as a PDF
... The G protein sequences of fourteen animal rhabdoviruses, representing all four recognized genera (Vesiculovirus, Lyssavirus, Ephemerovirus and Novirhabdovirus) and the ungrouped sigma virus, were aligned using CLUSTAL W and adjusted to account for obvious sequence similarities not detected by the a ...
... The G protein sequences of fourteen animal rhabdoviruses, representing all four recognized genera (Vesiculovirus, Lyssavirus, Ephemerovirus and Novirhabdovirus) and the ungrouped sigma virus, were aligned using CLUSTAL W and adjusted to account for obvious sequence similarities not detected by the a ...
SPSO: Synthetic Protein Sequence Oversampling for imbalanced
... oversampling (rHMMp). Our method (SPSO) outperforms the other two methods especially for families in which we have a low number of sequences, although the quality of the SMOTE is comparable to the SPSO method. ...
... oversampling (rHMMp). Our method (SPSO) outperforms the other two methods especially for families in which we have a low number of sequences, although the quality of the SMOTE is comparable to the SPSO method. ...
3did: a catalog of domain-based interactions of
... place within and between cells. However, they seldom act alone and it is their complex interrelationships that will ultimately determine the behavior of a biological system. For this reason, large efforts have been devoted to unveiling the complex network of interactions between proteins underlying ...
... place within and between cells. However, they seldom act alone and it is their complex interrelationships that will ultimately determine the behavior of a biological system. For this reason, large efforts have been devoted to unveiling the complex network of interactions between proteins underlying ...
The structure and function of proline
... region (Q approx. + 150 0). Surveys of prolines in crystal structures show that roughly 44 % of prolines are in the a region and 560% are in the ,3 region [4,5]. Second, the bulkiness of the N-CH2 group places restrictions on the conformation of the residue preceding proline [6], disfavouring the a- ...
... region (Q approx. + 150 0). Surveys of prolines in crystal structures show that roughly 44 % of prolines are in the a region and 560% are in the ,3 region [4,5]. Second, the bulkiness of the N-CH2 group places restrictions on the conformation of the residue preceding proline [6], disfavouring the a- ...
High Resolution Structure of the Neisseria gonorrhoeae Type IV
... enormously by the then new area detectors installed at SSRL according to John Tainer 2. Full length pilin structures were determined for Neisseria gonorrhoeae and Pseudomonas aeruginosa, and a truncated structure lacking the hydrophobic N-terminus was determined for Vibrio cholerae 2, 3. In a recent ...
... enormously by the then new area detectors installed at SSRL according to John Tainer 2. Full length pilin structures were determined for Neisseria gonorrhoeae and Pseudomonas aeruginosa, and a truncated structure lacking the hydrophobic N-terminus was determined for Vibrio cholerae 2, 3. In a recent ...
Structural disorder serves as a weak signal for
... danag/d-box/main.html, whereas KEN box content was determined by a sequence search for the KENxxxN/D motif. Low-complexity regions (LowComplex) were computed with program ‘‘seg’’ from the NCBI,30 and protein extinction coefficients (pExtCoeff) were calculated as described in.31 The influence of the ...
... danag/d-box/main.html, whereas KEN box content was determined by a sequence search for the KENxxxN/D motif. Low-complexity regions (LowComplex) were computed with program ‘‘seg’’ from the NCBI,30 and protein extinction coefficients (pExtCoeff) were calculated as described in.31 The influence of the ...
Data resource: In this database, 650 alternatively translated variants
... tree structure of species on the web page classifying the database entries of alternative translational initiation. When users click the leaf of the tree such as 'Metazoa--Vertebrata--Mammalia-- Bostaurus', the entries of this species are expanded. The program outputs an HTML-generated table of thes ...
... tree structure of species on the web page classifying the database entries of alternative translational initiation. When users click the leaf of the tree such as 'Metazoa--Vertebrata--Mammalia-- Bostaurus', the entries of this species are expanded. The program outputs an HTML-generated table of thes ...
A new method for predicting signal sequence cleavage sites
... a standard weight-matrix approach easily implemented even on a micro-ccmputer, it is possible to set up a prediction method that (i) provides a clean discrimination between signal sequences and the N-termlnal region in cytosollc proteins, and (li) can be expected to identify the correct cleavage sit ...
... a standard weight-matrix approach easily implemented even on a micro-ccmputer, it is possible to set up a prediction method that (i) provides a clean discrimination between signal sequences and the N-termlnal region in cytosollc proteins, and (li) can be expected to identify the correct cleavage sit ...
Supplementary Information (doc 48K)
... acidification. Peptides were extracted by acetonitrile/water and desalted and concentrated ...
... acidification. Peptides were extracted by acetonitrile/water and desalted and concentrated ...
No Slide Title
... Biochemistry 412 Analytical & Preparative Protein Chemistry II 4 February 2005 ...
... Biochemistry 412 Analytical & Preparative Protein Chemistry II 4 February 2005 ...
MH n
... High mass accuracy – what is it good for? All theoretical tryptic peptide masses from human IPI database Example Tryptic HSP-70 peptide: ...
... High mass accuracy – what is it good for? All theoretical tryptic peptide masses from human IPI database Example Tryptic HSP-70 peptide: ...
... modified and do not ionize. Show your work. Choice B: Determine the charge at pH 3.8 for the peptide discussed in the previous question. You may assume that the more acidic residue has a neutral charge when protonated, and the other a positive charge when protonated. Remember that the termini are mo ...
Gift of Protein Activity
... c. What does your finished bracelet (with the knot tied) represent? Explain. ...
... c. What does your finished bracelet (with the knot tied) represent? Explain. ...
Anti-UBR1 Antibody
... heart. In mouse embryo, UBR1 is primarily expressed in the branchial arches and in the tail and limb buds. UBR1 is located on mouse chromosome 2 and on human chromosome 15 in the syntenic region. The UBR1-selective antibodies were generated against unique N-terminal peptides characteristics of the p ...
... heart. In mouse embryo, UBR1 is primarily expressed in the branchial arches and in the tail and limb buds. UBR1 is located on mouse chromosome 2 and on human chromosome 15 in the syntenic region. The UBR1-selective antibodies were generated against unique N-terminal peptides characteristics of the p ...
1447437435_Sequence alignment GPU
... A pairwise semi-global alignment is like pairwise global alignment but ignoring start gaps, i.e. gaps that occur before the first character in a sequence, and end gaps, i.e., gaps that occur after the last character of a sequence. An overlap of two sequences is considered an alignment where start an ...
... A pairwise semi-global alignment is like pairwise global alignment but ignoring start gaps, i.e. gaps that occur before the first character in a sequence, and end gaps, i.e., gaps that occur after the last character of a sequence. An overlap of two sequences is considered an alignment where start an ...
7.06 Cell Biology EXAM #3 KEY
... sequence? If yes, which enzyme would remove the signal sequence from signal peptidase? Yes, by signal peptidase already present in the ER lumen. All cells come from other cells, so when a eukaryotic cell is born, it already has ER that came from the mother cell. This ER already has old signal peptid ...
... sequence? If yes, which enzyme would remove the signal sequence from signal peptidase? Yes, by signal peptidase already present in the ER lumen. All cells come from other cells, so when a eukaryotic cell is born, it already has ER that came from the mother cell. This ER already has old signal peptid ...
Structural Studies of DsbA and its Putative Partner, VKOR, in
... be re-oxidized by its putative partner, vitamin K epoxide reductase (VKOR). The intent of this study is to further investigate the molecular determinants of the interactions between DsbA and VKOR by X-ray crystallography. In order to achieve this, DsbA crystals were grown in order to be soaked with ...
... be re-oxidized by its putative partner, vitamin K epoxide reductase (VKOR). The intent of this study is to further investigate the molecular determinants of the interactions between DsbA and VKOR by X-ray crystallography. In order to achieve this, DsbA crystals were grown in order to be soaked with ...
Convolutional LSTM Networks for Subcellular Localization of Proteins
... Thus, its input is not only sequence, but also metadata derived from homology searches. ...
... Thus, its input is not only sequence, but also metadata derived from homology searches. ...
De Novo Sequencing and Homology Search with De Novo
... Problem: Two ion series defining partial sequences LSLV and LVES have been identified, but it is not known if these are y- or bions (i.e., the sequence direction is unknown). Solution: Since ion trap data often exhibits high mass b-ions, check to see if the highest mass ion in either series correspo ...
... Problem: Two ion series defining partial sequences LSLV and LVES have been identified, but it is not known if these are y- or bions (i.e., the sequence direction is unknown). Solution: Since ion trap data often exhibits high mass b-ions, check to see if the highest mass ion in either series correspo ...
Small-angle scattering studies of intrinsically disordered proteins
... proteins. In order to fully exploit the structural and dynamic information encoded in SAS data, it is necessary to use realistic three-dimensional (3D) models. However, the generation of conformational ensembles of disordered proteins is extremely challenging, mainly because of the flat energy lands ...
... proteins. In order to fully exploit the structural and dynamic information encoded in SAS data, it is necessary to use realistic three-dimensional (3D) models. However, the generation of conformational ensembles of disordered proteins is extremely challenging, mainly because of the flat energy lands ...
Caulobacter Export™ Manual
... or when inserted into a “permissive site” in the complete gene (6, 10, 11). In addition, the Slayer crystallization and surface attachment processes can also be remarkably tolerant of significant additions of foreign protein at selected permissive sites. There are no guarantees that any sequence wil ...
... or when inserted into a “permissive site” in the complete gene (6, 10, 11). In addition, the Slayer crystallization and surface attachment processes can also be remarkably tolerant of significant additions of foreign protein at selected permissive sites. There are no guarantees that any sequence wil ...
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.