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To deal with the situation that many protein sequences have no solved structures, some function prediction servers such as RaptorX are also developed that can first predict the 3D model of a sequence and then use structure-based method to predict functions based upon the predicted 3D model.
Structure- and sequence-based prediction of DNA-binding sites in DNA-binding proteins can be performed on several web servers listed below. DISIS predicts DNA binding sites directly from the amino acid sequence and hence is applicable for all known proteins.
Protegen is a web-based database and analysis system that curates, stores and analyzes protective antigens. Protegen includes basic antigen information and experimental evidence curated from peer-reviewed articles. It also includes detailed gene/protein information (e.g. DNA and protein sequences, and COG classification).
Moreover, the typical secondary structure prediction methods do not account for the influence of tertiary structure on formation of secondary structure; for example, a sequence predicted as a likely helix may still be able to adopt a beta-strand conformation if it is located within a beta-sheet region of the protein and its side chains pack ...
The principal difference between structural genomics and traditional structural prediction is that structural genomics attempts to determine the structure of every protein encoded by the genome, rather than focusing on one particular protein. With full-genome sequences available, structure prediction can be done more quickly through a ...
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 ...
Ab Initio gene prediction is an intrinsic method based on gene content and signal detection. Because of the inherent expense and difficulty in obtaining extrinsic evidence for many genes, it is also necessary to resort to ab initio gene finding, in which the genomic DNA sequence alone is systematically searched for certain tell-tale signs of protein-coding genes.
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.