Robert Edgar
@RobertEdgarPhD
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Joined August 2012
Search a structure against AFDB, PDB or BDFD with typical results in 2 to 5 minutes.
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Reseek achieves accurate E-values by using a novel null-model which accounts for non-random features. Preprint show that E-values scale to AFDB size.
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Standard significance estimates assume proteins are random, but unrelated structures commonly have non-random similarity.
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Accurate E-values are critially important because the vast majority of alignments are FPs.
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New preprint shows that DALI, TM-align and Foldseek overestimate protein structure alignment significance by 5-6 orders of magnitude https://t.co/rSA0mYtJID](https://t.co/rSA0mYtJID
biorxiv.org
Machine learning has generated millions of high-quality predicted protein structures, creating a need for computationally efficient structure search algorithms and robust estimates of statistical...
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"Protein structure alignment by Reseek improves sensitivity to remote homologs" published in Bioinformatics
academic.oup.com
AbstractMotivation. Recent breakthroughs in protein fold prediction from amino acid sequences have unleashed a deluge of new structures, presenting new opp
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Binaries for #usearch versions 5 through 11 are available under CC0-1.0 (public domain) ( https://t.co/LO1TtBEeri).
github.com
Executable files for usearch versions 5 through 11, donated to the public domain - rcedgar/usearch_old_binaries
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Source code for version 12 is available on GitHub under the GPL3.0 license ( https://t.co/OuyyyT9Yw5).
github.com
Open-source usearch. Contribute to rcedgar/usearch12 development by creating an account on GitHub.
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It's time to donate #usearch to the scientific community, with many sincere thanks to users who supported this research through license fees.
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(3/3) Secret sauce is sequence alignment using a structure-based alphabet with 85,899,345,920 states.
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(2/3) Sensitivity is roughly 2x DALI, TM-align and Foldseek on SCOP40 test
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(1/3) New protein structure alignment and search more accurate than DALI and faster than Foldseek https://t.co/Hsva6doYH5
biorxiv.org
Recent breakthroughs in protein fold prediction from amino acid sequences have unleashed a deluge of new structures, raising new opportunities for expanding insights into the universe of proteins and...
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Tara's figure showing high Arctic Ocean abundances for "Arctiviricota" is either greatly exaggerated or incorrectly calculated
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Predicted structures for new "phyla" have malformed palm domains inconsistent with viral RdRp
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