Center for Structural Biology
... Secondary- local Supersecondary (motifs)- intermediate Domains- independent folding units Tertiary- organization of a complete chain Quaternary- organization of multiple chains ...
... Secondary- local Supersecondary (motifs)- intermediate Domains- independent folding units Tertiary- organization of a complete chain Quaternary- organization of multiple chains ...
Proteins
... Held together by hydrogen bonds between hydrogen from the oxygen from the carbonyl group C=O and hydrogen from the amino group N – H that is four peptide bonds away Hair is an example ...
... Held together by hydrogen bonds between hydrogen from the oxygen from the carbonyl group C=O and hydrogen from the amino group N – H that is four peptide bonds away Hair is an example ...
A bioinformatika elméleti alapjai 4
... proteomics) Computational analysis of small fragments is accurate. ...
... proteomics) Computational analysis of small fragments is accurate. ...
Psi-blast
... 30%-50% sequence identity= 90% can be modeled <30% sequence identity =low accuracy (many errors) ...
... 30%-50% sequence identity= 90% can be modeled <30% sequence identity =low accuracy (many errors) ...
2 a - Atelier de BioInformatique
... • Cliques of “symbols” define similarity, e.g : - different overlapping sets of amino acids clustered by their properties (e.g. hydrophobic, hydrophilic, small, large, polar, charged, etc…) - different overlapping sets of amino acids clustered by setting a threshold value on their score in a similar ...
... • Cliques of “symbols” define similarity, e.g : - different overlapping sets of amino acids clustered by their properties (e.g. hydrophobic, hydrophilic, small, large, polar, charged, etc…) - different overlapping sets of amino acids clustered by setting a threshold value on their score in a similar ...
The subcomponents of biological molecules and their sequence
... storage. However, the cellulose made out of β glucose rings has a different purpose. It has a structural purpose rather than a storage purpose. ...
... storage. However, the cellulose made out of β glucose rings has a different purpose. It has a structural purpose rather than a storage purpose. ...
Thursday and Friday
... length of the two sequences under comparison. Algorithms of this nature are not particularly suited to the identification of genes that have evolved by recombination or insertion of unrelated regions of DNA. In instances such as this, a global similarity score will be greatly reduced. In cases where ...
... length of the two sequences under comparison. Algorithms of this nature are not particularly suited to the identification of genes that have evolved by recombination or insertion of unrelated regions of DNA. In instances such as this, a global similarity score will be greatly reduced. In cases where ...
Chemistry 160 Protein Structure Homework
... 2. What are prosthetic groups? 3. What are glycoproteins and lipoproteins? 4. Describe the 4 levels of protein structure. 5. Describe 3 types of interactions that stabilize protein structure. 6. What drives protein folding? 7. Give two ways amino acid sequences are determined. 8. A small protein was ...
... 2. What are prosthetic groups? 3. What are glycoproteins and lipoproteins? 4. Describe the 4 levels of protein structure. 5. Describe 3 types of interactions that stabilize protein structure. 6. What drives protein folding? 7. Give two ways amino acid sequences are determined. 8. A small protein was ...
PROTEIN STRUCTURE ANALYSIS ASSIGNMENTS Search from
... How many structures do you find? What methods have been used for their determination? How do they differ? Which one do you choose and why? Is it a crystallographic or NMR structure? What is resolution? How many chains are on the structure?What is the number of amino acids in the structure? What is t ...
... How many structures do you find? What methods have been used for their determination? How do they differ? Which one do you choose and why? Is it a crystallographic or NMR structure? What is resolution? How many chains are on the structure?What is the number of amino acids in the structure? What is t ...
Document
... -Amino acid distributions at individual position should not be taken as independent of one another. -Investigation of correlations between sequence positions in protein family leads to decomposition of the protein into groups of coevolving amino acids – “sectors”. ...
... -Amino acid distributions at individual position should not be taken as independent of one another. -Investigation of correlations between sequence positions in protein family leads to decomposition of the protein into groups of coevolving amino acids – “sectors”. ...
Basics of Molecular Biology
... Model or other statistical model for the family that is annotated with structural features, and align the new sequence to the model. Transfer structural information. ...
... Model or other statistical model for the family that is annotated with structural features, and align the new sequence to the model. Transfer structural information. ...
Introduction to Sequence Similarity
... The next few lectures will deal with the topic of “sequence similarity”, where the sequences under consideration might be DNA, RNA, or amino acid sequences. This is likely the most frequently performed task in computational biology. Its usefulness is predicated on the assumption that a high degree o ...
... The next few lectures will deal with the topic of “sequence similarity”, where the sequences under consideration might be DNA, RNA, or amino acid sequences. This is likely the most frequently performed task in computational biology. Its usefulness is predicated on the assumption that a high degree o ...
Seminar in structural bioinformatics
... reminded of the works of an Origami artist: Certain basic folding patterns are used over and over again and cleverly modified by minor adaptations to generate a wide variety of different protein structures. Where one such folding units is insufficient to generate the required complexity, multiple do ...
... reminded of the works of an Origami artist: Certain basic folding patterns are used over and over again and cleverly modified by minor adaptations to generate a wide variety of different protein structures. Where one such folding units is insufficient to generate the required complexity, multiple do ...
Basic Overview of Bioinformatics Tools and Biocomputing
... comparison of the two input sequences • Local Alignment looks for local stretches of similarity and tries to align the most similar segments • Algorithms used may be similar, but output different, statistics needed to assess results ...
... comparison of the two input sequences • Local Alignment looks for local stretches of similarity and tries to align the most similar segments • Algorithms used may be similar, but output different, statistics needed to assess results ...
COS 597c: Topics in Computational Molecular Biology Lecturer: Larry Brown
... we calculate its score (using dynamic programming) for all structures. Significance of a score for a particular structure is given by scoring a large sequence database against the structure and calculating z−score = ...
... we calculate its score (using dynamic programming) for all structures. Significance of a score for a particular structure is given by scoring a large sequence database against the structure and calculating z−score = ...
Bioinformatics and Phylogenetic Analysis
... Clustering algorithm analyzes the distance matrix to determine which sequences should be clustered. ...
... Clustering algorithm analyzes the distance matrix to determine which sequences should be clustered. ...
Crystallizing a clearer understanding of the protein
... the cellular level. Given the array of intelligent functions that proteins conduct in organisms, however, that moniker may not do them justice. Numbering in the millions, proteins—which are chains of amino acids—grow and repair cells, trigger chemical processes or transport molecules; they can be st ...
... the cellular level. Given the array of intelligent functions that proteins conduct in organisms, however, that moniker may not do them justice. Numbering in the millions, proteins—which are chains of amino acids—grow and repair cells, trigger chemical processes or transport molecules; they can be st ...
6. 3-D structure of proteins
... • The spatial arrangement of atoms in a protein is called its conformation. • Proteins in any of their functional folded conformations are called native proteins. • Stability can be defined as the tendency to ...
... • The spatial arrangement of atoms in a protein is called its conformation. • Proteins in any of their functional folded conformations are called native proteins. • Stability can be defined as the tendency to ...
Presentazione standard di PowerPoint
... MD simulations have been performed using the open-source software GROMACS, running in parallel (MPI) on the CRESCO clusters CRESCO1 and 2. The length of simulation was variable between 10 and 100 ns. In general, simulations were run on 96 nodes, obtaining a performance of 15 ns/day (previous benchma ...
... MD simulations have been performed using the open-source software GROMACS, running in parallel (MPI) on the CRESCO clusters CRESCO1 and 2. The length of simulation was variable between 10 and 100 ns. In general, simulations were run on 96 nodes, obtaining a performance of 15 ns/day (previous benchma ...
Biological Macromolecules Worksheet
... a. the number _____ of different nitrogenous bases in DNA b. the number _____ of different chemical classes of amino acids c. the number _____ of chains of nucleotides in a DNA molecule d. the number _____ of different nitrogenous bases in RNA e. the number _____ of different amino acids found in pr ...
... a. the number _____ of different nitrogenous bases in DNA b. the number _____ of different chemical classes of amino acids c. the number _____ of chains of nucleotides in a DNA molecule d. the number _____ of different nitrogenous bases in RNA e. the number _____ of different amino acids found in pr ...
November 19, 2012 3:00 PM Livermore Center 101 Isaac C. Sanchez
... separations. Using atomistic models, cavity size (free volume) distributions were determined by a combination of molecular dynamics (MD) and Monte Carlo methods for 6 thermally rearranged (TR) polyimides and their precursors. Diffusion, solubility, and permeation of gases in TR polymers and their pr ...
... separations. Using atomistic models, cavity size (free volume) distributions were determined by a combination of molecular dynamics (MD) and Monte Carlo methods for 6 thermally rearranged (TR) polyimides and their precursors. Diffusion, solubility, and permeation of gases in TR polymers and their pr ...
CMSE 520 BIOMOLECULAR STRUCTURE, FUNCTION AND
... What's E-Cell Project? E-Cell Project is an international research project aiming to model and reconstruct biological phenomena in silico, and developing necessary theoretical supports, technologies and software platforms to allow precise whole cell simulation. Metabolism model of the model cell co ...
... What's E-Cell Project? E-Cell Project is an international research project aiming to model and reconstruct biological phenomena in silico, and developing necessary theoretical supports, technologies and software platforms to allow precise whole cell simulation. Metabolism model of the model cell co ...
Freshman Seminar
... Sequence databases • What is a database? – An indexed set of records – Records retrieved using a query language – Database technology is well established ...
... Sequence databases • What is a database? – An indexed set of records – Records retrieved using a query language – Database technology is well established ...
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.