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Real-time structural motif searching in proteins using an inverted index strategy.

ABSTRACT: Biochemical and biological functions of proteins are the product of both the overall fold of the polypeptide chain, and, typically, structural motifs made up of smaller numbers of amino acids constituting a catalytic center or a binding site that may be remote from one another in amino acid sequence. Detection of such structural motifs can provide valuable insights into the function(s) of previously uncharacterized proteins. Technically, this remains an extremely challenging problem because of the size of the Protein Data Bank (PDB) archive. Existing methods depend on a clustering by sequence similarity and can be computationally slow. We have developed a new approach that uses an inverted index strategy capable of analyzing >170,000 PDB structures with unmatched speed. The efficiency of the inverted index method depends critically on identifying the small number of structures containing the query motif and ignoring most of the structures that are irrelevant. Our approach (implemented at motif.rcsb.org) enables real-time retrieval and superposition of structural motifs, either extracted from a reference structure or uploaded by the user. Herein, we describe the method and present five case studies that exemplify its efficacy and speed for analyzing 3D structures of both proteins and nucleic acids.

SUBMITTER: Bittrich S

PROVIDER: S-EPMC7746303 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature

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Real-time structural motif searching in proteins using an inverted index strategy.

Bittrich Sebastian S Burley Stephen K SK Rose Alexander S AS

PLoS computational biology 20201207 12

Biochemical and biological functions of proteins are the product of both the overall fold of the polypeptide chain, and, typically, structural motifs made up of smaller numbers of amino acids constituting a catalytic center or a binding site that may be remote from one another in amino acid sequence. Detection of such structural motifs can provide valuable insights into the function(s) of previously uncharacterized proteins. Technically, this remains an extremely challenging problem because of t ...[more]

PMID: 33284792

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Project description:The geometry of the characteristic element forming the artificial structure of an electromagnetic metamaterial defines the way the metamaterial will interact with electromagnetic waves, and accordingly, how it will transmit, reflect, and absorb electromagnetic energy. Metamaterials have been discovered that can manipulate electromagnetic waves to create perfect absorption of incident electromagnetic energy using relatively simple elemental geometries. But the phenomenon is confined to very narrow frequency bandwidths owing to the mono-resonance characteristics of simple cellular structures. Complex cellular geometries based on the combination of many different fundamental building blocks may be able to constructively couple many more resonances and broaden the perfect absorption bandwidth. We describe here a metasurface based upon geometric inversion of a set of conformal mapping contours. The resulting geometry forms a nearly continuous series of perfect absorption resonances within an ultrathin (λ/165) metasurface to develop broadband absorption in a frequency range of interest for downhole chemical spectroscopy. The metasurface is derived from a geometric inversion of the Rhodonea, or more commonly called four-leaf roses, conformal mapping contours and was found to exhibit a near zero index metamaterial (NZIM) behavior. An uncooled microbolometer design is described that uses the metasurface geometry on a single VO2 thermometric substrate leading to an infrared detector with predicted maximum absorption of 99.94% at 4.3 μm and an absorption bandwidth of 170% FWHM on 15.8 μm center wavelength, coincident with important chemical spectra of downhole hydrocarbons. The infrared detector design has a predicted maximum detectivity D* = 1.5 × 109 cm[Formula: see text]/W and noise equivalent difference temperature NEDT of 70 mK at a frame rate of 60 Hz. These levels of detector performance conventionally would be achievable only with cryogenically cooled technologies and could represent a significant step in the effort towards deploying an in situ infrared chemical spectroscopy sensor into downhole logging applications.

Dataset Information

Real-time structural motif searching in proteins using an inverted index strategy.

Publications

Real-time structural motif searching in proteins using an inverted index strategy.

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