![Predicting the Secondary Structure of Globular Proteins Using](http://s1.studyres.com/store/data/006086091_1-8df411a3aa06ef12e4fd338b67164db4-300x300.png)
Predicting the Secondary Structure of Globular Proteins Using
... network models are designed to mimic them. This study was inspired by a previous application of network .learning to the problem of text-to-speech. In the NETtalk system (Sejnowski & Rosenberg, 1987), the input to the network is strings of letters representing words and the output is strings of phon ...
... network models are designed to mimic them. This study was inspired by a previous application of network .learning to the problem of text-to-speech. In the NETtalk system (Sejnowski & Rosenberg, 1987), the input to the network is strings of letters representing words and the output is strings of phon ...
Cloning and structure of three rainbow trout C3
... C3-1 apparently lacks Con A-binding carbohydrates in its a-chain, where an N-glycosylation site is predicted. Since Con A recognizes only high-mannose carbohydrates, the presence of carbohydrates that do not bind Con A cannot be excluded. Because the a-chain carbohydrate moiety in human C3 is involv ...
... C3-1 apparently lacks Con A-binding carbohydrates in its a-chain, where an N-glycosylation site is predicted. Since Con A recognizes only high-mannose carbohydrates, the presence of carbohydrates that do not bind Con A cannot be excluded. Because the a-chain carbohydrate moiety in human C3 is involv ...
Defelipe, L.A, Dolghih E, Roitberg A.E., Nouzova M., Mayoral
... contrast, the amino acid identities between AeJHAMT and these four proteins varied between 62.6% (A. gambiae) and 40.6% (T. castaneum); furthermore, the important residues for catalysis and cofactor binding are well conserved. Using the Modeller9v4 program and the AeJHAMT homology model as template ...
... contrast, the amino acid identities between AeJHAMT and these four proteins varied between 62.6% (A. gambiae) and 40.6% (T. castaneum); furthermore, the important residues for catalysis and cofactor binding are well conserved. Using the Modeller9v4 program and the AeJHAMT homology model as template ...
The 10.8-AA structure of Saccharomyces cerevisiae
... (Radermacher, 1997, 2001) in 30° angular increments and a strongly low-pass-filtered reference (7 nm) to minimize the bias of the alignment by the reference. The aligned projections were used to create a new volume that, properly filtered to low resolution, was used as reference for the following alig ...
... (Radermacher, 1997, 2001) in 30° angular increments and a strongly low-pass-filtered reference (7 nm) to minimize the bias of the alignment by the reference. The aligned projections were used to create a new volume that, properly filtered to low resolution, was used as reference for the following alig ...
Essential Bioinformatics and Biocomputing
... • If we blindly interpret these results, we would erroneously conclude that motif VLADIMIR may have some functional importance for structure or function of the strawberry vein binding virus, and that TINWEE has to do with calciumdependent protein kinase in rice and possibly in Legionella pneumophila ...
... • If we blindly interpret these results, we would erroneously conclude that motif VLADIMIR may have some functional importance for structure or function of the strawberry vein binding virus, and that TINWEE has to do with calciumdependent protein kinase in rice and possibly in Legionella pneumophila ...
Abstract
... and study thermodynamics of the complex formation. Using these analyses it was established that the hook domain demonstrates extremely high stability of the metal mediated-dimer (logK12 = 20.74) and extensive structural changes upon Zn(II)-binding. It was established that the >650 000-fold increase ...
... and study thermodynamics of the complex formation. Using these analyses it was established that the hook domain demonstrates extremely high stability of the metal mediated-dimer (logK12 = 20.74) and extensive structural changes upon Zn(II)-binding. It was established that the >650 000-fold increase ...
Nucleic Acids Research
... Among the non-nucleic acid-binding is the cytochrome P450terp (1cpt) in which the large positive patch is known, to be functional, possibly involved in protein–protein interaction (22). In addition, we show a relative small patch found in the barstar protein (1bta) which does not have a known functi ...
... Among the non-nucleic acid-binding is the cytochrome P450terp (1cpt) in which the large positive patch is known, to be functional, possibly involved in protein–protein interaction (22). In addition, we show a relative small patch found in the barstar protein (1bta) which does not have a known functi ...
STING Millennium: a web-based suite of programs
... visualization of numerical value for any given parameter and for any amino acid in the sequence, might be easily achieved by color coding. This is the crucial difference between existing software packages (2,3) on one side and our SMS component—Protein Dossier. The constant increase in accumulation ...
... visualization of numerical value for any given parameter and for any amino acid in the sequence, might be easily achieved by color coding. This is the crucial difference between existing software packages (2,3) on one side and our SMS component—Protein Dossier. The constant increase in accumulation ...
What is NPN in feed, How does it work
... down the digestive tract. Simple stomach animal such as pigs and chickens cannot use NPN in large amounts because of the lack of bacteria and enzymes to break down the NPN to ammonia and synthesize it into proteins. The most common source of NPN used in feeds is urea. Other products include biuret ( ...
... down the digestive tract. Simple stomach animal such as pigs and chickens cannot use NPN in large amounts because of the lack of bacteria and enzymes to break down the NPN to ammonia and synthesize it into proteins. The most common source of NPN used in feeds is urea. Other products include biuret ( ...
ProRule: a new database containing functional
... the function or structure of a domain or protein. In the absence of the physico-chemical properties associated with them, the proper reaction cannot take place and the function or structure will be altered. The fact that profiles generally cover domains or proteins over their entire length makes the ...
... the function or structure of a domain or protein. In the absence of the physico-chemical properties associated with them, the proper reaction cannot take place and the function or structure will be altered. The fact that profiles generally cover domains or proteins over their entire length makes the ...
15 Tacks and a 4 Foot Toober
... After everyone has folded their toober as best they can, the teacher can point out: • Every toober had a different random sequence of tacks (amino acids) and therefore each toober (protein) folded into a different structure. • Some sequences of tacks were more easily folded into a reasonable structu ...
... After everyone has folded their toober as best they can, the teacher can point out: • Every toober had a different random sequence of tacks (amino acids) and therefore each toober (protein) folded into a different structure. • Some sequences of tacks were more easily folded into a reasonable structu ...
Basic Peptide Bonds
... that can be used to identify the protein structures involved in this process are still being investigated to better understand how this process works in the body naturally. The sequences of amino acids in polypeptides are controlled by codons which are located in the mRNA molecules that were used by ...
... that can be used to identify the protein structures involved in this process are still being investigated to better understand how this process works in the body naturally. The sequences of amino acids in polypeptides are controlled by codons which are located in the mRNA molecules that were used by ...
CIP Posters - International Potato Center
... factors involved in various physiologial processes in plants, including pathogen defence. WRKY transciption factors have been shown to act as both negative and positive regulators of defence, suggesting that they may operate through different regulatory complexes. The different roles can be partly d ...
... factors involved in various physiologial processes in plants, including pathogen defence. WRKY transciption factors have been shown to act as both negative and positive regulators of defence, suggesting that they may operate through different regulatory complexes. The different roles can be partly d ...
Divergent Evolution of Function in the ROK Sugar
... members of the functionally diverse ROK (repressor, open reading frame, kinase) superfamily. Previous work in our laboratory has demonstrated that AlsK and NanK possess weak phosphoryl transfer activity toward the alternate substrate D-glucose. To gain insight into the evolutionary mechanisms that f ...
... members of the functionally diverse ROK (repressor, open reading frame, kinase) superfamily. Previous work in our laboratory has demonstrated that AlsK and NanK possess weak phosphoryl transfer activity toward the alternate substrate D-glucose. To gain insight into the evolutionary mechanisms that f ...
Crystal structure of yeast hexokinase Pl in complex
... amino acid residue). If the amino acid distribution at the former position in the alignment varies (which is reflected in a high value for DDG stat), this means that for some reason, normally related to the structure and/or function of the protein, these two positions coevolved together, as suggeste ...
... amino acid residue). If the amino acid distribution at the former position in the alignment varies (which is reflected in a high value for DDG stat), this means that for some reason, normally related to the structure and/or function of the protein, these two positions coevolved together, as suggeste ...
Soy protein isolate
... Unlike most other beans, soybeans provide a “complete” protein profile. Soybeans contain all the essential amino acids that we need from our diet, because our bodies are simply not capable of synthesizing them. ...
... Unlike most other beans, soybeans provide a “complete” protein profile. Soybeans contain all the essential amino acids that we need from our diet, because our bodies are simply not capable of synthesizing them. ...
Can correct protein models be identified?
... The ability to separate correct models of protein structures from less correct models is of the greatest importance for protein structure prediction methods. Several studies have examined the ability of different types of energy function to detect the native, or native-like, protein structure from a ...
... The ability to separate correct models of protein structures from less correct models is of the greatest importance for protein structure prediction methods. Several studies have examined the ability of different types of energy function to detect the native, or native-like, protein structure from a ...
Microsoft Word - Lab05WalrusesWhalesWeasels
... 2. NOTE: Phylogenetic trees built with this software can only be used to make conclusions about common ancestry. They cannot be used to make conclusions about the timeframe of evolution. The length of branches is not a measure of evolutionary time. It is merely an artifact of physically arranging th ...
... 2. NOTE: Phylogenetic trees built with this software can only be used to make conclusions about common ancestry. They cannot be used to make conclusions about the timeframe of evolution. The length of branches is not a measure of evolutionary time. It is merely an artifact of physically arranging th ...
MOLECULAR VISUALIZATION LAB (replacing Ch 11) OF LDH
... "Databases May Put Drugs on Shelves Years Faster" they cited the increasing efforts by thousands of biotechnology firms to use available DNA sequence and protein structure data to supplement, or even replace, the high cost trial-and-error work of drug design. Scientists are manipulating almost every ...
... "Databases May Put Drugs on Shelves Years Faster" they cited the increasing efforts by thousands of biotechnology firms to use available DNA sequence and protein structure data to supplement, or even replace, the high cost trial-and-error work of drug design. Scientists are manipulating almost every ...
ppt - Bio 5068
... ~30 different small molecule-VP35 IID structures provides a comprehensive SAR dataset Currently, the efficacy and PD/PK characteristics are being tested. ...
... ~30 different small molecule-VP35 IID structures provides a comprehensive SAR dataset Currently, the efficacy and PD/PK characteristics are being tested. ...
Classification and Phylogenetic Analysis of the cAMP
... sition-specific iterated BLAST) (Altschul et al. 1997) set to search the nonredundant database using human RI␣ as the query sequence and a BLOSUM62 weight matrix (Henikoff and Henikoff 1992). Sequences identified in this first stage were used as query sequences for subsequent searches. Sequences une ...
... sition-specific iterated BLAST) (Altschul et al. 1997) set to search the nonredundant database using human RI␣ as the query sequence and a BLOSUM62 weight matrix (Henikoff and Henikoff 1992). Sequences identified in this first stage were used as query sequences for subsequent searches. Sequences une ...
Homology Modelling
... biological process of protein folding. A VERY DIFFICULT task because a protein chain can fold into millions of different conformations. Use it only when no detectable homologues are available. ...
... biological process of protein folding. A VERY DIFFICULT task because a protein chain can fold into millions of different conformations. Use it only when no detectable homologues are available. ...
Structural and functional features of Drosophila chorion proteins s36
... (V, L, I, F, W, Y, T, C; Ref. 17) which are out of phase. In s36 a nine-residue periodicity for/Y-turn formers and/3sheet formers is also out of phase. Prediction of secondary structure shows the prevalence of short fl-sheet strands alternating regularly with fl-turns in the central domain (Figure 2 ...
... (V, L, I, F, W, Y, T, C; Ref. 17) which are out of phase. In s36 a nine-residue periodicity for/Y-turn formers and/3sheet formers is also out of phase. Prediction of secondary structure shows the prevalence of short fl-sheet strands alternating regularly with fl-turns in the central domain (Figure 2 ...
The cyanide hydratase from Neurospora crassa forms a helix
... iterative helical real space reconstruction (IHRSR; Egelman 2000). Starting models were either a 12-nm-diameter featureless cylinder or a fiber generated by applying the helical symmetry operators to the homology model. All parameters indicative of correct alignment were monitored during the reconst ...
... iterative helical real space reconstruction (IHRSR; Egelman 2000). Starting models were either a 12-nm-diameter featureless cylinder or a fiber generated by applying the helical symmetry operators to the homology model. All parameters indicative of correct alignment were monitored during the reconst ...
Structural alignment
![](https://commons.wikimedia.org/wiki/Special:FilePath/Alignment_of_thioredoxins2.png?width=300)
Structural alignment attempts to establish homology between two or more polymer structures based on their shape and three-dimensional conformation. This process is usually applied to protein tertiary structures but can also be used for large RNA molecules. In contrast to simple structural superposition, where at least some equivalent residues of the two structures are known, structural alignment requires no a priori knowledge of equivalent positions. Structural alignment is a valuable tool for the comparison of proteins with low sequence similarity, where evolutionary relationships between proteins cannot be easily detected by standard sequence alignment techniques. Structural alignment can therefore be used to imply evolutionary relationships between proteins that share very little common sequence. However, caution should be used in using the results as evidence for shared evolutionary ancestry because of the possible confounding effects of convergent evolution by which multiple unrelated amino acid sequences converge on a common tertiary structure.Structural alignments can compare two sequences or multiple sequences. Because these alignments rely on information about all the query sequences' three-dimensional conformations, the method can only be used on sequences where these structures are known. These are usually found by X-ray crystallography or NMR spectroscopy. It is possible to perform a structural alignment on structures produced by structure prediction methods. Indeed, evaluating such predictions often requires a structural alignment between the model and the true known structure to assess the model's quality. Structural alignments are especially useful in analyzing data from structural genomics and proteomics efforts, and they can be used as comparison points to evaluate alignments produced by purely sequence-based bioinformatics methods.The outputs of a structural alignment are a superposition of the atomic coordinate sets and a minimal root mean square deviation (RMSD) between the structures. The RMSD of two aligned structures indicates their divergence from one another. Structural alignment can be complicated by the existence of multiple protein domains within one or more of the input structures, because changes in relative orientation of the domains between two structures to be aligned can artificially inflate the RMSD.