Multiple Sequence Alignments(pdf
... Progressive Multiple Sequence Alignment 1. First pairwise alignments of each sequence are made to form a guide tree 2. Guide tree is used to progressively add sequences to the alignment beginning with the most closely related and continuing until the most distant ...
... Progressive Multiple Sequence Alignment 1. First pairwise alignments of each sequence are made to form a guide tree 2. Guide tree is used to progressively add sequences to the alignment beginning with the most closely related and continuing until the most distant ...
LocalStructureBystro..
... • Learn a set of clusters or structure segments that can be identified from short local sequence • Combine a set of local structural predictions into one whole structure ...
... • Learn a set of clusters or structure segments that can be identified from short local sequence • Combine a set of local structural predictions into one whole structure ...
Computational Molecular Biology 2012
... substitution matrix (BLOSUM62) used in BLAST programs for proteins? 7) One of the 8 RNA fragments of the influenza A genome codes for a polymerase called PB1 of about 750 amino acids. It has been recently determined that the 5'-proximal part of this RNA fragment contains an overlapping open reading ...
... substitution matrix (BLOSUM62) used in BLAST programs for proteins? 7) One of the 8 RNA fragments of the influenza A genome codes for a polymerase called PB1 of about 750 amino acids. It has been recently determined that the 5'-proximal part of this RNA fragment contains an overlapping open reading ...
CSCE590/822 Data Mining Principles and Applications
... Randomized test: do a permutation test, find a length k such that <5% of random ORFs have lengths greater than k. ...
... Randomized test: do a permutation test, find a length k such that <5% of random ORFs have lengths greater than k. ...
Homology Modeling Zinc Fingers – Introduction zf
... A neighbor clustering algorithm was also applied to analyze the snapshots that were produced from the MD simulation. Each side chain was analyzed independent from the other side chains. The RMSD was calculated for all pairs of snapshots, and were clustered if the RMSD was within a 1.0 Å threshold. C ...
... A neighbor clustering algorithm was also applied to analyze the snapshots that were produced from the MD simulation. Each side chain was analyzed independent from the other side chains. The RMSD was calculated for all pairs of snapshots, and were clustered if the RMSD was within a 1.0 Å threshold. C ...
Document
... •Carboxyl-terminal helix fits into the major groove of DNA. •This motif is found in DNA-binding proteins, including l repressor, tryptophan repressor, catabolite activator protein (CAP) ...
... •Carboxyl-terminal helix fits into the major groove of DNA. •This motif is found in DNA-binding proteins, including l repressor, tryptophan repressor, catabolite activator protein (CAP) ...
Protein in disease
... • Study the effects of mutation on structure and function • Predict the effects of a novel mutation on structure or function (protein engineering -- beginning) • Design and build whole new proteins with novel functionality (protein engineering -- advanced) • Design drugs to interact with particular ...
... • Study the effects of mutation on structure and function • Predict the effects of a novel mutation on structure or function (protein engineering -- beginning) • Design and build whole new proteins with novel functionality (protein engineering -- advanced) • Design drugs to interact with particular ...
Lecture 8: Protein structure analysis
... Protein domains can be defined based on: Geometry: group of residues with a high contact density, number of contacts within domains is higher than the number of contacts between domains Kinetics: domain as an independently folding unit Physics: domain as a rigid body linked to other domains b ...
... Protein domains can be defined based on: Geometry: group of residues with a high contact density, number of contacts within domains is higher than the number of contacts between domains Kinetics: domain as an independently folding unit Physics: domain as a rigid body linked to other domains b ...
Sirota, Marina : Protein Multiple Alignment
... There are many types of sequence alignments. The two main branches of sequence comparison are global and local alignment. While global alignment examines the similarity between two sequences as a whole, local alignment looks at shorter highly conserved regions between two sequences. In this paper, I ...
... There are many types of sequence alignments. The two main branches of sequence comparison are global and local alignment. While global alignment examines the similarity between two sequences as a whole, local alignment looks at shorter highly conserved regions between two sequences. In this paper, I ...
4.2 - Alfred State College
... • The inner diameter of the helix (no side-chains) is about 4 – 5 Å Too small for anything to fit “inside” • The outer diameter of the helix (with side chains) is 10 – 12 Å Happens to fit well into the major groove of dsDNA ...
... • The inner diameter of the helix (no side-chains) is about 4 – 5 Å Too small for anything to fit “inside” • The outer diameter of the helix (with side chains) is 10 – 12 Å Happens to fit well into the major groove of dsDNA ...
Susan - Stanford University
... In other words, the most probable conformation is expected to be surrounded by lots of other low-energy conformations Goal: to use a hierarchical clustering method to select and rank docked conformations having the most “neighbors” given a defined cluster radius (in terms of C-alpha RMSD) ...
... In other words, the most probable conformation is expected to be surrounded by lots of other low-energy conformations Goal: to use a hierarchical clustering method to select and rank docked conformations having the most “neighbors” given a defined cluster radius (in terms of C-alpha RMSD) ...
PROTEINS Proteins play key roles in living systems
... – H-bonds formed between the amino and carbonyl groups of one residue and the carbonyl and amino groups of another single residue • Parallel – Both strands run from amino to carboxyl terminal – H-bonds formed between the amino and carbonyl groups of one residue on one strand, and the carbonyl and am ...
... – H-bonds formed between the amino and carbonyl groups of one residue and the carbonyl and amino groups of another single residue • Parallel – Both strands run from amino to carboxyl terminal – H-bonds formed between the amino and carbonyl groups of one residue on one strand, and the carbonyl and am ...
Background - Blue Valley Schools
... species name for the protein sequence (in this first case, Zea mays). Then, return to the Baylor website and “copy” just the protein sequence from the converted data, and “paste” it on the line following the “>Zea mays” identifier. 6. After you have finished this species, complete steps 1 through 5 ...
... species name for the protein sequence (in this first case, Zea mays). Then, return to the Baylor website and “copy” just the protein sequence from the converted data, and “paste” it on the line following the “>Zea mays” identifier. 6. After you have finished this species, complete steps 1 through 5 ...
what are proteins? - scie
... WHAT ARE PROTEINS? Proteins are condensation polymers made from amino acids. The structure, and therefore the function, of a protein depends entirely on the amino acid sequence. During digestion, proteins undergo hydrolysis and are split up into their component amino acids. The body can then use th ...
... WHAT ARE PROTEINS? Proteins are condensation polymers made from amino acids. The structure, and therefore the function, of a protein depends entirely on the amino acid sequence. During digestion, proteins undergo hydrolysis and are split up into their component amino acids. The body can then use th ...
Protein folding
... As they are synthesized they assume secondary and tertiary structure. Activity of proteins depend on the integrity of its final tertiary structure also reffered as the native form. The native form of protein is not very stable structure and it vulnerable to change by heat, high salt, reducing agents ...
... As they are synthesized they assume secondary and tertiary structure. Activity of proteins depend on the integrity of its final tertiary structure also reffered as the native form. The native form of protein is not very stable structure and it vulnerable to change by heat, high salt, reducing agents ...
Link to Poster - Rice IT
... more distinct structures than Monte Carlo, and complex neighbor generation scheme works best ...
... more distinct structures than Monte Carlo, and complex neighbor generation scheme works best ...
PPT - umber
... •DNA analysis: DNA translation (chapter 1), similarity searches (chapter 2), multiple alignments (chapter 4), restriction mapping (chapter 13); determination of gene structure through intron/exon prediction (chapter 10); inference of protein coding sequence through open reading frame (ORF) analysis ...
... •DNA analysis: DNA translation (chapter 1), similarity searches (chapter 2), multiple alignments (chapter 4), restriction mapping (chapter 13); determination of gene structure through intron/exon prediction (chapter 10); inference of protein coding sequence through open reading frame (ORF) analysis ...
Sequencing genomes
... Exploring amino acid residues that are important in the function and/or structure of a protein (multiple alignment of BLAST results, conserved residues). ...
... Exploring amino acid residues that are important in the function and/or structure of a protein (multiple alignment of BLAST results, conserved residues). ...
Sequencing genomes
... Exploring amino acid residues that are important in the function and/or structure of a protein (multiple alignment of BLAST results, conserved residues). ...
... Exploring amino acid residues that are important in the function and/or structure of a protein (multiple alignment of BLAST results, conserved residues). ...
Slide 1
... 1.5 Construct in both cases sequence logo and frequency plot. Can you identify (regulatory) sequence motifs? ...
... 1.5 Construct in both cases sequence logo and frequency plot. Can you identify (regulatory) sequence motifs? ...
Toward structural characterization of novel mechanism of inhibition
... need to be carefully evaluated. Therefore, we test several different conditions for proteins expression (time, temperature, type of the medium for growing bacteria), chromatographic procedures, and proteins stability and select the best ones for each of the proteins studies. The proteins whose produ ...
... need to be carefully evaluated. Therefore, we test several different conditions for proteins expression (time, temperature, type of the medium for growing bacteria), chromatographic procedures, and proteins stability and select the best ones for each of the proteins studies. The proteins whose produ ...
Symmetry
... can touch but not intersect. They may interpenetrate only in so far as there exist corresponding `holes' into which `knobs' can be fit. Furthermore, axes of rotational symmetry may not actually pass `through' a protein monomer ...
... can touch but not intersect. They may interpenetrate only in so far as there exist corresponding `holes' into which `knobs' can be fit. Furthermore, axes of rotational symmetry may not actually pass `through' a protein monomer ...
Sequence-Function Relationships
... α-carbon only All backbone atoms All backbone atoms + side chains (residues) Common conformation (positions) of side chain = rotamer ...
... α-carbon only All backbone atoms All backbone atoms + side chains (residues) Common conformation (positions) of side chain = rotamer ...
Proteins: 3D-Structure Protein Structure Terminology
... the detailed chemical mechanisms of an enzyme. ...
... the detailed chemical mechanisms of an enzyme. ...
Structural alignment
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.