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Found 8 papers, 2 papers with code
Decoding the Molecular Universe -- Workshop Report
Workshop attendees 1) explored what new understanding of biological and environmental systems could be revealed through the lens of small molecules; 2) characterized the similarities in current needs and technical challenges between each science or mission area for unambiguous and comprehensive determination of the composition and quantities of small molecules of any sample; 3) determined the extent to which technologies or methods currently exist for unambiguously and comprehensively determining the small molecule composition of any sample and in a reasonable time; and 4) identified the attributes of the ideal technology or approach for universal small molecule measurement and identification.
AI for Chemical Space Gap Filling and Novel Compound Generation
When considering large sets of molecules, it is helpful to place them in the context of a "chemical space" - a multidimensional space defined by a set of descriptors that can be used to visualize and analyze compound grouping as well as identify regions that might be void of valid structures.
DEIMoS: an open-source tool for processing high-dimensional mass spectrometry data
We present DEIMoS: Data Extraction for Integrated Multidimensional Spectrometry, a Python application programming interface (API) and command-line tool for high-dimensional mass spectrometry data analysis workflows that offers ease of development and access to efficient algorithmic implementations.
SPECTRe: Substructure Processing, Enumeration, and Comparison Tool Resource: An efficient tool to encode all substructures of molecules represented in SMILES
Functional groups and moieties are chemical descriptors of biomolecules that can be used to interpret their properties and functions, leading to the understanding of chemical or biological mechanisms.
Collision cross section specificity for small molecule identification workflows
The physical-chemical property of molecular collision cross section (CCS) is increasingly used to assist in small molecule identification; however, questions remain regarding the extent of its true utility in contributing to such identifications, especially given its correlation with mass.
A Validated Method for Predicting Small Molecule Ionization Sites using Gibb's Free Energies
Here, we present a new module for ISiCLE that addresses the sensitivity of CCS predictions to ionization site location.
Similarity Downselection: A Python implementation of a heuristic search algorithm for finding the set of the n most dissimilar items with an application in conformer sampling
Finding the set of the n most dissimilar items is different than simply sorting an array of numbers because there exists a pairwise relationship between each item and all other items in the population.
ISiCLE: A molecular collision cross section calculation pipeline for establishing large in silico reference libraries for compound identification
Comprehensive and confident identifications of metabolites and other chemicals in complex samples will revolutionize our understanding of the role these chemically diverse molecules play in biological systems.
Biomolecules Chemical Physics
