protein families
Functional coherence metrics in protein families
... given protein set (family) should characterize that ...each protein set or family as being its functional characteristic ...in protein families was to resort to term enrichment ...given ...
11
Cysteine associated distribution of aromatic residues in disulfide stabilized extracellular protein families
... Cysteine-dependent protein sequences were down- loaded from annotated database resources to gener- ate comprehensive EGF, Sushi, Laminin and Immu- noglobulin (IgC) motif-specific sequence ...each protein ...
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Tools and resources for identifying protein families, domains and motifs
... well-characterized protein family; derived from the litera- ture; from the results of sequence searches against SWISS- PROT and TrEMBL; or from sequence ...characterized protein families, may have ...
8
COGcollator: a web server for analysis of distant relationships between homologous protein families
... Reviewer 2: In this paper, Dibrova et al. present a web based tool, which enables detection of remote homology between protein families. The tool and underlying process for its development are well ...
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Comparative analysis of rigidity across protein families
... other protein families our data is obtained from single protein chains; for example, for hemoglobin we analyse α-hemoglobin ...a protein chain treated in isolation always has fewer constraints ...
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Ranking and compacting binding segments of protein families using aligned pattern clusters
... Our APC Process greatly reduces the number of APCs in comparison with other methods. This is due to the fact that the APC sstep starts with input patterns from the PD Step rather than the entire input search space. This ...
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Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems
... csf2, csf3 and csf4. The Csf2 protein is a Cas7 group RAMP closely related to the Csm3 subfamily. Csf3 is yet another diverged RAMP protein that might be function- ally analogous to the Cas5 group (Figure ...
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Concerted Evolution of Two Novel Protein Families in Caenorhabditis Species
... extremely stable, since it is orthologous and similarly structured in the three species examined, with a cumu- lative divergence of 200 MY. How the shared sequence is stably maintained is not immediately apparent. It is ...
13
Plant Heat Shock Protein Families: Essential Machinery for Development and Defense
... HSP90 has been reported to be involved in several biological processes. HSP90 has been reported to be actively expressed in root and shoot apices (Koning et al., 1992), flower buds (Krishna et al., 1995), during ...
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Understanding the sequence requirements of protein families: insights from the BioVis 2013 contests
... increase protein stability and function, the crippled phenotype is really an example of the reality that some towards-consensus mutants are damaging to the ...a protein contribute independently to its ...
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Privileged Structures and Polypharmacology within and between Protein Families.
... ABSTRACT: Polypharmacology is often a key contributor to the efficacy of a drug, but is also a potential risk. We investigated two hits discovered via a cell-based phenotypic screen, the CDK9 inhibitor CCT250006 1 and ...
13
Na+ dependent phosphate cotransporters: the NaPi protein families
... either cytoplasmic or extracellular domains. The large loop between hydrophobic regions three and four was found to be glycosylated and therefore extracellular (Hayes et al. 1994). The N and C termini were shown to face ...
8
Evolutionary analysis of protein structural families to assist comparative modelling of genome sequences
... additional protein domains) (Heringa &: Taylor, ...to protein, changes in the DNA sequence may have effects on the amino acid sequence of the protein it ...within protein sequences have ...
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Antibiotic Resistance Gene Diversity and Virulence Gene Diversity Are Correlated in Human Gut and Environmental Microbiomes
... Cooccurrence of AR and VFs belonging to the cell envelope. Our results suggest that cooccurrence of AR and VFs might be taking place amid bacterial communities. We wondered, however, which were the genetic traits that ...
13
Comparing the Bidirectional Baum-Welch Algorithm and the Baum-Welch Algorithm on Regular Lattice
... assigning protein sequences to protein ...a protein family, the information of the corresponding amino acid in the preceding sequence of residues in the PHMM can be ...ten protein ...
9
Comprehensive snake venomics of the Okinawa Habu pit viper, Protobothrops flavoviridis, by complementary mass spectrometry-guided approaches
... mentioned protein families, various bradykinin-potentiating peptides (BPP) and snake venom metalloproteinases inhibitor (svMP-i) are further constituents of snake ...
17
Endoglucanases: insights into thermostability for biofuel applications
... unfolding, number of Van der Waals contacts per resi- due, number of hydrogen bonds per residue, or number of residues involved in secondary structure). Other fac- tors such as Gibbs free energy change of hydration, ...
9
The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes
... the protein- coding genes are compared to protein families ...The protein se- quences are compared to COG PSSMs obtained from the CDD database [10] using the program RPS-BLAST at an e-value ...
5
What is gluten- why is it special?
... gluten protein families, and the presence of related types of protein which may also contribute to functional properties and impacts on ...gluten protein system at the level required by those ...
21
Assessing the Performances of Protein Function Prediction Algorithms from the Perspectives of Identification Accuracy and False Discovery Rate
... of protein function is essential for the study of biological processes, the understanding of disease mechanism and the exploration of novel therapeutic ...for protein function ...on protein sequence ...
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