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Link to original content: http://www.ncbi.nlm.nih.gov/pubmed/33119734
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. 2021 Jan 8;49(D1):D298-D308.
doi: 10.1093/nar/gkaa931.

DescribePROT: database of amino acid-level protein structure and function predictions

Bi Zhao  1 , Akila Katuwawala  1 , Christopher J Oldfield  1 , A Keith Dunker  2 , Eshel Faraggi  3 , Jörg Gsponer  4 , Andrzej Kloczkowski  3 , Nawar Malhis  4 , Milot Mirdita  5 , Zoran Obradovic  6 , Johannes Söding  5 , Martin Steinegger  7 , Yaoqi Zhou  8 , Lukasz Kurgan  1
Affiliations

DescribePROT: database of amino acid-level protein structure and function predictions

Bi Zhao et al. Nucleic Acids Res. .

Abstract

We present DescribePROT, the database of predicted amino acid-level descriptors of structure and function of proteins. DescribePROT delivers a comprehensive collection of 13 complementary descriptors predicted using 10 popular and accurate algorithms for 83 complete proteomes that cover key model organisms. The current version includes 7.8 billion predictions for close to 600 million amino acids in 1.4 million proteins. The descriptors encompass sequence conservation, position specific scoring matrix, secondary structure, solvent accessibility, intrinsic disorder, disordered linkers, signal peptides, MoRFs and interactions with proteins, DNA and RNAs. Users can search DescribePROT by the amino acid sequence and the UniProt accession number and entry name. The pre-computed results are made available instantaneously. The predictions can be accesses via an interactive graphical interface that allows simultaneous analysis of multiple descriptors and can be also downloaded in structured formats at the protein, proteome and whole database scale. The putative annotations included by DescriPROT are useful for a broad range of studies, including: investigations of protein function, applied projects focusing on therapeutics and diseases, and in the development of predictors for other protein sequence descriptors. Future releases will expand the coverage of DescribePROT. DescribePROT can be accessed at http://biomine.cs.vcu.edu/servers/DESCRIBEPROT/.

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Figures

Figure 1.
Figure 1.
Taxonomic distribution of the proteins (panel A) and proteomes (panel B) in DescribePROT.
Figure 2.
Figure 2.
An example results page generated by DescribePROT database for the human p53 protein (UniProt ID: P04637).
Figure 3.
Figure 3.
Spearman correlation coefficients (SCCs) between each pair of the numeric propensities produced by the 14 AA-level predictions of protein structure and function. The color-coded SCCs were computed over the AAs included in DescribePROT. The structure predictions include RSA by ASAquick, disordered linkers by DFLpred, helix, strand and coil conformations by PSIPRED, and intrinsic disorder by VSL2B. The function predictions cover disordered RNA-binding, DNA-binding and protein-binding by DisoRDPbind, MoRFs by MoRFchibi, structure-annotated DNA-binding and RNA-binding by DRNApred and structure-annotated protein-binding by SCRIBER. We also include sequence conservation computed from the profiles generated by MMSeqs2.
Figure 4.
Figure 4.
Distributions of the putative protein-level content of the structural, functional and sequence-derived descriptors included in DescribePROT. The boxplots represent the following 12 intervals, where the consecutive rectangles corresponding to 5–12.5, 12.5–20, 20–27.5, 27.5–35, 35–42.5, 42.5–50, 50–57.5, 57.5–65, 65–72.5, 72.5–80, 80–87.5, 87.5–95 percentile ranges. The black horizontal lines represent medians.
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References

    1. UniProt, C. UniProt: a worldwide hub of protein knowledge. Nucleic Acids Res. 2019; 47:D506–D515. - PMC - PubMed
    1. ww, P.D.B.c. Protein Data Bank: the single global archive for 3D macromolecular structure data. Nucleic Acids Res. 2019; 47:D520–D528. - PMC - PubMed
    1. Boutet E., Lieberherr D., Tognolli M., Schneider M., Bansal P., Bridge A.J., Poux S., Bougueleret L., Xenarios I.. UniProtKB/Swiss-Prot, the manually annotated section of the UniProt KnowledgeBase: how to use the entry view. Methods Mol. Biol. 2016; 1374:23–54. - PubMed
    1. Rost B. Prediction in 1D: secondary structure, membrane helices, and accessibility. Methods Biochem. Anal. 2003; 44:559–587. - PubMed
    1. Kurgan L., Disfani F.M.. Structural protein descriptors in 1-dimension and their sequence-based predictions. Curr. Protein Pept. Sci. 2011; 12:470–489. - PubMed

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