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Biomedical subjects

J S Garavelli

Publications and source records attributed to J S Garavelli.

8 recordsLinked to original sources
PubMed1999

The RESID Database of protein structure modifications.

Because the number of post-translational modifications requiring standardized annotation in the PIR-International Protein Sequence Database was large and steadily increasing, a database of protein structure modifications was constructed in 1993 to assist in producing appropriate feature annotations for covalent binding sites, modified sites and cross-links. In 1995 RESID was publicly released as a PIR-International text database distributed on CD-ROM and accessible through the ATLAS program. In 1998 it was made available on the PIR Web site at http://www-nbrf.georgetown.edu/pir/searchdb++ +.html . The RESID Database includes such information as: systematic and frequently observed alternate names; Chemical s Service registry numbers; atomic formulas and weights; enzyme activities; indicators forN-terminal, C-terminal or peptide chain cross-link modifications; keywords; and literature citations with database cross-references. The RESID Database can be used to predict atomic masses for peptides, and is being enhanced to provide molecular structures for graphical presentation on the PIR Web site using widely available molecular viewing programs.

Binding Sites↗
PubMed1999

The PIR-International Protein Sequence Database.

The Protein Information Resource (PIR; http://www-nbrf.georgetown. edu/pir/) supports research on molecular evolution, functional genomics, and computational biology by maintaining a comprehensive, non-redundant, well-organized and freely available protein sequence database. Since 1988 the database has been maintained collaboratively by PIR-International, an international association of data collection centers cooperating to develop this resource during a period of explosive growth in new sequence data and new computer technologies. The PIR Protein Sequence Database entries are classified into superfamilies, families and homology domains, for which sequence alignments are available. Full-scale family classification supports comparative genomics research, aids sequence annotation, assists database organization and improves database integrity. The PIR WWW server supports direct on-line sequence similarity searches, information retrieval, and knowledge discovery by providing the Protein Sequence Database and other supplementary databases. Sequence entries are extensively cross-referenced and hypertext-linked to major nucleic acid, literature, genome, structure, sequence alignment and family databases. The weekly release of the Protein Sequence Database can be accessed through the PIR Web site. The quarterly release of the database is freely available from our anonymous FTP server and is also available on CD-ROM with the accompanying ATLAS database search program.

Amino Acid Sequence↗
PubMed1998

The PIR-International Protein Sequence Database.

From its origin the Protein Information Resource (http://www-nbrf. georgetown.edu/pir/) has supported research on evolution and computational biology by designing and compiling a comprehensive, quality controlled, and well-organized protein sequence database. The database has been produced and updated on a regular schedule since 1984. Since 1988 it has been maintained collaboratively by the PIR-International, an association of data collection centers engaged in international cooperation for the development of this research resource during a period of explosive acquisition of new data. As of June 1997, essentially all sequence entries have been classified into families, allowing the efficient application of methods to propagate and standardize annotation among related sequences. The databases are available through the Internet by the World-Wide Web and FTP, or on CD-ROM and magnetic media.

Amino Acid Sequence↗
PubMed1997

The Protein Information Resource (PIR) and the PIR-International Protein Sequence Database.

From its origin, the PIR has aspired to support research in computational biology and genomics through the compilation of a comprehensive, quality controlled and well-organized protein sequence information resource. The resource originated with the pioneering work of the late Margaret O. Dayhoff in the early 1960s. Since 1988, the Protein Sequence Database has been maintained collaboratively by PIR-International, an association of macromolecular sequence data collection centers dedicated to fostering international cooperation as an essential element in the development of scientific databases. The work of the resource is widely distributed and is available on the World Wide Web, via FTP, E-mail server, CD-ROM and magnetic media. It is widely redistributed and incorporated into many other protein sequence data compilations including SWISS-PROT and theEntrezsystem of the NCBI.

Amino Acid Sequence↗
PubMed1991

Molecular modeling on the Commodore Amiga.

The Amiga 3000 is nearly ideal for desktop molecular modeling. It uses the Motorola 68030 32-bit processor, running at 16 or 25 MHz, with either the 68881 or 68882 math coprocessor and eight custom processing chips. The video system is NTSC compatible 15.75- or 31.5-KHz RGB analog or digital. The system video interface offers user selectable 320 x 200, 640 x 480, 768 x 480 or 1280 x 400 resolution with a displayable palette of 4,096 colors and interlaced, noninterlaced and overscan modes. NTSC compatibility permits simple and inexpensive video signal synchronization, so that composed monitor images can be displayed and recorded with standard video equipment. The processor, in conjunction with the custom video chips, can manipulate models mathematically at a sufficient rate to present moving or animated images in real time. Users can interact with the molecular image with mouse or joystick controls. A third-party manufacturer, Haitex Resources, has produced an inexpensive stereo image display interface for the Amiga. This stereo image display system consists of liquid crystal shutter goggles attached to a control module on one mouse/joystick port and synchronized at 60 Hz with alternating left/right screen displays. Several simple molecular graphics programs for the Amiga have been available in the public domain since 1988. The ease of video interfacing and the availability of stereo image display have stimulated several developers to begin assembling molecular modeling packages. At the National Biomedical Research Foundation the Amiga is being tested as an inexpensive stereo-image color graphics workstation for molecular modeling, biopolymer sequence analysis and medical imaging.(ABSTRACT TRUNCATED AT 250 WORDS)

Computer Graphics↗
PubMed1974

Structural and functional similarities between mitochondrial malate dehydrogenase and L-3-hydroxyacyl CoA dehydrogenase.

Pig heart mitochondrial malate dehydrogenase (EC 1.1.1.37), which has been obtained free of electrophoretic subforms, has been shown to have a molecular weight of 67,000 and to be composed of two polypeptide chains. Comparison of these and other properties, such as amino-acid composition, isoelectric point, and keto-substrate inhibition, with those of (L)-3-hydroxyaeyl CoA dehydrogenase (EC 1.1.1.35), another NAD(+)-dependent dehydrogenase of mitochondrial origin, suggests structural similarities of the type associated with proteins possessing common evolutionary origins. This conclusion is supported by immunological crossreactivity. In view of these observations, the dissimilarity in the stereospecificity of hydrogen transfer from cofactor to substrate catalyzed by the two enzymes is attributed to 180 degrees rotation in the binding orientation of the nicotinamide moiety of the NAD(+), rather than to gross differences in the geometry of the active site of the two enzymes.

Alcohol Oxidoreductases↗