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      CytokineDB: a database collecting biological information

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          Abstract

          Cytokines are subdivided in 12 sub-families and are described as multi-functional molecules that play an important biological activity in host defense system against pathogens, in homeostasis, tissue repair, cell growth and development. CytokineDB is an annotated database that collects biological information regarding the cytokines family in human and will be periodically updated by including new biological information. This database is freely available online and can be accessed at the URL: http://www.cro-m.eu/CytokineDB/

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          Is Open Access

          Data growth and its impact on the SCOP database: new developments

          The Structural Classification of Proteins (SCOP) database is a comprehensive ordering of all proteins of known structure, according to their evolutionary and structural relationships. The SCOP hierarchy comprises the following levels: Species, Protein, Family, Superfamily, Fold and Class. While keeping the original classification scheme intact, we have changed the production of SCOP in order to cope with a rapid growth of new structural data and to facilitate the discovery of new protein relationships. We describe ongoing developments and new features implemented in SCOP. A new update protocol supports batch classification of new protein structures by their detected relationships at Family and Superfamily levels in contrast to our previous sequential handling of new structural data by release date. We introduce pre-SCOP, a preview of the SCOP developmental version that enables earlier access to the information on new relationships. We also discuss the impact of worldwide Structural Genomics initiatives, which are producing new protein structures at an increasing rate, on the rates of discovery and growth of protein families and superfamilies. SCOP can be accessed at http://scop.mrc-lmb.cam.ac.uk/scop.
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            International union of pharmacology. XXII. Nomenclature for chemokine receptors.

            Chemokine receptors comprise a large family of seven transmembrane domain G protein-coupled receptors differentially expressed in diverse cell types. Biological activities have been most clearly defined in leukocytes, where chemokines coordinate development, differentiation, anatomic distribution, trafficking, and effector functions and thereby regulate innate and adaptive immune responses. Pharmacological analysis of chemokine receptors is at an early stage of development. Disease indications have been established in human immunodeficiency virus/acquired immune deficiency syndrome and in Plasmodium vivax malaria, due to exploitation of CCR5 and Duffy, respectively, by the pathogen for cell entry. Additional indications are emerging among inflammatory and immunologically mediated diseases, but selection of targets in this area still remains somewhat speculative. Small molecule antagonists with nanomolar affinity have been reported for 7 of the 18 known chemokine receptors but have not yet been studied in clinical trials. Virally encoded chemokine receptors, as well as chemokine agonists and antagonists, and chemokine scavengers have been identified in medically important poxviruses and herpesviruses, again underscoring the importance of the chemokine system in microbial pathogenesis and possibly identifying specific strategies for modulating chemokine action therapeutically. The purpose of this review is to update current concepts of the biology and pharmacology of the chemokine system, to summarize key information about each chemokine receptor, and to describe a widely accepted receptor nomenclature system, ratified by the International Union of Pharmacology, that is facilitating clear communication in this area.
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              A method for simultaneous alignment of multiple protein structures.

              Here, we present MultiProt, a fully automated highly efficient technique to detect multiple structural alignments of protein structures. MultiProt finds the common geometrical cores between input molecules. To date, most methods for multiple alignment start from the pairwise alignment solutions. This may lead to a small overall alignment. In contrast, our method derives multiple alignments from simultaneous superpositions of input molecules. Further, our method does not require that all input molecules participate in the alignment. Actually, it efficiently detects high scoring partial multiple alignments for all possible number of molecules in the input. To demonstrate the power of MultiProt, we provide a number of case studies. First, we demonstrate known multiple alignments of protein structures to illustrate the performance of MultiProt. Next, we present various biological applications. These include: (1) a partial alignment of hinge-bent domains; (2) identification of functional groups of G-proteins; (3) analysis of binding sites; and (4) protein-protein interface alignment. Some applications preserve the sequence order of the residues in the alignment, whereas others are order-independent. It is their residue sequence order-independence that allows application of MultiProt to derive multiple alignments of binding sites and of protein-protein interfaces, making MultiProt an extremely useful structural tool. Copyright 2004 Wiley-Liss, Inc.
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                Author and article information

                Journal
                Bioinformation
                Bioinformation
                Bioinformation
                Biomedical Informatics Publishing Group
                0973-2063
                2009
                30 September 2009
                : 4
                : 3
                : 92-93
                Affiliations
                [1 ]Centro Ricerche Oncologiche di Mercogliano “Fiorentino Lo Vuolo”, via Ammiraglio Bianco, 83013 Mercogliano (AV) Italy
                [2 ]Dipartimento di Biochimica e Biofisica e Centro di Ricerca Interdipartimentale di Scienze Computazionali e Biotecnologiche, Seconda Università di Napoli, 80131 Napoli, Italy
                [3 ]Istituto Nazionale per lo Studio e la Cura dei Tumori “Fondazione G. Pascale”, 80131 Napoli, Italy
                Author notes
                [* ]Susan Costantini: susan.costantini@ 123456unina2.it Phone: +39 0825 1911730; Fax: +39 0825 1911705
                Article
                002200042009
                2828895
                20198179
                e1198135-18f7-46d1-ab27-31476cc05a40
                © 2009 Biomedical Informatics Publishing Group

                This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium, for non-commercial purposes, provided the original author and source are credited.

                History
                : 11 May 2009
                : 27 June 2009
                : 03 July 2009
                Categories
                Hypothesis

                Bioinformatics & Computational biology
                database,cytokines,chemokines
                Bioinformatics & Computational biology
                database, cytokines, chemokines

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