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 DeepView (SwissPDB-Viewer). In brief, among these four packages, Protein Explorer is best...
Protean 3D's protein visualization and analysis tools let you explore macromolecular structure, motion, and function with graphically synchronized views!
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 software that we introduce provides a cross-platform, collaborative environment to view and modify data. Our solution allows for an immersive display of structures in a CAVE virtual reality environment, as well as full support for traditional desktop graphics environments. Via an auto-refresh ...
The structure module (Fig.3d) operates on a concrete 3D backbone structure using the pair representation and the original sequence row (single representation) of the MSA representation from the trunk. The 3D backbone structure is represented asNresindependent rotations and translations, each with respe...
However in spite of recent successes, the path to a high-resolution structure of a membrane protein still involves several bottlenecks including poor expression, limited extraction success, low purification yields and paucity of well-ordered 3D crystals (Fig. 1). Yet, the field of membrane protein...
1 Design rules of 3D protein crystals. a, Constrained degree of freedom (DOF): The angle of rotation at the designed dihedral crystal interface (Fig. 1a, right panel) must be precisely specified by the design process, where the C2 axis of the dihedral needs to coincide with the C2 axis ...
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 layer...
The MSM analysis shows that conformational transitions that involve global structural changes are notably slow in the crystal, occurring over μs to ms timescales (Fig.3d). Except for one instance, all characteristic rates in ff14SB are significantly faster than those in C36m (Fig.3d and Supple...
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]. NMR appr...