Presentation is loading. Please wait.

Presentation is loading. Please wait.

C E N T R F O R I N T E G R A T I V E B I O I N F O R M A T I C S V U E Master Course Sequence Alignment Lecture 10 Database searching Issues (1)

Published by Modified over 9 years ago

Similar presentations

Presentation on theme: "C E N T R F O R I N T E G R A T I V E B I O I N F O R M A T I C S V U E Master Course Sequence Alignment Lecture 10 Database searching Issues (1)"— Presentation transcript:

1 C E N T R F O R I N T E G R A T I V E B I O I N F O R M A T I C S V U E Master Course Sequence Alignment Lecture 10 Database searching Issues (1)

2

3

4 Protein main-chain and side-chain ‘R’ designates the side-chain

5

6 charge

7

8 (cysteine bridge)

9

10 VHLTPEEKSAVTALWGKVNVDE VGGEALGRLLVVYPWTQRFFE SFGDLSTPDAVMGNPKVKAHG KKVLGAFSDGLAHLDNLKGTFA TLSELHCDKLHVDPENFRLLGN VLVCVLAHHFGKEFTPPVQAAY QKVVAGVANALAHKYH PRIMARY STRUCTURE (amino acid sequence) QUATERNARY STRUCTURE (oligomers) SECONDARY STRUCTURE (helices, strands) TERTIARY STRUCTURE (fold) Protein structure hierarchical levels

11

12

13

14

15

16 Compared to preceding plot, RMSD is better able to pin-point relationships between more divergent sequences (RMSD stays relatively small for a longer time as compared to PAM distance). Note that the spread around RMSD is larger

17 Structural superpositioning

18

19

20

21

22

23

Download ppt "C E N T R F O R I N T E G R A T I V E B I O I N F O R M A T I C S V U E Master Course Sequence Alignment Lecture 10 Database searching Issues (1)"

Similar presentations

Proteins from Amino Acids

Proteins from Amino Acids
Evolution and proteins You can see the effects of evolution, not only in the whole organism, but also in its molecules - DNA and protein For a mutation.

Evolution and proteins You can see the effects of evolution, not only in the whole organism, but also in its molecules - DNA and protein For a mutation.
Protein Structure.

Protein Structure.
From: Protein Data Bank PDB ID: 1B0E Kalus, W., Zweckstetter, M., Renner, C., Sanchez, Y., Georgescu, J., Grol, M., Demuth, D., Schumacher, R., Dony, C.,

From: Protein Data Bank PDB ID: 1B0E Kalus, W., Zweckstetter, M., Renner, C., Sanchez, Y., Georgescu, J., Grol, M., Demuth, D., Schumacher, R., Dony, C.,
2 Nucleic Acids Convey Genetic Information Box 2-2Table Chapter 2-5.

2 Nucleic Acids Convey Genetic Information Box 2-2Table Chapter 2-5.
C E N T R F O R I N T E G R A T I V E B I O I N F O R M A T I C S V U E Master Course Sequence Alignment Lecture 9 Database searching (3)

C E N T R F O R I N T E G R A T I V E B I O I N F O R M A T I C S V U E Master Course Sequence Alignment Lecture 9 Database searching (3)
Master’s course Bioinformatics Data Analysis and Tools Centre for Integrative Bioinformatics FEW/FALW

Master’s course Bioinformatics Data Analysis and Tools Centre for Integrative Bioinformatics FEW/FALW
Sequence analysis course Lecture 8 Sequence databank searching 1.

Sequence analysis course Lecture 8 Sequence databank searching 1.
Lecture 1 BNFO 240 Usman Roshan. Course overview Perl progamming language (and some Unix basics) Sequence alignment problem –Algorithm for exact pairwise.

Lecture 1 BNFO 240 Usman Roshan. Course overview Perl progamming language (and some Unix basics) Sequence alignment problem –Algorithm for exact pairwise.
Protein structure Friday, 10 February 2006 Introduction to Bioinformatics Brigham Young University DA McClellan

Protein structure Friday, 10 February 2006 Introduction to Bioinformatics Brigham Young University DA McClellan
1. Primary Structure: Polypeptide chain Polypeptide chain Amino acid monomers Peptide linkages Figure 3.6 The Four Levels of Protein Structure.

1. Primary Structure: Polypeptide chain Polypeptide chain Amino acid monomers Peptide linkages Figure 3.6 The Four Levels of Protein Structure.
Resonance Assignment NMR analysis of proteins Sequential resonance assignment strategies Practical Issues.

Resonance Assignment NMR analysis of proteins Sequential resonance assignment strategies Practical Issues.
SnapDRAGON: protein 3D prediction-based DOMAINATION: based on PSI-BLAST Two methods to predict domain boundary sequence positions from sequence information.

SnapDRAGON: protein 3D prediction-based DOMAINATION: based on PSI-BLAST Two methods to predict domain boundary sequence positions from sequence information.
Proteins Structures Primary Structure.

Proteins Structures Primary Structure.
Amino acid side chains stabilise the enzyme shape.

Amino acid side chains stabilise the enzyme shape.
Daily Starter  Explain how a peptide bond is formed. (What is the reaction called and how does it happen?)

Daily Starter  Explain how a peptide bond is formed. (What is the reaction called and how does it happen?)
STRUCTURE OF PROTEIN Prepared by- Prepared by- Parikha Srivastav Parikha Srivastav (P.G.T CHEM.) (P.G.T CHEM.) K.V. BALRAMPUR K.V. BALRAMPUR.

STRUCTURE OF PROTEIN Prepared by- Prepared by- Parikha Srivastav Parikha Srivastav (P.G.T CHEM.) (P.G.T CHEM.) K.V. BALRAMPUR K.V. BALRAMPUR.
Protein Structures.

Protein Structures.
Protein Tertiary Structure Prediction

Protein Tertiary Structure Prediction
Pair-wise alignment quality versus sequence identity (Vogt et al., JMB 249, 816-831,1995)

Pair-wise alignment quality versus sequence identity (Vogt et al., JMB 249, ,1995)

Similar presentations

Ads by Google