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Constituent amino-acids can be analyzed to predict secondary, tertiary and quaternary protein structure. This list of protein structure prediction software summarizes notable used software tools in protein structure prediction, including homology modeling, protein threading, ab initio methods, secondary structure prediction, and transmembrane helix and signal peptide prediction.
RaptorX is the successor to the RAPTOR protein structure prediction system. RAPTOR was designed and developed by Dr. Jinbo Xu and Dr. Ming Li at the University of Waterloo. RaptorX was designed and developed by a research group led by Prof. Jinbo Xu at the Toyota Technological Institute branch at Chicago.
A protein structure database is a database that is modeled around the various experimentally determined protein structures. The aim of most protein structure databases is to organize and annotate the protein structures, providing the biological community access to the experimental data in a useful way.
An alpha-helix with hydrogen bonds (yellow dots) The α-helix is the most abundant type of secondary structure in proteins. The α-helix has 3.6 amino acids per turn with an H-bond formed between every fourth residue; the average length is 10 amino acids (3 turns) or 10 Å but varies from 5 to 40 (1.5 to 11 turns).
Ribbon diagrams, also known as Richardson diagrams, are 3D schematic representations of protein structure and are one of the most common methods of protein depiction used today. The ribbon depicts the general course and organization of the protein backbone in 3D and serves as a visual framework for hanging details of the entire atomic structure ...
Protein primary structure is the linear sequence of amino acids in a peptide or protein. [1] By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end. Protein biosynthesis is most commonly performed by ribosomes in cells. Peptides can also be synthesized in the ...
predict both 3-state and 8-state secondary structure using conditional neural fields from PSI-BLAST profiles: Webserver/downloadable: server download: 2011 GOR: Information theory/Bayesian inference: Many implementations: Basic GOR GOR V: 2002 (GOR V) Jpred: Multiple Neural network assignment from PSI-BLAST and HMMER profiles. Predicts ...
At the top level are all alpha proteins (domains consisting of alpha helices), all beta proteins (domains consisting of beta sheets), and mixed alpha helix/beta sheet proteins. While most proteins adopt a single stable fold, a few proteins can rapidly interconvert between one or more folds. These are referred to as metamorphic proteins. [5]