10 research outputs found
Gene3D: modelling protein structure, function and evolution
The Gene3D release 4 database and web portal () provide a combined structural, functional and evolutionary view of the protein world. It is focussed on providing structural annotation for protein sequences without structural representatives—including the complete proteome sets of over 240 different species. The protein sequences have also been clustered into whole-chain families so as to aid functional prediction. The structural annotation is generated using HMM models based on the CATH domain families; CATH is a repository for manually deduced protein domains. Amongst the changes from the last publication are: the addition of over 100 genomes and the UniProt sequence database, domain data from Pfam, metabolic pathway and functional data from COGs, KEGG and GO, and protein–protein interaction data from MINT and BIND. The website has been rebuilt to allow more sophisticated querying and the data returned is presented in a clearer format with greater functionality. Furthermore, all data can be downloaded in a simple XML format, allowing users to carry out complex investigations at their own computers
Atomically Thin Resonant Tunnel Diodes built from Synthetic van der Waals Heterostructures
Vertical integration of two-dimensional van der Waals materials is predicted
to lead to novel electronic and optical properties not found in the constituent
layers. Here, we present the direct synthesis of two unique, atomically thin,
multi-junction heterostructures by combining graphene with the monolayer
transition-metal dichalocogenides: MoS2, MoSe2, and WSe2.The realization of
MoS2-WSe2-Graphene and WSe2-MoSe2-Graphene heterostructures leads toresonant
tunneling in an atomically thin stack with spectrally narrow room temperature
negative differential resistance characteristics
The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis
The CATH database of protein domain structures (http://www.biochem.ucl.ac.uk/bsm/cath/) currently contains 43 229 domains classified into 1467 superfamilies and 5107 sequence families. Each structural family is expanded with sequence relatives from GenBank and completed genomes, using a variety of efficient sequence search protocols and reliable thresholds. This extended CATH protein family database contains 616 470 domain sequences classified into 23 876 sequence families. This results in the significant expansion of the CATHHMMmodel library to include models built from the CATH sequence relatives, giving a10%increase in coveragefor detecting remote homologues. An improved Dictionary of Homologous superfamilies (DHS) (http://www.biochem.ucl.ac.uk/bsm/dhs/) containing specific sequence, structural and functional information for each superfamily in CATH considerably assists manual validation of homologues. Information on sequence relatives in CATH superfamilies, GenBank and completed genomes is presented in the CATH associated DHS and Gene3D resources. Domain partnership information can be obtained from Gene3D (http://www.biochem.ucl.ac.uk/bsm/cath/Gene3D/). A new CATH server has been implemented (http://www.biochem.ucl.ac.uk/cgi-bin/cath/CathServer.pl) providing automatic classification of newly determined sequences and structures using a suite of rapid sequence and structure comparison methods. The statistical significance of matches is assessed and links are provided to the putative superfamily or fold group to which the query sequence or structure is assigned
The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution
We report the latest release (version 3.0) of the CATH protein domain database (). There has been a 20% increase in the number of structural domains classified in CATH, up to 86 151 domains. Release 3.0 comprises 1110 fold groups and 2147 homologous superfamilies. To cope with the increases in diverse structural homologues being determined by the structural genomics initiatives, more sensitive methods have been developed for identifying boundaries in multi-domain proteins and for recognising homologues. The CATH classification update is now being driven by an integrated pipeline that links these automated procedures with validation steps, that have been made easier by the provision of information rich web pages summarising comparison scores and relevant links to external sites for each domain being classified. An analysis of the population of domains in the CATH hierarchy and several domain characteristics are presented for version 3.0. We also report an update of the CATH Dictionary of homologous structures (CATH-DHS) which now contains multiple structural alignments, consensus information and functional annotations for 1459 well populated superfamilies in CATH. CATH is directly linked to the Gene3D database which is a projection of CATH structural data onto ∼2 million sequences in completed genomes and UniProt
Evolutionary and Functional Analyses of Protein Structural Families to Improve the Functional Annotation of Genomes
EThOS - Electronic Theses Online ServiceGBUnited Kingdo
Exploiting protein structure data to explore the evolution of protein function and biological complexity
Assessing strategies for improved superfamily recognition
There are more than 200 completed genomes and over 1 million nonredundant sequences in public repositories. Although the structural data are more sparse (~13,000 nonredundant structures solved to date), several powerful sequence-based methodologies now allow these structures to be mapped onto related regions in a significant proportion of genome sequences. We review a number of publicly available strategies for providing structural annotations for genome sequences, and we describe the protocol adopted to provide CATH structural annotations for completed genomes. In particular, we assess the performance of several sequence-based protocols employing Hidden Markov model (HMM) technologies for superfamily recognition, including a new approach (SAMOSA [sequence augmented models of structure alignments]) that exploits multiple structural alignments from the CATH domain structure database when building the models. Using a data set of remote homologs detected by structure comparison and manually validated in CATH, a single-seed HMM library was able to recognize 76% of the data set. Including the SAMOSA models in the HMM library showed little gain in homolog recognition, although a slight improvement in alignment quality was observed for very remote homologs. However, using an expanded 1D-HMM library, CATH-ISL increased the coverage to 86%. The single-seed HMM library has been used to annotate the protein sequences of 120 genomes from all three major kingdoms, allowing up to 70% of the genes or partial genes to be assigned to CATH superfamilies. It has also been used to recruit sequences from Swiss-Prot and TrEMBL into CATH domain superfamilies, expanding the CATH database eightfold
Realizing Large-Scale, Electronic-Grade Two-Dimensional Semiconductors
Atomically
thin transition metal dichalcogenides (TMDs) are of
interest for next-generation electronics and optoelectronics. Here,
we demonstrate device-ready synthetic tungsten diselenide (WSe<sub>2</sub>) via metal–organic chemical vapor deposition and provide
key insights into the phenomena that control the properties of large-area,
epitaxial TMDs. When epitaxy is achieved, the sapphire surface reconstructs,
leading to strong 2D/3D (<i>i.e.</i>, TMD/substrate) interactions
that impact carrier transport. Furthermore, we demonstrate that substrate
step edges are a major source of carrier doping and scattering. Even
with 2D/3D coupling, transistors utilizing transfer-free epitaxial
WSe<sub>2</sub>/sapphire exhibit ambipolar behavior with excellent
on/off ratios (∼10<sup>7</sup>), high current density (1–10
μA·μm<sup>–1</sup>), and good field-effect
transistor mobility (∼30 cm<sup>2</sup>·V<sup>–1</sup>·s<sup>–1</sup>) at room temperature. This work establishes
that realization of electronic-grade epitaxial TMDs must consider
the impact of the TMD precursors, substrate, and the 2D/3D interface
as leading factors in electronic performance