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...
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...
RESULTS: We introduce MSX-3D, a tool specifically geared to validate protein models using mass spectrometry. In addition to classical peptides identifications, it allows an interactive 3D visualization of the distance constraints derived from a cross-linking experiment. AVAILABILITY: Freely available at...
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 approaches require appropriate isotopic labelling of the protein and, in case of high molecular ...
Structure-based approaches depend upon the availability and quality of 3D structures, and most of these methods outperform sequence-based methods [20]. There are two main classes of structure-based methods, which are referred to here as “template-free” or “template-based” approaches. Template...
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 ...
Atomic-level three-dimensional (3D) structure data for biological macromolecules often prove critical to dissecting and understanding the precise mechanisms of action of cancer-related proteins and their diverse roles in oncogenic transformation, prolife
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...
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...