Protein Data Bank (PDB): database of three-dimensional structural information of biological macromolecules

The Protein Data Bank (PDB) at Brookhaven National Laboratory, is a database containing experimentally determined three-dimensional structures of proteins, nucleic acids and other biological macromolecules, with approximately 8000 entries. Data are easily submitted via PDB's WWW-based tool AutoDep, in either mmCIF or PDB format, and are most conveniently examined via PDB's WWW-based tool 3DB Browser.

Information management for complex systems: a case study in genomics

Genome mapping and sequencing projects push the frontiers of molecular biology and genetics toward information science. I will try to demonstrate that the information management characteristics of genome research may apply to other large-scale systematic studies of complex systems such as the brain.

Myosin light chain-actin interaction regulates cardiac contractility

The amino-terminal domain of the essential myosin light chain (MLC-1) binds to the carboxy terminus of the actin molecule. We studied the functional role of this interaction by two approaches: first, incubation of intact and chemically skinned human heart fibers with synthetic peptide corresponding to the sequences 5 through 14 (P5-14), 5 through 8 (P5-8), and 5 through 10 (P5-10) of the human ventricular MLC-1 (VLC-1) to saturate actin-binding sites, and second, incubation of skinned human heart fibers with a monoclonal antibody (MabVLC-1) raised against the actin-interacting N-terminal domain of human VLC-1 using P5-14 as antigen to deteriorate VLC-1 binding to actin. P5-14 increased isometric tension generation of skinned human heart fibers at both submaximal and maximal Ca2+ activation, the maximal effective peptide dosage being in the nanomolar range. A scrambled peptide of P5-14 with random sequence had no effects up to 10(-8) mol/L, ie, where P5-14 was maximally effective. P5-8 and P5-10 increased isometric force to the same extent as P5-14, but micromolar concentrations were required. Amplitude of isometric twitch contraction, rate of tension development, rate of relaxation, and shortening velocity at near-zero load of electrically driven intact human atrial fibers increased significantly on incubation with P5-14. These alterations were not associated with modulation of intracellular Ca2+ transients as monitored by fura 2 fluorescence measurements. Incubation of skinned human heart fibers with MabVLC-1 increased isometric tension at both submaximal and maximal Ca2+ activation levels, having a maximal effective concentration in the femtomolar range.

X-HUSAR, an X-based graphical interface for the analysis of genomic sequences

Management and analysis of nucleotide and protein sequence and structure data constitute a traditional area of bioinformatics. Since the analytical programs are frequently developed by researchers, rather than software engineers, they tend to suffer from idiosyncratic and non-ergonomic man-machine interfaces. We report on HUSAR, our 140+ collection of third-party, as well as in-house developed or adapted, sequence manipulation and analysis tools, well integrated into the UNIX operating system environment and accessible via consistent menu-aware interface. Most of the HUSAR programs can be completely specified by UNIX command-line options; they can thus be run in batches or combined into pipes. Adding such a program into the HUSAR environment is almost a 'plug-and-play' exercise. HUSAR has been recently complemented with a graphical client interface, X-HUSAR, to support users on UNIX platforms with X11 windowing systems. The whole X-HUSAR interface is based on a single generic program, COMLIGEN, and a number of specific configuration files. COMLIGEN interprets those files and renders appropriate windows, menus, and other interactive elements, which help the end user in selecting application programs and specifying their options. Efforts of extending both HUSAR and X-HUSAR are roughly linear to the size of the collection.

Characterizing heterogeneous molecular biology database systems

Molecular biology data are distributed among multiple databases. Although containing related data, these databases are often isolated and are characterized by various degrees of heterogeneity: they usually represent different views (schemas) of the scientific domain and are implemented using different data management systems. Currently, several systems support managing data in heterogeneous molecular biology databases. Lack of clear criteria for characterizing such systems precludes comprehensive evaluations of these systems or determining their relationships in terms of shared goals and facilities. In this paper, we propose criteria that would facilitate characterizing, evaluating, and comparing heterogeneous molecular biology database systems.

Prototype implementation of the integrated genomic database

We aim to develop an open software system to handle human genome data. The system, called Integrated Genomic Database (IGD), will integrate information from many genomic databases and experimental resources into a comprehensive target-end database (IGD TED). Users will access front-end client systems (IGD FRED) to download data of interest to their computers and merge them with their own local data. FREDs will provide persistent storage of, and instant access to, retrieved data; a friendly graphical interface; tools for querying, browsing, analyzing, and editing local data; interface to external analysis; and tools for communicating with the outside world. The TED will be accessible over the network (online and offline) as a read-only resource for multiple clients. It collects data from major databases for nucleotide and protein sequences and structures, genome maps, experimental reagents, phenotypes, and bibliographic data, and sets of raw data produced at genome centers and laboratories. Beside character-based access via Gopher, WAIS, FTP, and several query language interfaces to the TED, we will develop a specialized front-end client, IGD FRED, with its own database manager, based on the ACEDB program. The FRED will support graphical display methods for sequence feature maps, chromosomal genetic and physical maps, and experimental objects like clone grids, etc. FRED will also provide an interface to important analysis software packages and tools for submitting data to external databases in their own format.

Presence of antibody reactive with synthetic peptide derived from L2 open reading frame of human papillomavirus types 6b and 11 in human sera

Nine oligopeptides corresponding to segments of different open reading frame (ORF) proteins of human papillomavirus (HPV) 6b and HPV-16 were prepared and tested for reactivity with human sera in enzyme-immunoassay (ELISA). Of these only heptadecapeptide derived from L2 ORF of HPV-6b, and encoded also by L2 ORF of HPV 11, was reactive with some human sera. Over 400 human sera of different origin were tested for the presence of antibody to this antigen. While less than 15% of sera from healthy subjects or cervical carcinoma patients were found antibody positive, sera from the majority of condylomata accuminata (CA) patients were reactive. The antibody titres varied from 1:10 (initial serum dilution) to 1:80; in this respect there was no marked difference between sera from CA patients and the other subjects. The prevalence of antibody was higher among promiscuous than nonpromiscuous women. This is in line with the assumption that sexual intercourse is the most important route of HPV 6 and 11 transmission.