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SSFA-GPHR

http://www.ssfa-gphr.de Thyrotropin receptor (TSHR), follitropin receptor (FSHR) and lutropin/chorionic gonadotropin receptor (LHCGR) belong to the glycoprotein hormone receptors (GPHRs). They are a subgroup of family A GPCRs. This database and website have been designed to function as an information source on GPHR-related topics, collating and linking data from studies on i) naturally occurring mutations and site-directed mutations, ii) structures/structural models. Our aim is to facilitate the focused investigation of GPHRs to reveal new insights into the function and malfunction of these important receptors. SSFA-GPHR... * is a database for semi-quantitative Sequence- Structure- and Function- Analysis of GPHRs, * provides a condensed overview of available information such as mutagenesis data for GPHRs, * functional data are converted into unified scaled values to compare and to classify mutagenesis data from GPHR subtypes and different experimental approaches, * provides analyses of data by: focused extraction, comparison, projection and mapping on three-dimensional receptor structures and models. General Aims... * linking functional data with structural data for GPHR investigation, * contribution to new hypotheses regarding molecular interactions and activation mechanisms, * evaluation of data availability (including lack of information) and consistency. New features in the second database release... * a structure-based search for mutation data using three-dimensional structures or homology models, * structural morphings between basal and activated receptor conformations allow changes in amino acid interactions during activation to be traced, * inclusion of double and triple mutations, * improved handling and features for data analyses.

Telomerase database

http://telomerase.asu.edu/

Description :
Sequences and structures of the RNA and protein subunits of telomerase, mutations of telomerase components

CentrosomeDB

http://centrosome.dacya.ucm.es/

Description :
Active research on the biology of the centrosome during the past decades has allowed the identification and characterization of many centrosomal proteins. Unfortunately, the accumulated data are still dispersed among heterogeneous sources of information. Here we present CentrosomeDB, which intends to compile and integrate information related to the human centrosome. We have compiled a set of 383 likely human centrosomal genes, and recorded the associated supporting evidence. CentrosomeDB offers several perspectives to study the human centrosome, including evolution, function, and structure. The database contains information on orthology relationships with other species, including fungi, nematodes, arthropods, urochordates and vertebrates. Predictions of the domain organization of CentrosomeDB proteins are graphically represented in different sections of the database, including sets of alternative protein isoforms, interacting proteins, groups of orthologs, and the homologs identified with blast. CentrosomeDB also contains information related to function, gene-disease associations, SNPs and the 3D structure of proteins. Apart from important differences in the coverage of the set of centrosomal genes, our database differentiates from other similar initiatives in the way information is treated and analyzed. CentrosomeDB is publicly availablec.

Aknowledgement :
We would like to acknowledge César Vicente and the National Institute for Bioinformatics (INB) for technical support. This work has been partially funded by the Spanish grants S-Gen-0166/2006, BIO2007-67150-C03-02, CSD2006-00023 and TIN2005-5619. FA is a recipient of an I3P contract of the Spanish MEC. APM acknowledges the support of the Spanish Ramón y Cajal program.

NMPdb - Nuclear matrix associated proteins database

http://www.rostlab.org/db/NMPdb/

Description :
Nuclear matrix associated proteins database

SDR

http://paradox.harvard.edu/sdr

Description :
Predicted specificity-determining residues in protein families

ChromDB

http://www.chromdb.org/

Description :
Chromatin-associated proteins in a broad range of organisms

CREMOFAC

http://www.jncasr.ac.in/cremofac/

Description :
CREMOFAC is a dedicated web-database for ATP and Non-ATP dependent chromatin-remodeling factors. The database harbors factors from 49 different organisms reported in literature and facilitates a comprehensive search for them. It provides in-depth information for the factors reported in the three widely studied mammals namely, human, mouse and rat. Further, information on literature, pathways and phylogenetic relationships has also been covered.

Aknowledgement :
The authors are earnestly thankful to the reviewers of the first version of CREMOFAC for their constructive suggestions in improving the database, thereby making it more useful and valuable. Support from JNCASR, Bangalore for computational facilities and financial assistance is greatly acknowledged.

CyMoBase

http://www.motorproteins.de/cymobase/

Description :
CyMoBase is an online database for manually annotated protein sequences of cytoskeletal and motor proteins and associated information. It currently offers more than 3000 sequences from 26 proteins in more than 350 species. Meta information linked to sequences are: 564 Publications, NCBI nucleotide and protein IDs, coiled coil and domain predictions from parcoil2, pfam and prosite. Sequences are categorized into classes based on phylogenetic analysis. CyMoBase has a user friendly web interface with different search modules for precise and fast definition of complex search queries. Perspectives on search results ,featuring rich dynamically generated graphics, include: Sequence details, protein inventory by species, domain composition, class composition, molecular weight histogram and FASTA file download. Additionally, searches can be saved and monitored. CyMoBase is accessible from http://www.motorproteins.de/cymobase/.

Recent develoments :
Recently we added versioning to sequence releases, fulltext search on abstacts, doubled the number of proteins and added the possibility to save searches.

Aknowledgement :
This work has been supported by the Max-Planck-Society and funded by grant I80798 of the VolkswagenStiftung.

References :
Odronitz F, Kollmar M. (2006) Pfarao: a web application for protein family analysis customized for cytoskeletal and motor proteins (CyMoBase). BMC Genomics. 7:300

DB-PABP

http://ppa.bcf.ku.edu/DB_PABP/

Description :
Database of experimentally characterized polyanion-binding proteins

Heme Protein Database

http://heme.chem.columbia.edu/heme.php

Description :
Heme types, protein structures, axial ligands and Em values

Knottin database

http://knottin.cbs.cnrs.fr/

Description :
Database of knottins - small proteins with an unusual "disulfide through disulfide" knot

PeroxiBase

http://peroxibase.isb-sib.ch/index.php

Description :
Peroxidases from plants, bacteria and fungi

PlantTFDB

http://planttfdb.cbi.pku.edu.cn/

Description :
Plant Transcription Factor Database

PlantTribes

http://fgp.huck.psu.edu/tribedb/index.pl

Description :
Families of protein-coding genes from five sequenced plant species

SelenoDB

http://www.selenodb.org/

Description :
A database of selenoprotein genes, proteins and SECIS elements

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