Search PubMed⌕ Search

Biomedical subjects

F H Allen

Publications and source records attributed to F H Allen.

At least 37 records · Page 2Linked to original sources
PubMed1994

Shape information from a critical point analysis of calculated electron density maps: application to DNA-drug systems.

A computational method is described for mapping the volume within the DNA double helix accessible to the groove-binding antibiotic netropsin. Topological critical point analysis is used to locate maxima in electron density maps reconstructed from crystallographically determined atomic coordinates. The peaks obtained in this way are represented as ellipsoids with axes related to local curvature of the electron density function. Combining the ellipsoids produces a single electron density function which can be probed to estimate effective volumes of the interacting species. Close complementarity between host and ligand in this example shows the method to give a good representation of the electron density function at various resolutions. At the atomic level, the ellipsoid method gives results which are in close agreement with those from the conventional spherical van der Waals approach.

Base Sequence↗
PubMed1993

Molecular scene analysis: the integration of direct-methods and artificial-intelligence strategies for solving protein crystal structure.

A knowledge-based approach to crystal structure determination is presented. The approach integrates direct-methods and artificial-intelligence strategies to rephrase the structure determination process as an exercise in scene analysis. A general joint probability distribution framework, which allows the incorporation of isomorphous replacement, anomalous scattering and a priori structural information, forms the basis of the direct-methods strategies. The accumulated knowledge on crystal and molecular structures is exploited through the use of artificial-intelligence strategies, which include techniques of knowledge representation, search and machine learning.

Journal Article↗
PubMed1993

Pharmacophoric pattern matching in files of three-dimensional chemical structures: characterization and use of generalized torsion angle screens.

This paper describes the use of generalized torsion angles for the screening of conformational searches in databases of three-dimensional chemical structures. A generalized torsion angle is defined as the dihedral angle between two vectors, A1-A2 and A3-A4, in which none, some, or all of the vectors A1-A2, A2-A3, and A3-A4 correspond to formal chemical bonds. The screens consist of a set of four atoms together with an associated angular range, and are identified by a statistical analysis of the frequencies of occurrence of these features in the Cambridge Structural Database. These frequencies are discussed, and the effectiveness of the screens is demonstrated by an extensive series of searches for representative pharmacophoric patterns.

Databases, Factual↗
PubMed1991

Pharmacophoric pattern matching in files of three-dimensional chemical structures: characterization and use of generalized valence angle screens.

This paper describes the use of generalized valence angles for the screening of pharmacophoric pattern searches in databases of three-dimensional chemical structures. A generalized valence angle is defined as the angle between two vectors, AB and BC, which have a common vertex B, and in which both vectors correspond to formal chemical bonds; one vector corresponds to a bond and the other to a non-bonded interaction; or both vectors correspond to non-bonded interactions. The screens are identified by a statistical analysis of the frequencies of occurrence of these angle-based features in the Cambridge Structural Database. The occurrence frequencies are discussed and shown to be explicable in terms of small, commonly occurring structural features. The effectiveness of the screens is demonstrated by an extensive series of searches for representative pharmacophoric patterns. The results are compared with those obtained from a similar series of searches using distance-based screens: The latter are found to give a better level of performance, and evidence is presented to suggest that this is due to a high degree of association between the assignments of the angle-based screens.

Computers↗
PubMed1984

Estimating the recombination frequency for the PTC-Kell linkage.

Two data sets are analyzed for linkage between the PTC and Kell blood group loci. The original report of close linkage for these loci was that of Conneally et al. (1976), where the maximum likelihood estimate of theta was 0.05. These two new data sets give a combined maximum likelihood estimate of theta m = f = 0.28. Estimating the recombination frequency for the sexes separately gave theta m = 0.29, theta f = 0.23. The combined maximum likelihood estimate over all published data sets including this report is theta m = f = 0.14, Zmax = 8.94. There is statistically significant evidence of heterogeneity among the published studies.

Blood Group Antigens↗
PubMed1984

Genetic linkage analysis in primary torsion dystonia.

We studied five families, each containing two siblings affected with torsion dystonia and having phenotypically normal parents, for linkage of dystonia to 18 marker systems, including HLA. Analysis assumed an autosomal recessive mode of inheritance. Linkage was not found. Two markers, HLA and MN, were excluded from tight linkage, and evidence against tight linkage to ABO, Rh, GC, and GLO was obtained.

Adolescent↗
PubMed1983

Shared HLA antigens and reproductive performance among Hutterites.

Shared histocompatibility antigens between spouses may affect reproductive outcome adversely as a result of prenatal selection against compatible fetuses. Evidence from both animal and human studies suggest that histocompatible fetuses may not initiate a maternal immunologic response that prevents rejection of the embryo. Therefore, parents sharing HLA antigens may produce compatible fetuses and consequently experience a greater frequency of early fetal losses and show poorer reproductive outcome than couples not sharing antigens. In the Hutterites, an inbred human isolate that proscribes contraception, we tested the hypothesis that couples sharing HLA antigens have poorer reproductive outcomes than couples who do not. The Hutterites are characterized by high fertility and large family sizes. Couples that share zero (no. = 21), one (no. = 15), and more than one (no. = 10) HLA-A or HLA-B antigens were compared for reproductive performance. Median intervals between births were larger among couples that share more than one antigen in eight of 11 intervals examined. In addition, the median intervals from marriage to first, fifth, and tenth birth were consistently larger among couples that share more than one antigen. Differences among the groups appear to become larger with increasing parity, suggesting that the effect of histocompatibility on reproductive performance becomes more evident in later pregnancies. These differences in reproductive performance between couples that share zero, one, or more than one HLA-A or HLA-B antigens may have significant evolutionary consequences. However, our results demonstrate that sharing HLA antigens does not preclude normal pregnancy and caution should be exercised before concluding that shared HLA antigens are solely responsible for repeated fetal losses.

Birth Intervals↗
PubMed1980

Comparison of real-time cholecystosonography and oral cholecystography.

To evaluate the efficacy of real-time ultrasonography in detecting cholelithiasis, a series of outpatients and inpatients was examined by oral cholecystography and real-time cholecystosonography. In 163 patients, real-time cholecystosonography achieved a sensitivity of 0.91 and a specificity of 0.99. These values are equal to or better than those usually obtained in current B-mode cholecystosonography or some reported series of oral cholecystography. However, technically excellent and meticulously performed oral cholecystography achieves slightly better sensitivity and specificity than real-time cholecystosonography. The latter is suggested as the initial examination for hospitalized patients, those with abnormal liver function studies or gastric outlet obstruction, and pregnant women. Real-time ultrasonography should also be used when the gallbladder is not adequately opacified on initial oral cholecystography if a sequential dose examination cannot be readily accomplished.

Cholecystography↗
PubMed1979

Deletion mapping: further evidence for the location of acid phosphatase (ACP1) within 2p23.

The human red cell acid phosphatase (ACP1) locus was assigned to region 2p23 leads to 2pter by Ferguson-Smith et al [3], more specifically to 2p23 by Hamerton et al [5]. We describe two unrelated patients with deletion of chromosome 2, with similar breakpoints in the distal portion of band p23 (del(2) (p23)). ACP1 typing in both patients revealed heterozygous BA phenotypes. Thus, we assign the locus for ACP1 to the distal portion of 2p23.

Abnormalities, Multiple↗