PMC:5056895 / 7843-9551
Annnotations
{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/5056895","sourcedb":"PMC","sourceid":"5056895","source_url":"https://www.ncbi.nlm.nih.gov/pmc/5056895","text":"Protein structure prediction and validation of drug target\nThe sequence of NS3 protein (accession No. YP_009227202) of ZIKV was retrieved from NCBI database [27]. Phyre2 servers predict the three-dimensional (3D) structure of a protein sequence using the principles and techniques of homology modeling. Because the structure of a protein is more conserved in evolution than its amino acid sequence, a protein sequence of interest (the target) can be modeled with reasonable accuracy on a very distantly related sequence of known structure (the template), provided that the relationship between target and template can be discerned through sequence alignment. Phyre2 was used for modelling the 3D structure of NS3 protein, it is a suite of tools available on the web to predict and analyze protein structure, function and mutations. The focus of Phyre2 is to provide biologists with a simple and intuitive interface to state-of-the-art protein bioinformatics tools [29]. The refined model reliability was assessed through, ProSA-web, the ProSA program (Protein Structure Analysis) is an established tool which has a large user base and is frequently employed in the refinement and validation of experimental protein structures [29], and ProQ is a neural network based predictor that based on a number of structural features predicts the quality of a protein model [30]. Further the refined model was verified by ERRAT server, ERRAT is a program for verifying protein structures determined by crystallography. Error values are plotted as a function of the position of a sliding 9-residue window. The error function is based on the statistics of non-bonded atom-atom interactions in the reported structure [31].","divisions":[{"label":"Title","span":{"begin":0,"end":58}}],"tracks":[{"project":"2_test","denotations":[{"id":"27729840-17517781-44841860","span":{"begin":965,"end":967},"obj":"17517781"},{"id":"27729840-17517781-44841861","span":{"begin":1227,"end":1229},"obj":"17517781"},{"id":"27729840-12717029-44841862","span":{"begin":1364,"end":1366},"obj":"12717029"},{"id":"27729840-8401235-44841863","span":{"begin":1704,"end":1706},"obj":"8401235"}],"attributes":[{"subj":"27729840-17517781-44841860","pred":"source","obj":"2_test"},{"subj":"27729840-17517781-44841861","pred":"source","obj":"2_test"},{"subj":"27729840-12717029-44841862","pred":"source","obj":"2_test"},{"subj":"27729840-8401235-44841863","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#93ec9d","default":true}]}]}}