EyeCue Video Gallery

GPCR Drug Discovery

Druggability of the S1PR2 pocket

Druggability assessment of S1PR2 identifies three potential binding pockets, with one emerging as a promising buried transmembrane cavity featuring complementary polar and hydrophobic interactions for ligand binding and strategically positioned cysteines enabling covalent ligand design.

Structural Basis of S1P Recognition in S1PR2

S1P, a bioactive signaling lipid, maintains stable binding within the rigid transmembrane cavity throughout the simulation. Its polar head group is stabilized by electrostatic interactions, while the hydrophobic tail is accommodated within a complementary hydrophobic pocket.

Siponimod in S1PR1: a hydrophobic pocket with a single polar anchor

A 1-μs all-atom MD simulation of docked siponimod in S1PR1 identified that binding is predominantly driven by hydrophobic packing along with a principal polar interaction with Tyr77. The pocket remained conformationally rigid whereas the most mobile intracellular loop was located 32 Å from the binding site.

Kinase Drug Discovery

An inhibitor bound past the p38α gatekeeper

Molecular dynamics of PDB entry 1W82 shows an inhibitor that binds to p38α without the usual hinge interaction, opens a hidden hydrophobic back pocket, and then uses its larger structure to fill that pocket. Because the back pocket is far less conserved across the kinome than the hinge, its shape offers a structural rationale for selectivity.

Ligand Unbinding Dynamics

Capturing the Unbinding Pathway of a Factor Xa Inhibitor

Scaled molecular dynamics captures the dissociation of a Factor Xa inhibitor from its binding site, revealing the dynamic nature of ligand unbinding and the molecular interactions governing inhibitor residence within the active site.

EyeCue Gallery

GPCR Drug Discovery

Druggability of the S1PR2 pocket

Structural Basis of S1P Recognition in S1PR2

Siponimod in S1PR1: a hydrophobic pocket with a single polar anchor

Kinase Drug Discovery

An inhibitor bound past the p38α gatekeeper

Ligand Unbinding Dynamics

Capturing the Unbinding Pathway of a Factor Xa Inhibitor

How OCT4 reads DNA

Surfactant-Fabric Simulations

Why a nonionic surfactant sticks to cotton and a cationic one doesn't

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