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In biochemistry, a Ramachandran plot (also known as a Rama plot, a Ramachandran diagram or a [φ,ψ] plot), originally developed in 1963 by G. N. Ramachandran, C. Ramakrishnan, and V. Sasisekharan, [1] is a way to visualize energetically allowed regions for backbone dihedral angles ( also called as torsional angles , phi and psi angles ) ψ ...
PyMol allows you to save its current internal state, including all molecules you have loaded, all selections, objects, and representations, and all display settings in a PyMol session file, which has the file extension .pse. This is very useful for saving intermediate states of complex manipulations, especially since PyMol does not have a ...
Molecular geometries can be specified in terms of 'bond lengths', 'bond angles' and 'torsional angles'. The bond length is defined to be the average distance between the nuclei of two atoms bonded together in any given molecule. A bond angle is the angle formed between three atoms across at least two bonds.
PyMOL can produce high-quality 3D images of small molecules and biological macromolecules, such as proteins. PyMOL is widely used. PyMOL is one of the few mostly open-source model visualization tools available for use in structural biology. The Py part of the software's name refers to the program having been written in the programming language ...
A protein can be represented by a sequence of these nine "torsion angle letters". Thrifty is using these sequences of torsion angle letters to identify good templates in a database of ~18,500 nonredundant PDB structures that have had their structures converted to the nine-letter Ramachandran "alphabet".
a torsion angle between ±90° and 180° is called anti (a) a torsion angle between 30° and 150° or between −30° and −150° is called clinal (c) a torsion angle between 0° and ±30° or ±150° and 180° is called periplanar (p) a torsion angle between 0° and ±30° is called synperiplanar (sp), also called syn-or cis-conformation
ICM also is a programming environment for various tasks in computational chemistry and computational structural biology, sequence analysis and rational drug design.The original goal was to develop algorithms for energy optimization of several biopolymers with respect to an arbitrary subset of internal coordinates such as bond lengths, bond angles torsion angles and phase angles.
PREDITOR (PREDIction of TORsion angles) is a freely available web-server for the prediction of protein torsion angles from chemical shifts. [1] For many years it has been known that protein chemical shifts are sensitive to protein secondary structure, which in turn, is sensitive to backbone torsion angles.