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The University of Minnesota Pathway Prediction System (UM-PPS) is a web tool that recognizes functional groups in organic compounds that are potential targets of microbial catabolic reactions and predicts transformations of these groups based on biotransformation rules. Multi-level predictions are made. (bio.tools entry) [116]
The prediction is made by "threading" (i.e. placing, aligning) each amino acid in the target sequence to a position in the template structure, and evaluating how well the target fits the template. After the best-fit template is selected, the structural model of the sequence is built based on the alignment with the chosen template.
In palmitoleoylation, a palmitoleoyl group (derived from palmitoleic acid, pictured above) is added.. Palmitoleoylation is type of protein lipidation where the monounsaturated fatty acid palmitoleic acid is covalently attached to serine or threonine residues of proteins.
Name Method description Type Link Initial release RaptorX-SS8 : predict both 3-state and 8-state secondary structure using conditional neural fields from PSI-BLAST profiles ...
De novo protein structure prediction methods attempt to predict tertiary structures from sequences based on general principles that govern protein folding energetics and/or statistical tendencies of conformational features that native structures acquire, without the use of explicit templates. Research into de novo structure prediction has been ...
The Chou–Fasman method is an empirical technique for the prediction of secondary structures in proteins, originally developed in the 1970s by Peter Y. Chou and Gerald D. Fasman. [ 1 ] [ 2 ] [ 3 ] The method is based on analyses of the relative frequencies of each amino acid in alpha helices , beta sheets , and turns based on known protein ...
In this mode the input is a project file that can be generated by the DeepView (Swiss Pdb Viewer) visualization and structural analysis tool, [4] to allow the user to examine and manipulate the target-template alignment in its structural context. In all three cases the output is a pdb file with atom coordinates of the model or a DeepView ...