We will also utilize the domain-centric protein sequence and structural analyses to understand the potential functions of the ... Seven genomes of Lso haplotypes are available in NCBI GenBank database, including Lso haplotype A (NZ1, GCA_000968085.1; HenneA ...

... is a database of annotated comparative protein structure models. The models are calculated by ModPipe, an automated modeling ... ModBase currently contains almost 30 million reliable models for domains in 4.7 million unique protein sequences. ModBase ... Structural Bioinformatics Unit, Structural Biology and Chemistry department, Institut Pasteur, 25 rue du Docteur Roux, 75015 ... a database of annotated comparative protein structure models and associated resources Nucleic Acids Res. 2014 Jan;42(Database ...

Crystal structure of Alcohol dehydrogenase zinc-binding domain protein from Burkholderia ambifaria ... Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID). Revision History (Full details and ... Alcohol dehydrogenase zinc-binding domain protein. A. 383. Burkholderia ambifaria MC40-6. Mutation(s): 0 Gene Names: BamMC406_ ... Crystal structure of Alcohol dehydrogenase zinc-binding domain protein from Burkholderia ambifaria. Abendroth, J., Mayclin, S.J ...

Plasmodium falciparum Erythrocyte Membrane Protein 1 (PfEMP1) encoded by the var2CSA gene is believed to be the main parasite ... Three-dimensional structural models of various DBL domains were built and analysed with a view to assessing conservation of CSA ... These structural insights have clear implications in using CSA-binding DBL domains for vaccines against placental malaria as it ... Structural comparisons of the three-dimensional structures of CSA-binding DBL domains indicates that the proposed CSA ...

YAKUSA: A fast structural database scanning method. Proteins. 2005;61(1):137-151. ... If given a known protein domain, VAST can return structural neighbors in seconds using pre-calculated results. However, if ... First, for domain searches, SSM is working with the SCOP 1.73 database, so accordingly we operate RUPEE on SCOP 1.73 domains to ... Given a protein domain identifier, whole chain identifier or an uploaded PDB file, RUPEE can search for matches among domains ...

... pyrin domain of apoptosis-associated speck-like protein) filament at atomic resolution. ... Support for Structural Bioinformatics Computational structural biology is an increasingly important multidisciplinary field ... Pulse Program Database We are currently developing a web platform for NMR pulse programs. This platform allows the archival and ... Integrative Structural Biology Figure 2. Structure determination protocol (left), ChhC solid state NMR spectrum (top), electron ...

... although the hCTR contains an insert of 16 amino acids between transmembrane domain I and II. The structural differences may ... but is not significantly related to other G protein-coupled receptor sequences now in the data bases. ... these receptors comprise a distinct family of G protein-coupled seven transmembrane domain receptors. Interestingly, the hCTR ... The cloned cDNA encodes a putative peptide of 490 amino acids with seven potential transmembrane domains. The amino acid ...

A TH domain missense mutation has also been described in BTK. [1] A database of BTK mutations (BTKbase: Mutation registry for X ... The putative structural implications of all of the missense mutations are provided in the database. [4, 5, 6, 7] ... The definitive determinant of XLA is the complete absence of BTK ribonucleic acid (RNA) or protein. Specific molecular analysis ... Mutations in each of the 5 domains of BTK can lead to disease. The single most common genetic event is a missense mutation. ...

ReferencesOLDERADO: On‐line database of ensemble representatives and domains. LA Kelley, MJ Sutcliffe, Protein science 6 (12), ... Protein Eng. Jan;11(1):1-9. (1998)Enhanced genome annotation using structural profiles in the program 3D-PSSM. LA Kelley, RM ... On-Line Database of Ensemble Representatives and Domains [1] - to look at the results. Each morning I would go on the internet ... and that reason is the mystery of protein folding. The person that solves the protein folding problem (at least I hope its a ...

Structural and functional characterization of an RNase HI domain from the bifunctional protein Rv2228c from Mycobacterium ... The N-terminal domain is homologous with prokaryotic and eukaryotic RNase H domains and the C-terminal domain with alpha- ... The open reading frame Rv2228c from Mycobacterium tuberculosis is predicted to encode a protein composed of two domains, each ... The open reading frame Rv2228c from Mycobacterium tuberculosis is predicted to encode a protein composed of two domains, each ...

RUN domain and cysteine-rich domain containing Beclin 1-interacting protein; SLE: systemic lupus erythematosus; SQSTM1/p62: ... Therefore, care is required when interpreting data based on ATG8 in order to conclude whether a signal relates to the canonical ... view abstract Nature structural & molecular biology, PMID: 23262492 2013 Autophagy proteins in macroendocytic engulfment. ... Overexpression of a 2xFYVE(Hrs) domain fusion protein abolished this response demonstrating that the effect of PI3K-C2beta on ...

Here, we present results of a recent search of the protein sequence database for new DS domains using generalized profiles, a ... NMR Structure of the Mouse MFG-E8 C2 Domain. 2orx. Structural Basis for Ligand Binding and Heparin Mediated Activation of ... Click on the protein counts, or double click on taxonomic names to display all proteins containing FA58C domain in the selected ... Evolution (species in which this domain is found). * Taxonomic distribution of proteins containing FA58C domain.. This tree ...

... which provides structural information about individual proteins; and the Conserved Domain Database (CDD), which provides a ... Once a protein structure has been identified, the domains within the protein, as well as domain "neighbors" (i.e., those with ... these two databases allow scientists to retrieve and view structures, find structurally similar proteins to a protein of ... structures of proteins center around two databases: the Molecular Modeling Database (MMDB), ...

Keratin (/ˈkɛrətɪn/[1][2]) is one of a family of structural fibrous proteins also known as scleroproteins. Alpha-keratin (α- ... Protein sequence alignment of human keratin 1, 2A, 3,4, 5, 6A, 7, and 8 (KRT1 - KRT8). Only the first rod domain is shown above ... "GeneCards - Human Genes , Gene Database".. *^ Hanukoglu, Israel; Fuchs, Elaine (November 1982). "The cDNA sequence of a human ... Limited interior space is the reason why the triple helix of the (unrelated) structural protein collagen, found in skin, ...

By mapping the protein domains between different databases, I can analyze and add new, otherwise not apparent information. ... I am augmenting the computational resources available on the Structural Classification of Proteins (SCOP) database by mapping ... Enriching the SCOP Database with Phylogenetic and Protein Function Data. Different protein databases classify and organize ... The Uniprot-GOA mapping will be used to assign protein functions to the Protein Data Bank entries in SCOP and improve the ...

... might give insight on acceptability of its particular structural model out of a confusion set of models generated from database ... The result obtained from a widely varying structural class of proteins indicated that speed of protein structure evaluation can ... It showed that, once structure models of a protein were obtained through homology technique, the problem of selection of a best ... It was intriguing to observe that direct experimental knowledge of the concerned protein, however simple it may be, ...

SSToSS is a database which provides sequence-structural templates of single member protein domain superfamilies like PASS2. ... 3D interacting domains The database of 3D Interaction Domains (3did) is a collection of domain-domain interactions in proteins ... Protein Structure Change Database The Protein Structural Change DataBase (PSCDB) presents the structural changes found in ... Protein Model Database The Protein Model DataBase (PMDB) is a database that stores three dimensional protein models obtained by ...

As a result, antibody responses to the receptor binding domain (RBD), N, and non-structural protein 8 (NSP8) were induced ... ZF2001 is a recombinant protein vaccine based on SARS-CoV-2 receptor-binding domain (RBD) subunit which contains aluminum ... The WHO Covid-19 Research Database is a resource created in response to the Public Health Emergency of International Concern ( ... Compared to E and M proteins, N and S activated a higher proportion of specific T-cells with broader functions. The predominant ...

These results suggested that the active domains of the enzyme from our isolate have the considerable identity with the database ... In this study, we report the characterization and structural analysis of choline dehydrogenase in E. coli. Moreover, the ... 4). Upon analysis of betA protein, the predicted charge at pH 7.0 was 15.45 with the isoelectric point of 5.52. ... Upon structural analysis, both Chou-Fasman and Garnier-Robson prediction of alpha helix structures showed a maximum similarity ...

The lack of covalent bonding in the Env proteins of these two genera correlates with the lack of a particular cysteine in the ... hypothesizing that the structural difference associated with the two TM types would have implications for host range that had ... lack of an immunosuppressive domain (ISD) and a longer membrane proximal external region (MPER). We took advantage of these ... sequence features to screen the NCBI genomic databases for TM sequences of each type, ...

Pfam - A database of protein families and domains. Protein families are classified based on sequence similarity, structural ... PROSITE - Database of protein domains, families and functional sites. Patterns and profiles to identify the protein domains, ... protein-protein, protein-nucleic acid, or protein-ligand binding).. threonine (Thr, T) - Alpha amino acid with a uncharged, ... SCOP - The Structural Classification of Proteins (SCOP) database aims to provide detailed, comprehensive descriptions of the ...

One protein containing peptides Eisenhower and Kennedy, the MPER and the membrane spanning domain of gp41, called LIPO-gp41 and ... However, this protein showed certain structural instability and propensity to self-associate at physiological pH, which may be ... In order to obtain a broad data base for the identification of parameters important for E. coli gene expression a new approach ... However protein mixed in gel could be unstable. For this reason, it was recommended to mix the protein to the gel immediately ...

UniProt (Universal Protein Resource). *CDD Search (Conserved Domain Database). Analyze:. Predict TMSs (Predict number of ... 1] "Synthesis of the heteropolysaccharide O antigen of Escherichia coli O52 requires an ABC transporter: structural and genetic ... Heteropolysaccharide O-antigen exporter, Wzm/Wzt (Feng et al., 2004). The C-terminal cytoplasmic domain of Wzt (an IgG-like β- ... large structural changes within the nucleotide-binding and transmembrane regions push conserved hydrophobic residues at the ...

... the tonoplast intrinsic proteins (TIPs), the nodulin 26-like intrinsic proteins (NIPs), the small basic intrinsic proteins ( ... Protein structure evaluation showed a hydrophilic aromatic/arginine (ar/R) selectivity filter (SF) in PIPs whereas other ... SIPs), and the uncharacterized intrinsic proteins (XIPs). A notable exception was the XIP subfamily where XIP1 group was ... analysis showed similar numbers of AQPs clustered in five distinct subfamilies including the plasma membrane intrinsic proteins ...

... database. The S1 subunit (PDB I.D-6VSB) of the spike protein being reported to acts as receptor binding domain (RBD), binding ... Huang SY, Zou X. Ensemble docking of multiple protein structures: considering protein structural variations in molecular ... Huang SY, Zou, X. An iterative knowledge?based scoring function for protein-protein recognition Proteins 2008;72(2):557-79. ... Structural and functional properties of SARS-CoV-2 spike protein: potential antivirus drug development for COVID-19. Acta ...

Three broad themes emerge: cGST domains as enzymes, as chloride ion channels and as protein-protein interaction mediators. As ... The EBI AlphaFold Protein Structure Database (for example) contains over 230 million structures. In this study, these data have ... has emerged as a powerful tool in the field of structural biology. AI-based algorithms have been used to analyze large amounts ... A total of 39 proteins were found, including the alpha-, mu-, pi-, sigma-, zeta- and omega-class GSTs, intracellular chloride ...

In a carrot primary culture system (PCS), this tool allowed identifying an early peak related with structural biomass formation ... In a carrot primary culture system (PCS), this tool allowed identifying an early peak related with structural biomass formation ... Rambaldi, D., and Ciccarelli, F. D. (2009). FancyGene: dynamic visualization of gene structures and protein domain ... Phylogenetic studies included data retrieved from public web-based databases, freely available (NCBI)3, Plaza4; e!EnsemblPlants ...

... including topological and structural classification in biochemistry, and prediction of protein-protein and domain-domain ... Efficient Algorithms for Structural Recall in Databases (Hao Wang, Patra Volarath, and Robert W. Harrison) ... Computational Approaches to Predict Protein-Protein and Domain-Domain Interactions (Raja Jothi and Teresa M. Przytycka) ... Algorithmic approaches in structural and systems biology, ... Part V: Structural and Systems Biology.. 19. Topological ...

The use of the protein database offers the possibility of determining the similarity of the novel protein of interest with ... This could also be compared to discrete motifs and domains in the protein where there is complete sequence similarity with that ... Structural similarity, serological and sequence homology; the principal aim of this is to determine whether and to what level ... This means that there is a need for improving the methods that are used in plant profiling of their proteins as well as ...

GenDiS database update with improved approach and features to recognize homologous sequences of protein domain superfamilies.. ... survey of remote homologues for protein domain superfamilies of known structure reveals unequal distribution across structural ...