Modeling in Biology - Server users.dimi.uniud.it
... identification, characterization and classification of the logical and informational modules that operate in cells. For example, the types of modules that may be involved in the dynamics of intracellular communication include feedback loops, switches, timers, oscillators and amplifiers. Many of thes ...
... identification, characterization and classification of the logical and informational modules that operate in cells. For example, the types of modules that may be involved in the dynamics of intracellular communication include feedback loops, switches, timers, oscillators and amplifiers. Many of thes ...
VSV Poster - Wake Forest College
... negative sense single-stranded RNA viruses. Rabies, Ebola, and influenza A are examples of other viruses in this family but these viruses are infectious and potentially deadly to humans, making them difficult to study. Thus the cellular biochemistry of VSV is fundamentally interesting as it may serv ...
... negative sense single-stranded RNA viruses. Rabies, Ebola, and influenza A are examples of other viruses in this family but these viruses are infectious and potentially deadly to humans, making them difficult to study. Thus the cellular biochemistry of VSV is fundamentally interesting as it may serv ...
Structural basis of ubiquitylation Andrew P VanDemark and
... Doc domain adopts a ‘jelly roll’ fold, which has been seen in many other protein structures and typically functions to bind a ligand, such as a sugar, nucleotide, phospholipid, nucleic acid or protein. Interestingly, the conserved APC10 residues cluster at the putative ligand-binding cleft and a tem ...
... Doc domain adopts a ‘jelly roll’ fold, which has been seen in many other protein structures and typically functions to bind a ligand, such as a sugar, nucleotide, phospholipid, nucleic acid or protein. Interestingly, the conserved APC10 residues cluster at the putative ligand-binding cleft and a tem ...
Wheat Quality Analysis - Commodity Inspection Services
... Test weight is obtained by pouring (until it just overflows) a well-mixed sample into a Schopper Chondrometer which consists of a half litre aluminium measuring cylinder equipped with a cup and a striking blade. The Chondrometer is weighed empty prior to use and in testing a grain sample with the us ...
... Test weight is obtained by pouring (until it just overflows) a well-mixed sample into a Schopper Chondrometer which consists of a half litre aluminium measuring cylinder equipped with a cup and a striking blade. The Chondrometer is weighed empty prior to use and in testing a grain sample with the us ...
Tyrosine cross-linking of extracellular matrix is catalyzed by Duox, a
... and consists of a COOH-terminal flavoprotein domain containing the NADPH-binding site (Rotrosen et al., 1992; Segal et al., 1992; Taylor et al., 1993; Takeshige and Sumimoto, 1994) and an NH2-terminal hydrophobic region comprised of five to six transmembrane helices and harboring the two heme grou ...
... and consists of a COOH-terminal flavoprotein domain containing the NADPH-binding site (Rotrosen et al., 1992; Segal et al., 1992; Taylor et al., 1993; Takeshige and Sumimoto, 1994) and an NH2-terminal hydrophobic region comprised of five to six transmembrane helices and harboring the two heme grou ...
INFERRING PROPERTY SELECTION PRESSURE FROM
... single amino acid present, all properties will have zero variance. In addition, a variance-based measure is inadequate because it fails to penalize for residues that have not been observed. Figure 2 illustrates this point for an example protein. Shown is the distribution of amino acids at position 8 ...
... single amino acid present, all properties will have zero variance. In addition, a variance-based measure is inadequate because it fails to penalize for residues that have not been observed. Figure 2 illustrates this point for an example protein. Shown is the distribution of amino acids at position 8 ...
Prediction of protease substrates using sequence
... cells. While substrates for both types of proteases have been determined experimentally, there are many more yet to be discovered in humans and other metazoans. Here, we present a bioinformatics method based on support vector machine (SVM) learning that identifies sequence and structural features imp ...
... cells. While substrates for both types of proteases have been determined experimentally, there are many more yet to be discovered in humans and other metazoans. Here, we present a bioinformatics method based on support vector machine (SVM) learning that identifies sequence and structural features imp ...
Based Method for Identification of Horizontal Gene Transfer in Bacteria
... Horizontal gene transfer (HGT) or lateral gene transfer is the passing of genetic material from one organism to another, other than by descent in which genetic information travels through the generations as the cell divides. In nature, gene transfer occurs between two same species or closely related ...
... Horizontal gene transfer (HGT) or lateral gene transfer is the passing of genetic material from one organism to another, other than by descent in which genetic information travels through the generations as the cell divides. In nature, gene transfer occurs between two same species or closely related ...
HHMI meeting, FOLDING
... This was a “chemical logic”. However, although protein folding intermediates (like MG) were found for many proteins, the main question as to how the protein chain can find its native structure among zillions of alternatives remained unanswered. A progress in the understanding was achieved when studi ...
... This was a “chemical logic”. However, although protein folding intermediates (like MG) were found for many proteins, the main question as to how the protein chain can find its native structure among zillions of alternatives remained unanswered. A progress in the understanding was achieved when studi ...
Study of the arginine repressor in different organisms
... Arginine repressors bind as hexamers to a tandem pair of ARG boxes, each consisting of a 18 bp imperfect palindromic sequence. The repressor makes contacts with two major groove segments and the intermediate minor groove segment of each box at the same face of the DNA helix. ArgR proteins and their ...
... Arginine repressors bind as hexamers to a tandem pair of ARG boxes, each consisting of a 18 bp imperfect palindromic sequence. The repressor makes contacts with two major groove segments and the intermediate minor groove segment of each box at the same face of the DNA helix. ArgR proteins and their ...
Amino Acid Starter Kit
... Amino Acids are small molecules used by cells to make proteins. There are 20 Amino Acids and each one consists of two parts — a Backbone and a Sidechain. The backbone is the same in all 20 Amino Acids and the sidechain is different in each one. Each sidechain consists of a unique combination of atom ...
... Amino Acids are small molecules used by cells to make proteins. There are 20 Amino Acids and each one consists of two parts — a Backbone and a Sidechain. The backbone is the same in all 20 Amino Acids and the sidechain is different in each one. Each sidechain consists of a unique combination of atom ...
Is structural flexibility of antigen-binding loops
... preceding studies, because replacement mutations occurred at random, and differed in numbers and positions in CDR and FR, we could not correlate changes between primary ...
... preceding studies, because replacement mutations occurred at random, and differed in numbers and positions in CDR and FR, we could not correlate changes between primary ...
Koi Food facts and Nutrition myths Duncan Griffiths
... protein as opposed to lower more staple food winter argument, has raged for ages, and it’s a real complex issue and there is no specific answer as we are dealing with captive carp V’s wild carp and the requirement or rather what’s available to wild carp differs immensely. But when you look at real w ...
... protein as opposed to lower more staple food winter argument, has raged for ages, and it’s a real complex issue and there is no specific answer as we are dealing with captive carp V’s wild carp and the requirement or rather what’s available to wild carp differs immensely. But when you look at real w ...
Dm1-MMP, a Matrix Metalloproteinase from Drosophila with a
... residue that distinguishes MMPs from other metalloproteinases. This catalytic domain also has a Met residue seven residues COOH-terminal to the zinc-binding site, conserved in all MMPs and proposed to play an essential role in the structure of the active sites of these enzymes (37). Finally, the ded ...
... residue that distinguishes MMPs from other metalloproteinases. This catalytic domain also has a Met residue seven residues COOH-terminal to the zinc-binding site, conserved in all MMPs and proposed to play an essential role in the structure of the active sites of these enzymes (37). Finally, the ded ...
A toolbox for validation of mass spectrometry peptides identification
... assigned to each peptide spectrum matches (PSMs). For each query, PSMs are ranked according to their score. Mascot then groups PSMs into protein hits. A hit contains not only all proteins covered by the same set of PSMs but also all proteins covered by a subset of these PSMs. A hit score, based on ...
... assigned to each peptide spectrum matches (PSMs). For each query, PSMs are ranked according to their score. Mascot then groups PSMs into protein hits. A hit contains not only all proteins covered by the same set of PSMs but also all proteins covered by a subset of these PSMs. A hit score, based on ...
WrkSht4-AAroles-Mutations
... amino acids were equally represented in DHFR, there would be approximately 159 residues/20 = 8 of each. Amino acids that occur much more often than that in DHFR include Asp (14), Ala (13), and Ile (12). What is the least common hydrophobic amino acid in DHFR? ___________ with _______ examples Kinema ...
... amino acids were equally represented in DHFR, there would be approximately 159 residues/20 = 8 of each. Amino acids that occur much more often than that in DHFR include Asp (14), Ala (13), and Ile (12). What is the least common hydrophobic amino acid in DHFR? ___________ with _______ examples Kinema ...
The Art of Multiple Sequence Alignment in R
... with another sequence, merging with another set of sequences, and so-forth until all the sequences are aligned. This process is iterated to further refine the alignment. There are other functions that extend use of AlignSeqs for different purposes: 1. The first is AlignTranslation, which will align ...
... with another sequence, merging with another set of sequences, and so-forth until all the sequences are aligned. This process is iterated to further refine the alignment. There are other functions that extend use of AlignSeqs for different purposes: 1. The first is AlignTranslation, which will align ...
Genes affecting starch biosynthesis exert pleiotropic effects on the
... protein or starch. There are therefore two methods for modifying the protein content of the dry seed: ®rstly, to manipulate those genes which directly affect the synthesis of the proteins themselves; secondly, to shift partitioning of carbon towards protein by reducing the synthesis of starch. A num ...
... protein or starch. There are therefore two methods for modifying the protein content of the dry seed: ®rstly, to manipulate those genes which directly affect the synthesis of the proteins themselves; secondly, to shift partitioning of carbon towards protein by reducing the synthesis of starch. A num ...
Protein Interactions Techniques and Challenges
... There are a lot of false positive solutions that produce similar scores In some cases the correct solution is not among the first ranked results Thessaloniki, October 2009 ...
... There are a lot of false positive solutions that produce similar scores In some cases the correct solution is not among the first ranked results Thessaloniki, October 2009 ...
Attributes Tutorial
... Apply. The coloring shows that many positions in or near the binding site are highly conserved. The Render by Attribute dialog also lists the residue attribute mavPercentConserved. Whereas mavConservation changes along with the Conservation calculation method, mavPercentConserved is always the perce ...
... Apply. The coloring shows that many positions in or near the binding site are highly conserved. The Render by Attribute dialog also lists the residue attribute mavPercentConserved. Whereas mavConservation changes along with the Conservation calculation method, mavPercentConserved is always the perce ...
PERG Survey (2007) Bottlenecks in Protein Expression The goal of
... 5. What systems do people use and what are the success rates? 6. Utility and benefits of large-scale mammalian cell culture 7. Final buffer configurations to minimize aggregation 8. Purification conditions 9. How do people handle protein solubility problems? ...
... 5. What systems do people use and what are the success rates? 6. Utility and benefits of large-scale mammalian cell culture 7. Final buffer configurations to minimize aggregation 8. Purification conditions 9. How do people handle protein solubility problems? ...
Protein thermal stability: insights from atomic displacement
... shortening of loops, increased hydrophobicity and decreased flexibility of α-helical segments and subunit interfaces (Kelly et al., 1993; Russell et al., 1997) have been proposed as important factors conferring thermal stability. In the case of Che Y protein from Thermotoga maritama, thermal stabili ...
... shortening of loops, increased hydrophobicity and decreased flexibility of α-helical segments and subunit interfaces (Kelly et al., 1993; Russell et al., 1997) have been proposed as important factors conferring thermal stability. In the case of Che Y protein from Thermotoga maritama, thermal stabili ...
AlgPred: prediction of allergenic proteins and mapping of
... used as an input vector of dimension 20 for training and testing of SVM (33–35). The performance of SVM-based methods has been optimized by tuning SVM parameters, in order to achieve maximum accuracy with nearly equal sensitivity and specificity. As shown in Table 1, we achieved accuracy around 85% ...
... used as an input vector of dimension 20 for training and testing of SVM (33–35). The performance of SVM-based methods has been optimized by tuning SVM parameters, in order to achieve maximum accuracy with nearly equal sensitivity and specificity. As shown in Table 1, we achieved accuracy around 85% ...
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.