PubMed Health⌕ Search
Home/Archive/PubMed

PubMed · 15141111

Application of chemoinformatics to high-throughput screening: practical considerations.

Christian N Parker·Suzanne K Schreyer
View original source ↗Export metadata ↓

Abstract

The objective of this chapter is to summarize and evaluate some of the most common chemoinformatic methods that are applied to the analysis of high-throughput-screening data. The chapter will briefly describe current high-throughput-screening practices and will stress how the major constraint on the application of chemoinformatics is often the quality of high-throughput-screening data. Discussion of the NCI dataset and how it differs from most high-throughput-screening datasets will be made to highlight this point.

Explore related subjects

Chemical PhenomenaChemistryInformation ServicesNational Institutes of Health (U.S.)United StatesJournal ArticleReview

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Christian N Parker, Suzanne K Schreyer. 2004. Application of chemoinformatics to high-throughput screening: practical considerations.. https://doi.org/10.1385/1-59259-802-1%3A085

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

PubMed2007

Hydrogen-bonded nucleic acid base pairs containing unusual base tautomers: complete basis set calculations at the MP2 and CCSD(T) levels.

The total interaction energies of altogether 15 hydrogen-bonded nucleic acid base pairs containing unusual base tautomers were calculated. The geometry properties of all selected adenine-thymine and guanine-cytosine hydrogen-bonded base pairs enable their incorporation into DNA. Unusual base pairing patterns were compared with Watson-Crick H-bonded structures of the adenine-thymine and guanine-cytosine pairs. The complete basis set (CBS) limit of the MP2 interaction energy and the CCSD(T) correction term, determined as the difference between the CCSD(T) and MP2 interaction energies, was evaluated. Extrapolation to the MP2 CBS limit was done using the aug-cc-pVDZ and aug-cc-pVTZ results, and the CCSD(T) correction term was determined with the 6-31G*(0.25) basis set. Final interaction energies were corrected while taking into account both tautomeric penalization determined at the CBS level and solvation/desolvation free energies. The situation for the adenine-thymine pairs is straightforward, and tautomeric pairs are significantly less stable than the Watson-Crick pair consisting of the canonical forms. In the case of the guanine-cytosine pair, the Watson-Crick structure made by canonical forms is again the most stable. The other two structures are, however, energetically rather similar (by 5 and 6 kcal/mol), which provides a very small but non-negligible chance of detecting these structures in the DNA double helix (1:5000). Due to the fact that DNA bases and base pairs incorporated into DNA are solvated less favorably than in isolated systems, this probability represents the very upper limit. The results clearly show how precisely the canonical building blocks of DNA molecules were chosen and how well their stability is maintained.

Chemical Phenomena↗
PubMed2007

Effect of moisture content during dry-heating on selected physicochemical and functional properties of dried egg white.

This article addresses the effect of moisture content (0.8-9.9%) during dry-heating (80 degrees C) on selected physicochemical (solubility, turbidity, residual denaturation enthalpy, aggregation, surface hydrophobicity, and sulfhydryl content) and functional (foaming ability, foam density, and stability) properties of freeze-dried egg white (FDEW). Moisture content during dry-heating proved to be a parameter determining the functionality of the resulting egg white powder. The degree of conformational changes induced in the egg white proteins by dry-heating was strongly dependent on the amount of water present. Preferentially, dry-heating at 80 degrees C should be performed on egg white powder with a moisture content below 6.8%, as the loss of protein solubility above this value is extensive. In addition to insoluble aggregates, soluble, strongly stabilized aggregates were also formed, especially at higher moisture contents. The decrease in denaturation enthalpy, increase in surface hydrophobicity, and exposure of SH groups previously hidden in the protein core and their subsequent oxidation were more pronounced at prolonged dry-heating times and at higher moisture contents. These conformational changes resulted in improved foaming ability and foams with lower density. No effect of dry-heating on the foam stability was observed.

Chemical Phenomena↗
PubMed2007

Kohlrausch regulating function and other conservation laws in electrophoresis.

The Kohlrausch regulating function (KRF) is a conservation law (conservation function), which is held in electrophoresis and which enables calculation of the so-called adjusted concentrations of constituents. The KRF is not the only conservation function and, depending on the complexity of the electrophoretic system, other conservation laws may be obeyed having a broader range of applicability. The conservation laws are tightly related to system eigenmobilities and system zones (system peaks). In principle, no system eigenmobility is exactly zero, but in most practical cases at least one system's eigenmobility is close to zero. The existence of the close-to-zero eigenmobility inherently points to the existence of a conservation function and a system zone which is stationary. The stationary system zone is called injection zone, stagnant zone, water peak, or solvent dip. Electrophoretic (electromigration) systems can be divided into two types: (i) conservation systems, in which the absolute value of at least one system eigenmobility is close to zero and where at least one conservation law is obeyed and (ii) nonconservation systems, where no system eigenmobility is close to zero and no conservation law is obeyed. The paper reviews work dealing with conservation functions in electromigration, derives some "historical" conservation functions in a new way, derives several conservation functions for systems of multivalent electrolytes, and discusses electrophoretic systems that have nonconservation behavior. In some typical instances, the conservation functions are simulated by means of a dynamic simulation tool and depicted graphically.

Chemical Phenomena↗