TransportDB 2.0: a database for exploring membrane transporters in sequenced genomes from all domains of life
All cellular life contains an extensive array of membrane transport proteins. The vast majority of these transporters have not been experimentally characterized. We have developed a bioinformatic pipeline to identify and annotate complete sets of transporters in any sequenced genome. This pipeline is now fully automated enabling it to better keep pace with the accelerating rate of genome sequencing. This manuscript describes TransportDB 2.0 (http://www.membranetransport.org/transportDB2/), a completely updated version of TransportDB, which provides access to the large volumes of data generated by our automated transporter ...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Elbourne, L. D. H., Tetu, S. G., Hassan, K. A., Paulsen, I. T. Tags: Database Issue Source Type: research
The SWISS-MODEL Repository--new features and functionality
SWISS-MODEL Repository (SMR) is a database of annotated 3D protein structure models generated by the automated SWISS-MODEL homology modeling pipeline. It currently holds >400 000 high quality models covering almost 20% of Swiss-Prot/UniProtKB entries. In this manuscript, we provide an update of features and functionalities which have been implemented recently. We address improvements in target coverage, model quality estimates, functional annotations and improved in-page visualization. We also introduce a new update concept which includes regular updates of an expanded set of core organism models and UniProtKB-based tar...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Bienert, S., Waterhouse, A., de Beer, T. A. P., Tauriello, G., Studer, G., Bordoli, L., Schwede, T. Tags: Database Issue Source Type: research
RepeatsDB 2.0: improved annotation, classification, search and visualization of repeat protein structures
RepeatsDB 2.0 (URL: http://repeatsdb.bio.unipd.it/) is an update of the database of annotated tandem repeat protein structures. Repeat proteins are a widespread class of non-globular proteins carrying heterogeneous functions involved in several diseases. Here we provide a new version of RepeatsDB with an improved classification schema including high quality annotations for ~5400 protein structures. RepeatsDB 2.0 features information on start and end positions for the repeat regions and units for all entries. The extensive growth of repeat unit characterization was possible by applying the novel ReUPred annotation method ov...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Paladin, L., Hirsh, L., Piovesan, D., Andrade-Navarro, M. A., Kajava, A. V., Tosatto, S. C. E. Tags: Database Issue Source Type: research
PCDDB: new developments at the Protein Circular Dichroism Data Bank
The Protein Circular Dichroism Data Bank (PCDDB) has been in operation for more than 5 years as a public repository for archiving circular dichroism spectroscopic data and associated bioinformatics and experimental metadata. Since its inception, many improvements and new developments have been made in data display, searching algorithms, data formats, data content, auxillary information, and validation techniques, as well as, of course, an increase in the number of holdings. It provides a site (http://pcddb.cryst.bbk.ac.uk) for authors to deposit experimental data as well as detailed information on methods and calculations ...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Whitmore, L., Miles, A. J., Mavridis, L., Janes, R. W., Wallace, B. A. Tags: Database Issue Source Type: research
ECOD: new developments in the evolutionary classification of domains
Evolutionary Classification Of protein Domains (ECOD) (http://prodata.swmed.edu/ecod) comprehensively classifies protein with known spatial structures maintained by the Protein Data Bank (PDB) into evolutionary groups of protein domains. ECOD relies on a combination of automatic and manual weekly updates to achieve its high accuracy and coverage with a short update cycle. ECOD classifies the approximately 120 000 depositions of the PDB into more than 500 000 domains in ~3400 homologous groups. We show the performance of the weekly update pipeline since the release of ECOD, describe improvements to the ECOD website and avai...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Schaeffer, R. D., Liao, Y., Cheng, H., Grishin, N. V. Tags: Database Issue Source Type: research
CATH: an expanded resource to predict protein function through structure and sequence
This article describes developments to the CATH-Gene3D resource over the last two years since the publication in 2015, including: significant increases to our structural and sequence coverage; expansion of the functional families in CATH; building a support vector machine (SVM) to automatically assign domains to superfamilies; improved search facilities to return alignments of query sequences against multiple sequence alignments; the redesign of the web pages and download site. (Source: Nucleic Acids Research)
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Dawson, N. L., Lewis, T. E., Das, S., Lees, J. G., Lee, D., Ashford, P., Orengo, C. A., Sillitoe, I. Tags: Database Issue Source Type: research
Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures
The Protein Data Bank Japan (PDBj, http://pdbj.org), a member of the worldwide Protein Data Bank (wwPDB), accepts and processes the deposited data of experimentally determined macromolecular structures. While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins. We herein outline the updated web user interfaces together with RESTful web services and the backend relational database that support the former. To enhance the interoperability of the PDB data, we have previously developed PDB/RDF, PDB data in th...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Kinjo, A. R., Bekker, G.-J., Suzuki, H., Tsuchiya, Y., Kawabata, T., Ikegawa, Y., Nakamura, H. Tags: Database Issue Source Type: research
WERAM: a database of writers, erasers and readers of histone acetylation and methylation in eukaryotes
In this work, we developed a database WERAM (http://weram.biocuckoo.org/) for histone acetyltransferases, histone deacetylases, histone methyltransferases, histone demethylases and acetyl- or methyl-binding proteins, which catalyze, remove and recognize histone acetylation and methylation sites as ‘writers’, ‘erasers’ and ‘readers’, and synergistically determine the ‘histone code’. From the scientific literature, we totally collected over 580 experimentally identified histone regulators from eight model organisms, including Homo sapiens, Mus musculus, Rattus norvegicus, Droso...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Xu, Y., Zhang, S., Lin, S., Guo, Y., Deng, W., Zhang, Y., Xue, Y. Tags: Database Issue Source Type: research
mutLBSgeneDB: mutated ligand binding site gene DataBase
Mutations at the ligand binding sites (LBSs) can influence protein structure stability, binding affinity with small molecules, and drug resistance in cancer patients. Our recent analysis revealed that ligand binding residues had a significantly higher mutation rate than other parts of the protein. Here, we built mutLBSgeneDB (mutated Ligand Binding Site gene DataBase) available at http://zhaobioinfo.org/mutLBSgeneDB. We collected and curated over 2300 genes (mutLBSgenes) having ~12 000 somatic mutations at ~10 000 LBSs across 16 cancer types and selected 744 drug targetable genes (targetable_mutLBSgenes) by incorporating k...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Kim, P., Zhao, J., Lu, P., Zhao, Z. Tags: Database Issue Source Type: research
Membranome: a database for proteome-wide analysis of single-pass membrane proteins
The Membranome database was developed to assist analysis and computational modeling of single-pass (bitopic) transmembrane (TM) proteins and their complexes by providing structural information about these proteins on a genomic scale. The database currently collects data on >6000 bitopic proteins from Homo sapiens, Arabidopsis thaliana, Dictyostelium discoideum, Saccharomyces cerevisiae, Escherichia coli and Methanocaldococcus jannaschii. It presents the following data: (i) hierarchical classification of bitopic proteins into 15 functional classes, 689 structural superfamilies and 1404 families; (ii) 446 complexes of bit...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Lomize, A. L., Lomize, M. A., Krolicki, S. R., Pogozheva, I. D. Tags: Database Issue Source Type: research
LinkProt: a database collecting information about biological links
Protein chains are known to fold into topologically complex shapes, such as knots, slipknots or complex lassos. This complex topology of the chain can be considered as an additional feature of a protein, separate from secondary and tertiary structures. Moreover, the complex topology can be defined also as one additional structural level. The LinkProt database (http://linkprot.cent.uw.edu.pl) collects and displays information about protein links — topologically non-trivial structures made by up to four chains and complexes of chains (e.g. in capsids). The database presents deterministic links (with loops closed, e.g. ...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Dabrowski-Tumanski, P., Jarmolinska, A. I., Niemyska, W., Rawdon, E. J., Millett, K. C., Sulkowska, J. I. Tags: Database Issue Source Type: research
JET2 Viewer: a database of predicted multiple, possibly overlapping, protein-protein interaction sites for PDB structures
The database JET2 Viewer, openly accessible at http://www.jet2viewer.upmc.fr/, reports putative protein binding sites for all three-dimensional (3D) structures available in the Protein Data Bank (PDB). This knowledge base was generated by applying the computational method JET2 at large-scale on more than 20 000 chains. JET2 strategy yields very precise predictions of interacting surfaces and unravels their evolutionary process and complexity. JET2 Viewer provides an online intelligent display, including interactive 3D visualization of the binding sites mapped onto PDB structures and suitable files recording JET2 analyses. ...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Ripoche, H., Laine, E., Ceres, N., Carbone, A. Tags: Database Issue Source Type: research
FuzDB: database of fuzzy complexes, a tool to develop stochastic structure-function relationships for protein complexes and higher-order assemblies
FuzDB (http://protdyn-database.org) compiles experimentally observed fuzzy protein complexes, where intrinsic disorder (ID) is maintained upon interacting with a partner (protein, nucleic acid or small molecule) and directly impacts biological function. Entries in the database have both (i) structural evidence demonstrating the structural multiplicity or dynamic disorder of the ID region(s) in the partner bound form of the protein and (ii) in vitro or in vivo biological evidence that indicates the significance of the fuzzy region(s) in the formation, function or regulation of the assembly. Unlike the other intrinsically di...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Miskei, M., Antal, C., Fuxreiter, M. Tags: Database Issue Source Type: research
ATGC database and ATGC-COGs: an updated resource for micro- and macro-evolutionary studies of prokaryotic genomes and protein family annotation
The Alignable Tight Genomic Clusters (ATGCs) database is a collection of closely related bacterial and archaeal genomes that provides several tools to aid research into evolutionary processes in the microbial world. Each ATGC is a taxonomy-independent cluster of 2 or more completely sequenced genomes that meet the objective criteria of a high degree of local gene order (synteny) and a small number of synonymous substitutions in the protein-coding genes. As such, each ATGC is suited for analysis of microevolutionary variations within a cohesive group of organisms (e.g. species), whereas the entire collection of ATGCs is use...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Kristensen, D. M., Wolf, Y. I., Koonin, E. V. Tags: Database Issue Source Type: research
ADPriboDB: The database of ADP-ribosylated proteins
ADP-ribosylation refers to the addition of one or more ADP-ribose units onto proteins post-translationally. This protein modification is often added by ADP-ribosyltransferases, commonly known as PARPs, but it can also be added by other enzymes, including sirtuins or bacterial toxins. While past literature has utilized a variety of methods to identify ADP-ribosylated proteins, recent proteomics studies bring the power of mass spectrometry to determine sites of the modification. To appreciate the diverse roles of ADP-ribosylation across the proteome, we have created ADPriboDB – a database of ADP-ribosylated proteins (h...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Vivelo, C. A., Wat, R., Agrawal, C., Tee, H. Y., Leung, A. K. L. Tags: Database Issue Source Type: research
