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Total 408160 results found since Jan 2013.

INFERYS Rescoring: boosting peptide identifications and scoring confidence of database search results
Rapid Commun Mass Spectrom. 2021 May 20:e9128. doi: 10.1002/rcm.9128. Online ahead of print.ABSTRACTDatabase search engines for bottom-up proteomics largely ignore peptide fragment ion intensities during the automated scoring of tandem mass spectra against protein databases. Recent advances in deep learning allow the accurate prediction of peptide fragment ion intensities. Using these predictions to calculate additional intensity-based scores help to overcome this drawback. Here, we describe a processing workflow termed INFERYS™ Rescoring for the intensity-based rescoring of Sequest HT search engine results in Thermo Sci...
Source: Rapid Communications in Mass Spectrometry : RCM - May 20, 2021 Category: Chemistry Authors: Daniel P Zolg Siegfried Gessulat Carmen Paschke Michael Graber Magnus Rathke-Kuhnert Florian Seefried Kai Fitzemeier Frank Berg Daniel Lopez-Ferrer David Horn Christoph Henrich Andreas Huhmer Bernard Delanghe Martin Frejno Source Type: research

Understanding the Target Search by Multiple Transcription Factors on Nucleosomal DNA
In this study, by developing a theoretical model based on a discrete-state stochastic approach, we investigated the target search mechanism of multiple TFs on nucleosomal DNA. Experimental kinetic rate constants of different TFs are taken as input to estimate the Mean-First-Passage time to recognize the binding motifs by two TFs on a dynamic nucleosome model. The theory systematically analyzes when the TFs search their binding motifs hierarchically and when simultaneously by proceeding via the formation of a protein-protein complex. Our results, validated by extensive Monte Carlo simulations, elucidate the molecular basis ...
Source: Chemphyschem - January 5, 2023 Category: Chemistry Authors: Sujeet Kumar Mishra Arnab Bhattacherjee Source Type: research

Evidential significance of automotive paint trace evidence using a pattern recognition based infrared library search engine for the Paint Data Query Forensic Database.
Abstract A prototype library search engine has been further developed to search the infrared spectral libraries of the paint data query database to identify the line and model of a vehicle from the clear coat, surfacer-primer, and e-coat layers of an intact paint chip. For this study, search prefilters were developed from 1181 automotive paint systems spanning 3 manufacturers: General Motors, Chrysler, and Ford. The best match between each unknown and the spectra in the hit list generated by the search prefilters was identified using a cross-correlation library search algorithm that performed both a forward and ba...
Source: Talanta - July 31, 2016 Category: Chemistry Authors: Lavine BK, White CG, Allen MD, Fasasi A, Weakley A Tags: Talanta Source Type: research

The SMILES Substructure Search Fallacy
ConclusionText matching on SMILES strings seems like a natural, simple solution to the substructure search problem. But this is a mirage. The futility of this approach may only become apparent after weeks or even months of effort. Regardless of the specific implementation, any robust solution must compare molecules as graphs.
Source: Depth-First - April 13, 2019 Category: Chemistry Authors: Richard L. Apodaca Source Type: blogs

In Search of Hosts for Blue OLEDs:  Computational Design and Experimental Validation
Chemistry. 2022 Dec 22. doi: 10.1002/chem.202203282. Online ahead of print.ABSTRACTConsidering the difficulties associated with the traditional 'trial and error' approach for a complete analysis of a giant molecular space, we took the aid of computational pathway (DFT) in screening a large space search of 780 (12×13×5) molecules to search for a host for the blue emitter. The selection process was completed in three Tiers with the conditions of highest theoretical triplet energy (>2.81 eV), aligned HOMO/LUMO levels w.r.t blue dopant (FIrpic), and position of substituents to meet the optimal requirements as host materia...
Source: Chemistry - December 22, 2022 Category: Chemistry Authors: Diksha Thakur Mangey Ram Nagar Sunil Kumar Shahnawaz Shahnawaz Anju Tomar Anirban Karmakar Subrata Banik Jwo-Huei Jou Subrata Ghosh Source Type: research

Intensity-dependent mass search for improving metabolite database matches in chemical isotope labeling LC-QTOF-MS-based metabolomics
Anal Chim Acta. 2023 Sep 1;1272:341467. doi: 10.1016/j.aca.2023.341467. Epub 2023 Jun 1.ABSTRACTLiquid chromatography mass spectrometry (LC-MS) has been increasingly used for metabolome analysis. One of the critical steps in the LC-MS metabolome analysis workflow is related to metabolite identification. Among the measured parameters, peak mass is commonly used to search against a database for potential metabolite matches. Higher accuracy mass measurement allows the use of a narrower mass tolerance window for mass search. While various types of mass analyzers can routinely measure a peak mass with an error of less than a fe...
Source: Analytica Chimica Acta - June 24, 2023 Category: Chemistry Authors: Yunong Li Hao Li Taibo Luo Guohui Lin Liang Li Source Type: research