A physical map of human Alu repeats cleavage by restriction endonucleases

<p>Abstract</p> <p>Background</p> <p>Alu repetitive elements are the abundant sequences in human genome. Diversity of DNA sequences of these elements makes difficult the construction of theoretical patterns of Alu repeats cleavage by restriction endonucleases. We have proposed a method of restriction analysis of Alu repeats sequences <it>in silico</it>.</p> <p>Results</p> <p>Simple software to analyze Alu repeats database has been suggested and Alu repeats digestion patterns for several restriction enzymes' recognition sites have been constructed. Restriction maps of Alu repeats cleavage for corresponding restriction enzymes have been calculated and plotted. Theoretical data have been compared with experimental results on DNA hydrolysis with restriction enzymes, which we obtained earlier.</p> <p>Conclusion</p> <p>Alu repeats digestions provide the main contribution to the patterns of human chromosomal DNA cleavage. This corresponds to the experimental data on total human DNA hydrolysis with restriction enzymes.</p

AI is a viable alternative to high throughput screening: a 318-target study

: High throughput screening (HTS) is routinely used to identify bioactive small molecules. This requires physical compounds, which limits coverage of accessible chemical space. Computational approaches combined with vast on-demand chemical libraries can access far greater chemical space, provided that the predictive accuracy is sufficient to identify useful molecules. Through the largest and most diverse virtual HTS campaign reported to date, comprising 318 individual projects, we demonstrate that our AtomNet® convolutional neural network successfully finds novel hits across every major therapeutic area and protein class. We address historical limitations of computational screening by demonstrating success for target proteins without known binders, high-quality X-ray crystal structures, or manual cherry-picking of compounds. We show that the molecules selected by the AtomNet® model are novel drug-like scaffolds rather than minor modifications to known bioactive compounds. Our empirical results suggest that computational methods can substantially replace HTS as the first step of small-molecule drug discovery

A physical map of human Alu repeats cleavage by restriction endonucleases-4

Wn at top, whereas those for the complete set of annotated Alu repeats are shown at bottom. The highest peak values are indicated.<p><b>Copyright information:</b></p><p>Taken from "A physical map of human Alu repeats cleavage by restriction endonucleases"</p><p>http://www.biomedcentral.com/1471-2164/9/305</p><p>BMC Genomics 2008;9():305-305.</p><p>Published online 26 Jun 2008</p><p>PMCID:PMC2443384.</p><p></p

A physical map of human Alu repeats cleavage by restriction endonucleases-3

Electrophoregrams of human genomic DNA enzymatic cleavage (8% PAAG) and lengths of fragments are shown at left. A correspondence of predicted DNA fragments (arrows) to the bands in electrophoregrams is shown by dotted lines. M – DNA ladder pUC19/MspI (the lengths of visible fragments are: 501, 489, 404, 331, 242, 190, 147, 111+110, 67 and 34 bp, from top to bottom). "sat" – α-satellite DNA cleavage products.<p><b>Copyright information:</b></p><p>Taken from "A physical map of human Alu repeats cleavage by restriction endonucleases"</p><p>http://www.biomedcentral.com/1471-2164/9/305</p><p>BMC Genomics 2008;9():305-305.</p><p>Published online 26 Jun 2008</p><p>PMCID:PMC2443384.</p><p></p

Distribution diagrams of AluI and AsuHPI recognition sites in all Alu repeats sequences

<p><b>Copyright information:</b></p><p>Taken from "A physical map of human Alu repeats cleavage by restriction endonucleases"</p><p>http://www.biomedcentral.com/1471-2164/9/305</p><p>BMC Genomics 2008;9():305-305.</p><p>Published online 26 Jun 2008</p><p>PMCID:PMC2443384.</p><p></p

A physical map of human Alu repeats cleavage by restriction endonucleases-0

Wn at top, whereas those for the complete set of annotated Alu repeats are shown at bottom. The highest peak values are indicated.<p><b>Copyright information:</b></p><p>Taken from "A physical map of human Alu repeats cleavage by restriction endonucleases"</p><p>http://www.biomedcentral.com/1471-2164/9/305</p><p>BMC Genomics 2008;9():305-305.</p><p>Published online 26 Jun 2008</p><p>PMCID:PMC2443384.</p><p></p