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At least 1,135 records · Page 63Linked to original sources
PubMed1999

DOMPLOT: a program to generate schematic diagrams of the structural domain organization within proteins, annotated by ligand contacts.

A program is described for automatically generating schematic linear representations of protein chains in terms of their structural domains. The program requires the co-ordinates of the chain, the domain assignment, PROSITE information and a file listing all intermolecular interactions in the protein structure. The output is a PostScript file in which each protein is represented by a set of linked boxes, each box corresponding to all or part of a structural domain. PROSITE motifs and residues involved in ligand interactions are highlighted. The diagrams allow immediate visualization of the domain arrangement within a protein chain, and by providing information on sequence motifs, and metal ion, ligand and DNA binding at the domain level, the program facilitates detection of remote evolutionary relationships between proteins.

Adenosine Diphosphate↗
PubMed2006

Dividing the large glycoside hydrolase family 13 into subfamilies: towards improved functional annotations of alpha-amylase-related proteins.

Family GH13, also known as the alpha-amylase family, is the largest sequence-based family of glycoside hydrolases and groups together a number of different enzyme activities and substrate specificities acting on alpha-glycosidic bonds. This polyspecificity results in the fact that the simple membership of this family cannot be used for the prediction of gene function based on sequence alone. In order to establish robust groups that show an improved correlation between sequence and enzymatic specificity, we have performed a large-scale analysis of 1691 family GH13 sequences by combining clustering, similarity search and phylogenetic methods. About 80% of the sequences could be reliably classified into 35 subfamilies. Most subfamilies appear monofunctional (i.e. contain enzymes with the same substrate and the same product). The close examination of the other, apparently polyspecific, subfamilies revealed that they actually group together enzymes with strongly related (or even sometimes virtually identical) activities. Overall our subfamily assignment allows to set the limits for genomic function prediction on this large family of biologically and industrially important enzymes.

Amino Acid Sequence↗
PubMed2004

Pediatricians advocating for children: an annotated bibliography.

PURPOSE OF REVIEW: Pediatricians have for many years been strong advocates for the health and safety of children. This article reviews the health literature to provide a historical perspective of advocacy efforts of pediatricians and examples of advocacy for patients at the bedside, in the community, and through local, state, and federal legislation, as well as policymaking. Studying these advocacy activities and incorporating them into pediatric practice and education of residents will surely result in stronger, healthier, safer, and happier children and families. RECENT FINDINGS: Some of the cited works relate to pediatric advocacy in general, and some relate to advocacy for specific pediatric topics. Also, articles relating to the education of medical students and pediatric residents are reviewed; they may be of benefit to educators who develop advocacy curriculum. SUMMARY: A review of the MEDLINE literature database from 1966 through October 2003 was performed looking for the terms advocacy (child advocacy, consumer advocacy, legislative advocacy, patient advocacy), as well as advocacy education and training, and was limited to children from birth through 18 years. The titles and many of the abstracts of 4580 articles were reviewed, and 104 articles were read in full. From these, 68 were selected for review here; they were thought to be of particular interest to practicing pediatricians and pediatric educators.

Child↗
PubMed1997

Sequencing and functional annotation of the Bacillus subtilis genes in the 200 kb rrnB-dnaB region.

The 200 kb region of the Bacillus subtilis chromosome spanning from 255 to 275 degrees on the genetic map was sequenced. The strategy applied, based on use of yeast artificial chromosomes and multiplex Long Accurate PCR, proved to be very efficient for sequencing a large bacterial chromosome area. A total of 193 genes of this part of the chromosome was classified by level of knowledge and biological category of their functions. Five levels of gene function understanding are defined. These are: (i) experimental evidence is available of gene product or biological function; (ii) strong homology exists for the putative gene product with proteins from other organisms; (iii) some indication of the function can be derived from homologies with known proteins; (iv) the gene product can be clustered with hypothetical proteins; (v) no indication on the gene function exists. The percentage of detected genes in each category was: 20, 28, 20, 15 and 17, respectively. In the sequenced region, a high percentage of genes are implicated in transport and metabolic linking of glycolysis and the citric acid cycle. A functional connection of several genes from this region and the genes close to 140 degrees in the chromosome was also observed.

Bacillus subtilis↗