Biomedical subjects

R H Higa

Publications and source records attributed to R H Higa.

4 recordsLinked to original sources

PubMed2006

The Star STING server: a multiplatform environment for protein structure analysis.

Star STING is the latest version of the STING suite of programs and corresponding database. We report on five important aspects of this package that have acquired some new characteristics, designed to add key advantages to the whole suite: 1) availability for most popular platforms and browsers, 2) introduction of the STING_DB quality assessment, 3) improvement in algorithms for calculation of three STING parameters, 4) introduction of five new STING modules, and 5) expansion of the existing modules. Star STING is freely accessible at: http://sms.cbi.cnptia.embrapa.br/SMS/, http://trantor.bioc.columbia.edu/SMS, http://www.es.embnet.org/SMS/, http://gibk26.bse.kyutech.ac.jp/SMS/ and http://www.ar.embnet.org/SMS.

Algorithms↗

PubMed2004

STING Contacts: a web-based application for identification and analysis of amino acid contacts within protein structure and across protein interfaces.

UNLABELLED: Amino acid contacts in terms of atomic interactions are essential factors to be considered in the analysis of the structure of a protein and its complexes. Consequently, molecular biologists do require specific tools for the identification and visualization of all such contacts. Graphical contacts (GC) and interface forming residue graphical contacts (IFRgc) presented here, calculate atomic contacts among amino acids based on a table of predefined pairs of the atom types and their distances, and then display them using number of different forms. The inventory of currently listed contact types by GC and IFRgc include hydrogen bonds (in nine different flavors), hydrophobic interactions, charge-charge interactions, aromatic stacking and disulfide bonds. Such extensive catalog of the interactions, representing the forces that govern protein folding, stability and binding, is the key feature of these two applications. GC and IFRgc are part of STING Millennium Suite. AVAILABILITY: http://sms.cbi.cnptia.embrapa.br/SMS, http://trantor.bioc.columbia.edu/SMS, http://mirrors.rcsb.org//SMS, http://www.es.embnet.org/SMS and http://www.ar.embnet.org/SMS (Options: Graphical Contacts and IFR Graphical Contacts).

Algorithms↗

PubMed2004

ConSSeq: a web-based application for analysis of amino acid conservation based on HSSP database and within context of structure.

SUMMARY: A web-based application to analyze protein amino acids conservation-Consensus Sequence (ConSSeq) is presented. ConSSeq graphically represents information about amino acid conservation based on sequence alignments reported in homology-derived structures of proteins. Beyond the relative entropy for each position in the alignment, ConSSeq also presents the consensus sequence and information about the amino acids, which are predominant at each position of the alignment. ConSSeq is part of the STING Millennium Suite and is implemented as a Java Applet. AVAILABILITY: http://sms.cbi.cnptia.embrapa.br/SMS/STINGm/consseq/, http://trantor.bioc.columbia.edu/SMS/STINGm/consseq/, http://mirrors.rcsb.org//SMS/STINGm/consseq/, http://www.es.embnet.org/SMS/STINGm/consseq/ and http://www.ar.embnet.org/SMS/STINGm/consseq/

Amino Acids↗

PubMed2004

Defining 3D residue environment in protein structures using SCORPION and FORMIGA.

SUMMARY: Two web-based applications to analyze amino acids three-dimensional (3D) local environment within protein structures-SCORPION and FORMIGA-are presented. SCORPION and FORMIGA produce a graphical presentation for simple statistical data showing the frequency of residue occurrence within a given sphere (defined here as the 3D contacts). The center of that sphere is placed at the Calpha and at the last heavy atom in the side chain of the selected amino acid. Further depth of detail is given in terms of a secondary structure to which the profiled amino acid belongs. Results obtained with those two applications are relevant for estimating the importance of the amino acid 3D local environment for protein folding and stability. Effectively, SCORPION and FORMIGA construct knowledge-based force fields. The difference between SCORPION and FORMIGA is in that the latter operates on protein interfaces, while the former only functions for a single protein chain. Both applications are implemented as stand-alone components of STING Millennium Suite. AVAILABILITY: http://sms.cbi.cnptia.embrapa.br/SMS, http://trantor.bioc.columbia.edu/SMS, http://mirrors.rcsb.org/SMS, http://www.es.embnet.org/SMS and http://www.ar.embnet.org/SMS. [options: Scorpion, Formiga]

Algorithms↗