Dot plot
... • What is the function of P05049? • P05049 is a serine protease. Would you run a wet lab experiment ...
... • What is the function of P05049? • P05049 is a serine protease. Would you run a wet lab experiment ...
294_2005_38_MOESM43_ESM - Springer Static Content Server
... protein, with the exceptions of S. pombe and U. maydis, which both have three different histidine kinases lacking transmembrane domains. The sequences from S. kluyveri and D. hansenii were significantly shorter due to frameshifts, presumably resulting from sequencing errors. For S. kluyveri, the DNA ...
... protein, with the exceptions of S. pombe and U. maydis, which both have three different histidine kinases lacking transmembrane domains. The sequences from S. kluyveri and D. hansenii were significantly shorter due to frameshifts, presumably resulting from sequencing errors. For S. kluyveri, the DNA ...
Relationships between amino acid sequence and backbone torsion
... torsional potentials. In the first approach, we use PDBderived knowledge-based potentials to characterize the pairwise distributions of angles for residues. The knowledge-based potentials are extracted as averages over the native states of large number, low homology proteins. In the second approac ...
... torsional potentials. In the first approach, we use PDBderived knowledge-based potentials to characterize the pairwise distributions of angles for residues. The knowledge-based potentials are extracted as averages over the native states of large number, low homology proteins. In the second approac ...
Structural biology and drug design
... • The method is absolutely depending on formation of protein crystals • Many proteins form crystals under optimal conditions (which are normally not known in advance, hence crystal screening is nessesary) • Thousands of combinations of diffrent protein forms and crystallization conditions may have t ...
... • The method is absolutely depending on formation of protein crystals • Many proteins form crystals under optimal conditions (which are normally not known in advance, hence crystal screening is nessesary) • Thousands of combinations of diffrent protein forms and crystallization conditions may have t ...
SystemsBiologyPaper
... cells in siRNA and injection [13]. Plasmids and viral vectors have also been constructed to produce specific siRNA within a cell population through transfection. There are many methods that are currently being optimized for RNAi based studies [13]. These studies let researchers block the action of a ...
... cells in siRNA and injection [13]. Plasmids and viral vectors have also been constructed to produce specific siRNA within a cell population through transfection. There are many methods that are currently being optimized for RNAi based studies [13]. These studies let researchers block the action of a ...
IOSR Journal of Computer Engineering (IOSR-JCE)
... whole. Conversely, a local sequences alignment is to detect regions of similarity between compared sequences. In local sequence alignment, a number of similar subsequent can be produced. Furthermore, sequences in different species may be similar over short conserved regions and dissimilar over remai ...
... whole. Conversely, a local sequences alignment is to detect regions of similarity between compared sequences. In local sequence alignment, a number of similar subsequent can be produced. Furthermore, sequences in different species may be similar over short conserved regions and dissimilar over remai ...
2-Oxoacid dehydrogenase multienzyme complexes
... volcanii ORF3 encodes an E2-like protein. If this is indeed the case, then the boundaries of typical E2 structural domains and motifs should be identifiable within the predicted amino acid sequence. However, before this can be investigated, account must be taken of the sequence alignments which show ...
... volcanii ORF3 encodes an E2-like protein. If this is indeed the case, then the boundaries of typical E2 structural domains and motifs should be identifiable within the predicted amino acid sequence. However, before this can be investigated, account must be taken of the sequence alignments which show ...
Gene Section MTCP1 (mature T cell proliferation 1) in Oncology and Haematology
... splicing from exon 1 to exon 2; initiation of the transcription: an alternative site of initiation of the transcription in intron 1 has been found in one tumour with a translocation breakpoint in intron 1. ...
... splicing from exon 1 to exon 2; initiation of the transcription: an alternative site of initiation of the transcription in intron 1 has been found in one tumour with a translocation breakpoint in intron 1. ...
Algorithm
... It is apparent that the above array operation can begin at any of a number of points along the borders of the array, which is equivalent to a comparison of N-terminal residues or C-terminal residues only. As long as the appropriate rules for pathways are followed, the maximum match will be the same. ...
... It is apparent that the above array operation can begin at any of a number of points along the borders of the array, which is equivalent to a comparison of N-terminal residues or C-terminal residues only. As long as the appropriate rules for pathways are followed, the maximum match will be the same. ...
Database Modeling in Bioinformatics
... Standardized transfer of annotation from characterized proteins in SWISS-PROT to TrEMBL entries • TrEMBL entry is reliably recognized by a given method as a member of a certain group of proteins • corresponding group of proteins in SWISS-PROT shares certain annotation • common annotation is transfe ...
... Standardized transfer of annotation from characterized proteins in SWISS-PROT to TrEMBL entries • TrEMBL entry is reliably recognized by a given method as a member of a certain group of proteins • corresponding group of proteins in SWISS-PROT shares certain annotation • common annotation is transfe ...
CIP Posters with 2 logos - International Potato Center
... The groups previously classified in Arabidopsis [1] were identified: Group 1 proteins contain 2 WRKY domains and based on the C-terminal WRKY domain alone do not form a clearly supported group in phylogenetic tree. Part of the group 2b proteins cluster together with group 2a proteins. However, these ...
... The groups previously classified in Arabidopsis [1] were identified: Group 1 proteins contain 2 WRKY domains and based on the C-terminal WRKY domain alone do not form a clearly supported group in phylogenetic tree. Part of the group 2b proteins cluster together with group 2a proteins. However, these ...
environmental life cycle assessment of alternative protein sources
... Since our food production are responsible for approx. 1/3 of global environmental impact – and feed production are a major contributor – it is important to explore possibilities to reduce this impact For comparing and improving the environmental impact of alternative protein sources – life cycle ass ...
... Since our food production are responsible for approx. 1/3 of global environmental impact – and feed production are a major contributor – it is important to explore possibilities to reduce this impact For comparing and improving the environmental impact of alternative protein sources – life cycle ass ...
ppt file
... Notice that these are defined from N to C terminus, using main chain atoms only. A residue’s conformation is usually listed as (,), since is close to 180 for almost all residues. ...
... Notice that these are defined from N to C terminus, using main chain atoms only. A residue’s conformation is usually listed as (,), since is close to 180 for almost all residues. ...
An archaebacterial homolog of pelota, a meiotic cell division protein
... protein, but is absent from the predicted PelA protein. The negatively charged carboxy-terminus characteristic of all these eukaryotic pelota homologs is likewise absent from PelA. Both of these features are thus predicted to reflect the presence or function of this protein specifically within eukar ...
... protein, but is absent from the predicted PelA protein. The negatively charged carboxy-terminus characteristic of all these eukaryotic pelota homologs is likewise absent from PelA. Both of these features are thus predicted to reflect the presence or function of this protein specifically within eukar ...
Protein and the Runner
... getting much notice these days; namely the ‘Zone’ and ‘Atkins’ diets. Diets such as these, with extremely low dietary carbohydrate intake, have many negative side effects including decreases in endurance performance, decreased ability to recover after workouts and races, and many potential long-term ...
... getting much notice these days; namely the ‘Zone’ and ‘Atkins’ diets. Diets such as these, with extremely low dietary carbohydrate intake, have many negative side effects including decreases in endurance performance, decreased ability to recover after workouts and races, and many potential long-term ...
Basic Local Alignment Search Tool
... The p-value relates the score returned for an alignment to the likelihood of it having arisen by chance In general, the closer the value approaches zero the greater the con dence that the match is real = 4e-45 (4 x 10−45 ), 4e-16 (4 x 10−16 ), or 1e-05 (1 x 10−05 ) 1e-05 (1 x 10−5 ) indicates that t ...
... The p-value relates the score returned for an alignment to the likelihood of it having arisen by chance In general, the closer the value approaches zero the greater the con dence that the match is real = 4e-45 (4 x 10−45 ), 4e-16 (4 x 10−16 ), or 1e-05 (1 x 10−05 ) 1e-05 (1 x 10−5 ) indicates that t ...
Humans are living significantly longer than ever before, and
... Unfortunately, these variants can incur growth defects at 37°C, probably due to off-target effects (Jackrel et al, 2015). Therefore, engineering more substrate-specific variants represents a priority if Hsp104 is to be used to mitigate the effects of protein aggregation in neurodegeneration. As it h ...
... Unfortunately, these variants can incur growth defects at 37°C, probably due to off-target effects (Jackrel et al, 2015). Therefore, engineering more substrate-specific variants represents a priority if Hsp104 is to be used to mitigate the effects of protein aggregation in neurodegeneration. As it h ...
Multiple Sequence Alignment
... Discouraging too many gaps • If there is no gap opened, then the GOP is increased if the position is within 8 residues of an existing gap. • This discourages gaps that are too close together. • At any position within a run of hydrophilic residues, the GOP is decreased. • These runs usually indicate ...
... Discouraging too many gaps • If there is no gap opened, then the GOP is increased if the position is within 8 residues of an existing gap. • This discourages gaps that are too close together. • At any position within a run of hydrophilic residues, the GOP is decreased. • These runs usually indicate ...
Scottish Phylogeny Discussion Group The James Hutton
... Jim Procter, University of Dundee Abstract: Jalview (www.jalview.org) is a BBSRC funded open source tool for the visualisation and analysis of protein and nucleic acid sequence alignments that is widely used in teaching and research. Available as a web based applet, or Desktop application, version 2 ...
... Jim Procter, University of Dundee Abstract: Jalview (www.jalview.org) is a BBSRC funded open source tool for the visualisation and analysis of protein and nucleic acid sequence alignments that is widely used in teaching and research. Available as a web based applet, or Desktop application, version 2 ...
Cancer Prone Disease Section Chediak-Higashi Syndrome Atlas of Genetics and Cytogenetics
... The first of these domains has been referred to as the BEACH domain. The BEACH domain contains a consensus 'WIDL' amino acid stretch as well as several other conserved amino acids that define members of the CHS protein family. The second domain contains a WD-40 repeat region, indicative of a protein ...
... The first of these domains has been referred to as the BEACH domain. The BEACH domain contains a consensus 'WIDL' amino acid stretch as well as several other conserved amino acids that define members of the CHS protein family. The second domain contains a WD-40 repeat region, indicative of a protein ...
sv-lncs - Department of Computer Science and Engineering
... finding the proteins which host a domain. The number of domains is the vector’s size. Every domain has a unique id where the id is the index in the vector. Every domain also has a linked list of proteins. This list contains all the proteins which host this domain. A data structure is also needed in ...
... finding the proteins which host a domain. The number of domains is the vector’s size. Every domain has a unique id where the id is the index in the vector. Every domain also has a linked list of proteins. This list contains all the proteins which host this domain. A data structure is also needed in ...
Chao, Elizabeth: Critical Analysis of secondary Structure Prediction Algorithms
... database does not allow the evaluation of parameters required for an exact treatment of the problem. GOR IV considers all possible pair frequencies within a window of 17 amino acid residues, improving GOR I to a mean accuracy of 64.4% for a three state prediction (Q3). The predicted secondary struct ...
... database does not allow the evaluation of parameters required for an exact treatment of the problem. GOR IV considers all possible pair frequencies within a window of 17 amino acid residues, improving GOR I to a mean accuracy of 64.4% for a three state prediction (Q3). The predicted secondary struct ...
Homology modeling
Homology modeling, also known as comparative modeling of protein, refers to constructing an atomic-resolution model of the ""target"" protein from its amino acid sequence and an experimental three-dimensional structure of a related homologous protein (the ""template""). Homology modeling relies on the identification of one or more known protein structures likely to resemble the structure of the query sequence, and on the production of an alignment that maps residues in the query sequence to residues in the template sequence. It has been shown that protein structures are more conserved than protein sequences amongst homologues, but sequences falling below a 20% sequence identity can have very different structure.Evolutionarily related proteins have similar sequences and naturally occurring homologous proteins have similar protein structure.It has been shown that three-dimensional protein structure is evolutionarily more conserved than would be expected on the basis of sequence conservation alone.The sequence alignment and template structure are then used to produce a structural model of the target. Because protein structures are more conserved than DNA sequences, detectable levels of sequence similarity usually imply significant structural similarity.The quality of the homology model is dependent on the quality of the sequence alignment and template structure. The approach can be complicated by the presence of alignment gaps (commonly called indels) that indicate a structural region present in the target but not in the template, and by structure gaps in the template that arise from poor resolution in the experimental procedure (usually X-ray crystallography) used to solve the structure. Model quality declines with decreasing sequence identity; a typical model has ~1–2 Å root mean square deviation between the matched Cα atoms at 70% sequence identity but only 2–4 Å agreement at 25% sequence identity. However, the errors are significantly higher in the loop regions, where the amino acid sequences of the target and template proteins may be completely different.Regions of the model that were constructed without a template, usually by loop modeling, are generally much less accurate than the rest of the model. Errors in side chain packing and position also increase with decreasing identity, and variations in these packing configurations have been suggested as a major reason for poor model quality at low identity. Taken together, these various atomic-position errors are significant and impede the use of homology models for purposes that require atomic-resolution data, such as drug design and protein–protein interaction predictions; even the quaternary structure of a protein may be difficult to predict from homology models of its subunit(s). Nevertheless, homology models can be useful in reaching qualitative conclusions about the biochemistry of the query sequence, especially in formulating hypotheses about why certain residues are conserved, which may in turn lead to experiments to test those hypotheses. For example, the spatial arrangement of conserved residues may suggest whether a particular residue is conserved to stabilize the folding, to participate in binding some small molecule, or to foster association with another protein or nucleic acid. Homology modeling can produce high-quality structural models when the target and template are closely related, which has inspired the formation of a structural genomics consortium dedicated to the production of representative experimental structures for all classes of protein folds. The chief inaccuracies in homology modeling, which worsen with lower sequence identity, derive from errors in the initial sequence alignment and from improper template selection. Like other methods of structure prediction, current practice in homology modeling is assessed in a biennial large-scale experiment known as the Critical Assessment of Techniques for Protein Structure Prediction, or CASP.