conformation in refinement is by using torsion …

The conformation of the idopyranose ring revisited: How subtle O-substituent induced changes can be deduced from vicinal 1H-NMR coupling constants

CAG Haasnoot, R de Gelder, H Kooijman… - Carbohydrate …, 2020 - Elsevier
The idopyranose ring plays a pivotal role in the conformational, dynamical, and
intermolecular binding aspects of glycosaminoglycans like heparin and dermatan sulfate …