Structural Biochemistry in AR

Molecular modeling kit

Virtual modeling kit

Display *any* molecule from its atomic coordinates, to explore its structure and its motions in AR.

Virtual modeling kit 2.0

Display any molecule to explore its structure and dynamics. Now with two markers, the option to draw your own molecules and a forcefield to see molecular motions and interactions

Virtual modeling kit 3.0

Explore the structures and interactions of all the molecules you want, contained inside a simulation box.

Provide a PDB structure and choose how to represent its proteins, nucleic acids, and small molecules, getting back webAR sessions ready to use with a cube marker or in your space without markers. Useful to quickly build AR views from atomic coordinates.

Orbitals and molecular shapes

Atomic orbitals and VSEPR theory

Visualize and compare all the most common pure and hybrid atomic orbitals, and the basic molecular geometries as in the valence shell electron repulsion theory (VSEPR).

Molecular orbitals and shapes

Visualize and compare all the molecular orbitals precalculated for several small molecules.

Molecular shapes by VSEPR

Examples molecules for each of the main kinds of shapes according to Valence Shell Electron Pair Repulsion (VSEPR) theory.

Web remake of Martinez-Hung et al 2017

Examples of crystalline structures, TRPEV shapes and water complexes from a previous publication by Martinez-Hung et al Revista Cubana de Quimica 2017, repurposed for webAR.

Hydrogen bonding, acids and bases

Equilibria of water protonation

Explore how two water molecules establish hydrogen bonds and transfer protons interconverting between hydronium cation, neutral water and hydroxide anion. The equilibrium is dynamic and gives rise to the water dissociation constant Kw.

Equilibria of acid deprotonation in water

Explore how an acetic acid molecule establishes hydrogen bonds with a water molecule and transfers a proton becoming negatively charged and forming a hydronium cation. Grey atoms are C, red ones are O, white are Hs. This dynamic equilibrium gives rise to the acidic constant, Ka.

Equilibria of ammonia protonation in water

Explore how an ammonia molecule establishes hydrogen bonds with a water molecule and takes a proton becoming positively charged and forming a hydroxide anion. Grey atoms are C, red ones are O, white are Hs, blue is N. This dynamic equilibrium gives rise to the basic constant, Kb.

Equilibrium between acidic and basic amino acid side chains

Explore how the side chains of glutamate and lysine interconvert between charged and neutral species by exchanging protons. Grey atoms are C, red ones are O, white are Hs, blue is N. The yellow dots show the hydrogen bonds between H and O or N.

Atomistic structure of biological macromolecules

Protein-DNA complex

Dock a do1main of a transcription factor onto its cognate DNA; check the electrostatic interactions formed. This example comes from an experimental structure, PDB 1FJL.

Dock peptide on electron density

Dock two portions of a peptide into the electron density map determined by x-ray diffraction. This example gives you a sense of how experimental structures are obtained. It comes from an experimental structure, PDB 3HYD.7

Protein secondary structures and stabilizing interactions

Inspect the detailed atomic structure, hydrogen bonds and salt bridges that stabilize protein secondary structures. You have an alpha helix on one AR marker and a beta sheet on the other.

Compilation of atomistic structures of biomolecules

Inspect a set of pre-made views of biological macromolecules.

Protein-protein and protein-DNA interactions in a B-zip transcription factor

Inspect in detail all the interactions that stabilize the dimeric leucine-zip-based transcription factor, and how it interacts with its target DNA

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