A Concise Review of Biomolecule Visualization

Abstract

The structural characteristics of biomolecules are a major focus in the field of structural biology. Molecular visualization plays a crucial role in displaying structural information in an intuitive manner, aiding in the understanding of molecular properties. This paper provides a comprehensive overview of core concepts, key techniques, and tools in molecular visualization. Additionally, it presents the latest research findings to uncover emerging trends and highlights the challenges and potential directions for the development of the field.

Keywords: augmented reality; computer graphics; level of detail; molecular visualization; representation models.

Figure 1

The development of molecular visualization. Specically, the figure contains various molecular graphics: the CPK model of the green fluorescent protein (PDB ID: 1EMA), the cartoon model of ribonuclease (PDB ID: 1M07), the SES surface of protein isomerase (PDB ID: 1OGZ), the AO rendering effect of viral protein (PDB ID: 1RB8), the cartoon model of visual pigment (PDB ID: 3PQR), and the medium-scale model of HIV. These graphics were generated using Materials Studio (https://www.3ds.com/products-services/biovia/products/molecular-modeling-simulation/biovia-materials-studio/ (accessed on 15 October 2023)) [13], MegaMol (https://megamol.org/ (accessed on 15 October 2023)) [14], Molstar (https://molstar.org/ (accessed on 15 October 2023)) [15], YASARA View (http://www.yasara.org/ (accessed on 15 October 2023)) [16], and the molecular viewer integrated in RCSB PDB (https://www.rcsb.org/3d-view/ (accessed on 15 October 2023)).

Figure 2

The different representation models of Ribonuclease (PDB ID: 1M07) including: (A) lines model, (B) stick model, (C) ball-and-stick model, (D) HyperBall model, (E) cartoon model, (F) ribbon model, (G) backbone model, (H) trace model, (I) vdW surface (space-filling model), (J) SAS surface, (K) SES surface, and (L) Gaussian surface. UnityMol (http://www.baaden.ibpc.fr/umol/ (accessed on 15 October 2023)) [26], MegaMol (https://megamol.org/ (accessed on 15 October 2023)) [14], and the integrated molecular viewer in RCSB PDB (https://www.rcsb.org/3d-view/ (accessed on 15 October 2023)) are used for visualization. Different colors represent separate chains within a molecule.

Figure 3

The protease inhibitor (PDB ID: 4KTC) can be rendered in four different ways: (A) local illumination rendering, (B) ambient occlusion rendering, (C) illustrative rendering, and (D) PDB-101 style illustration. Molstar [15] and Illustrate [47] are used for visualization. Different colors represent separate chains within a molecule.

Figure 4

YASARA View (http://www.yasara.org/ (accessed on 15 October 2023)) [16] is used to visualize HIV at a mesoscopic level. The LOD technique is used with the appropriate level of detail. The color scheme is adjusted adaptively.

Figure 5

The uncertainty visualization of the bacterial protein (PDB ID: 1M5Q) using PyMol [70] and UnityMol [26]. (A) Sausage representation, (B) molecular surface.