![Protein](http://s1.studyres.com/store/data/005749520_1-d0021557abea0bb200007198a8301742-300x300.png)
No Slide Title
... Note how the region of a conserved histidine (▼) varies depending on which algorithm is used ...
... Note how the region of a conserved histidine (▼) varies depending on which algorithm is used ...
Similarity
... similarity but have two different functions. For example, human gamma-crystallin is a lens protein that has no known enzymatic activity. It shares a high percentage of identity with E. coli quinone oxidoreductase. These proteins likely had a common ancestor but their functions diverged. ...
... similarity but have two different functions. For example, human gamma-crystallin is a lens protein that has no known enzymatic activity. It shares a high percentage of identity with E. coli quinone oxidoreductase. These proteins likely had a common ancestor but their functions diverged. ...
Alignment scoring statistics and scoring matrices
... random sequences -> harder to assess the significance of a global alignment • Can approximate a score by shuffling the sequences and realigning but this can be misleading • Alignment scores follow the extreme value Gumbel distribution, not a normal distribution ...
... random sequences -> harder to assess the significance of a global alignment • Can approximate a score by shuffling the sequences and realigning but this can be misleading • Alignment scores follow the extreme value Gumbel distribution, not a normal distribution ...
RNA_Structure
... Genetic information copied from DNA is transferred to 3 types of RNA: __________ RNA: mRNA Copy of information in DNA that is brought to the ribosome and translated into PROTEIN by tRNA & rRNA. ( 2%) , 100,000 KINDS. __________ RNA: rRNA Most of the RNA in cells is associated with structures known a ...
... Genetic information copied from DNA is transferred to 3 types of RNA: __________ RNA: mRNA Copy of information in DNA that is brought to the ribosome and translated into PROTEIN by tRNA & rRNA. ( 2%) , 100,000 KINDS. __________ RNA: rRNA Most of the RNA in cells is associated with structures known a ...
Amino acid
... They are characterized by an irregular series of conformational angles that fold the chain back on itself. Turns are often very compact and well ordered, though they are hot-spots for evolution. Sometimes they are sites of flexibility, at other times they are quite rigid. Need to look carefully at t ...
... They are characterized by an irregular series of conformational angles that fold the chain back on itself. Turns are often very compact and well ordered, though they are hot-spots for evolution. Sometimes they are sites of flexibility, at other times they are quite rigid. Need to look carefully at t ...
Lecture 6: Sequence Alignment – Local Alignment
... • It takes a band of 32 letters centered on the init1 segment for calculating the optimal local alignment. • After all sequences in the database are searched the program plots the scores of each database sequence in a histogram, and calculates the statistical significance of each. • The so-called E- ...
... • It takes a band of 32 letters centered on the init1 segment for calculating the optimal local alignment. • After all sequences in the database are searched the program plots the scores of each database sequence in a histogram, and calculates the statistical significance of each. • The so-called E- ...
File
... • How are amino acids linked to form polypeptides – the primary structure of proteins? • How are polypeptides arranged to form the secondary structure and then the tertiary structure of a protein? • How is the quaternary structure of a protein formed? • How are proteins identified? ...
... • How are amino acids linked to form polypeptides – the primary structure of proteins? • How are polypeptides arranged to form the secondary structure and then the tertiary structure of a protein? • How is the quaternary structure of a protein formed? • How are proteins identified? ...
Sturctural and functional prediction of shigella
... multiplication of the organism. • Hydorolase: Play decisive role in synthesis, lysis, invasion of host cells. These processes are essential for survival, growth and development of living organism. We have identified 85 HPs as hydrolase protein. • Lyase: Enzymes playing that may be involved in the re ...
... multiplication of the organism. • Hydorolase: Play decisive role in synthesis, lysis, invasion of host cells. These processes are essential for survival, growth and development of living organism. We have identified 85 HPs as hydrolase protein. • Lyase: Enzymes playing that may be involved in the re ...
Direct-Coupling Analysis (DCA)
... 1) exert selective pressures on each other 2) evolve in response to each other • Molecular co-evolution can be due to specific co-adaptation between the two co-evolving elements, where changes in one of them are compensated by changes in the other, or by a less specific external force affecting the ...
... 1) exert selective pressures on each other 2) evolve in response to each other • Molecular co-evolution can be due to specific co-adaptation between the two co-evolving elements, where changes in one of them are compensated by changes in the other, or by a less specific external force affecting the ...
condensed version - FSU Biology
... The source of the structure and its resolution is always given. Secondary structure boundaries, sequence data, and reference information are often associated with the coordinate data, but it is the 3D data that really matters, not the annotation. ...
... The source of the structure and its resolution is always given. Secondary structure boundaries, sequence data, and reference information are often associated with the coordinate data, but it is the 3D data that really matters, not the annotation. ...
FlexWeb
... Proteins • The ability of proteins to change their conformation is important to their function as biological machines. ...
... Proteins • The ability of proteins to change their conformation is important to their function as biological machines. ...
Watching proteins fold one molecule at a time
... ruled out by measurement of fluorescence polarization, which confirmed that the AK molecules were moving freely within the vesicles. •Jump of the fluorescent labels, thereby modifyng the FRET efficiency. This is not the case because NO FRET transitions are seen under native conditions, where orienta ...
... ruled out by measurement of fluorescence polarization, which confirmed that the AK molecules were moving freely within the vesicles. •Jump of the fluorescent labels, thereby modifyng the FRET efficiency. This is not the case because NO FRET transitions are seen under native conditions, where orienta ...
1.0 Å Cα RMSD for 249 residues
... EFDVILKAAGANKVAVIKAVRGATGLGLKEAKDLVESAPAALKEGVSKDDAEALKKALEEAGAEVEVK ...
... EFDVILKAAGANKVAVIKAVRGATGLGLKEAKDLVESAPAALKEGVSKDDAEALKKALEEAGAEVEVK ...
Toober variations
... Some students will randomly generate a sequence of tacks that is very difficult to fold into a shape that simultaneously satisfies all 3 (or 4) laws of chemistry. This is a good “teaching moment” in that the teacher can use these examples to emphasize that such “proteins” would not have been selecte ...
... Some students will randomly generate a sequence of tacks that is very difficult to fold into a shape that simultaneously satisfies all 3 (or 4) laws of chemistry. This is a good “teaching moment” in that the teacher can use these examples to emphasize that such “proteins” would not have been selecte ...
Joey Barnett, Ph.D. Vice Chair, Department of Pharmacology
... Modeling)? - Collaborations with biology/math depts. - joint programs? Small molecule screens? (interactions with industry) Intellectual Property and Patenting? (ditto) More genomics/genetics? Structure based inhibitors/activators? Structural Biology? Administration? Ph.D/MBA programs? ...
... Modeling)? - Collaborations with biology/math depts. - joint programs? Small molecule screens? (interactions with industry) Intellectual Property and Patenting? (ditto) More genomics/genetics? Structure based inhibitors/activators? Structural Biology? Administration? Ph.D/MBA programs? ...
BLAST- bioinformatics
... ask whether and how sequence-level changes result in functional changes. Can be done for coding or non-coding (i.e. regulatory regions) . ...
... ask whether and how sequence-level changes result in functional changes. Can be done for coding or non-coding (i.e. regulatory regions) . ...
EGEE07_FP_October1st2007
... application for users that are not familiar with the grid, it was decided to integrate it in a web portal based on the GridSphere Portal Framework. ...
... application for users that are not familiar with the grid, it was decided to integrate it in a web portal based on the GridSphere Portal Framework. ...
In general, animal proteins are considered complete proteins. A complete... essential amino acids. Vegetable (plant-based) proteins are considered incomplete proteins...
... protein with a method known as complimentary protein, where you combine certain foods that will create a complete protein. For more information email: [email protected] ...
... protein with a method known as complimentary protein, where you combine certain foods that will create a complete protein. For more information email: [email protected] ...
1+1+1 - Computer Science, Columbia University
... Remote homology detection and domain segmentation are crucial steps for studying genes with no close homology. Query sequence ...
... Remote homology detection and domain segmentation are crucial steps for studying genes with no close homology. Query sequence ...
MolecularViewers
... Threading, alluded to earlier, is a mechanism to address the alignment of two sequences that have <30% identity and are typically considered non-homologous. Essentially, one fits—or threads—the unknown sequence onto the known structure and evaluates the resulting structure’s fitness using environmen ...
... Threading, alluded to earlier, is a mechanism to address the alignment of two sequences that have <30% identity and are typically considered non-homologous. Essentially, one fits—or threads—the unknown sequence onto the known structure and evaluates the resulting structure’s fitness using environmen ...
Lecture Notes - Math
... The Tertiary structure of proteins There are a wide variety of ways in which the various helix, sheets & loop elements can combine to produce a complete structure. At the level of tertiary structure, the side chains play a much more active role in creating the final structure. ...
... The Tertiary structure of proteins There are a wide variety of ways in which the various helix, sheets & loop elements can combine to produce a complete structure. At the level of tertiary structure, the side chains play a much more active role in creating the final structure. ...
Protein Structure
... state depends strongly on its local environment. This feature is often exploited and histidine is used as a molecular switch. ...
... state depends strongly on its local environment. This feature is often exploited and histidine is used as a molecular switch. ...
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.