The NCBI structure viewer iCn3D 2.20.0 is now available on the NCBI web site and from GitHub. You can now view the electrostatic potential map for any subset of 3D structures within 30,000 atoms. The potential is calculated using the DelPhi program by solving a linear Poisson-Boltzmann equation. You can show the potential on a surface or show a equipotential map. The potential map shows the effect of charges on molecular interactions qualitatively.
The example in Figure 1 below shows the electrostatic potential for the binding of Gleevec to the human Abl2 protein. This new feature can be accessed from the menu “Analysis > DelPhi Potential.” You can also download the PQR file format with assigned partial charges.
Figure 1: 3GVU: The crystal structure of human ABL2 in complex with GLEEVEC. The ligand shows the -25 mV (red) and +25 mV (blue) equipotential map with a grid size 65, salt concentration 0.15 M, and pH 7. The protein shows the surface potential with a gradient from -75 mV (red) to +75 mV (blue).
Other recently introduced features listed below and more are shown as linked examples on the iCn3D documentation.
- Visualization of observed sequence variation for selected SARS-CoV-2 structures
- Availability of iCn3D in the Jupyter Notebook with the widget “icn3dpy”
- Visualization of a binding site or an interaction interface
- Ability to export models for 3D printing
- Displaying transmembrane proteins
- Showing the surface map, EM map, or electron density map
- Viewing 1D sequences and 2D interactions
- Aligning two structures, two chains, or a protein sequence to a structure and realigning these alignments
- Addition of custom tracks in various formats (FASTA, bed file, etc.)
- Showing a force-directed graph for interactions
- Calculating and displaying solvent accessible surface area (SASA)
- Showing symmetry when available