Free molecular visualization software of excellent quality is now available. Protein Explorer is featured because it is easiest to use, yet quite powerful. It is compared with Cn3D, WebLab Viewer Lite and DeepV
Understanding the structure of a protein is critical to understanding protein function, but many protein analysis tools miss the crucial connection between analysis of protein structure and biophysical properties of the protein sequence. Protean 3D, the foundation ofLasergene Protein, rises above other p...
Homologous proteins often have similar structures. Protein structural alignment software can be a valuable tool for identifying these similarities by comparing the shape and 3D conformation between structures. Protein structural alignment is also a valuable tool for comparingNovaFold predicted modelsto templa...
The 3D visualization is based on JSmol [17] which is a java-independent tool supported by all operating systems and major browsers without the need to install additional software or plu- gins. The site is composed of three main layers: an input layer, hits selection laye...
Next, we used MaSIF-search to predict the structure of known protein–protein complexes. Ideally, one would be able to predict whether two proteins interact simply by comparing their respective fingerprints, avoiding a time-consuming, systematic exploration of the 3D docking space. We find that ...
shown with coloring based on predicted probability, ranging from low (white) to high (dark blue). The partner protein is shown in cartoon representation (gray transparent). Visualization software, ChimeraX59. Full size image We evaluated three models on the PPBS dataset: (1) ScanNet, (2) a...
shown in Figure3C, and a simplistic linear interpolation could be used to calculate a normal (x-axis) and binormal (y-axis) for each point. However, a much smoother interpolation can be achieved by using the spherical linear interpolation (SLERP) parameterized equation shown in Figure3D[35–...
Geometry-based methods locate cavities by analyzing the molecular surface, generally using a 3D grid, spheres or tessellation techniques, and comprise a majority of available software. Examples include LIGSITE [3], CAST [4], SURFNET [5], PASS [6], SCREEN [7], POCASA [8], PocketPicker [9...
is mandatory to understand molecular requisites of proteins interaction with their cognate ligands. The high-resolution 3D structure of a protein can be assessed using X-ray crystallography [1],NMR spectroscopy[2] or the recent and revolutionary cryo-electron microscopy (cryo-EM) [3].NMRapproaches...
Concerning the network visualizations, the tool is capable of providing four different visualization options including 3D structure view, 3D network view, 2D contact maps and distance matrix view. Using these options, one can study molecular interactions of active site residues and ligand binding ...