3DM: Protein Super-family Platforms 3DM Protein super-family data integration Tom van den Bergh Bio-Prodict.

Slides:

Advertisements

Similar presentations

1 Introduction to Sequence Analysis Utah State University – Spring 2012 STAT 5570: Statistical Bioinformatics Notes 6.1.

Advertisements

Protein Structure Database Introduction Database of Comparative Protein Structure Models ModBase 生資所 g 詹濠先.

Pfam(Protein families )

Chemotaxis Pathway How can physics help? Davi Ortega.

©CMBI 2005 Exploring Protein Sequences - Part 2 Part 1: Patterns and Motifs Profiles Hydropathy Plots Transmembrane helices Antigenic Prediction Signal.

Intro to Bioinformatics Summary. What did we learn Pairwise alignment – Local and Global Alignments When? How ? Tools : for local blast2seq, for global.

Sequence Similarity Searching Class 4 March 2010.

Archives and Information Retrieval

Ion Channels. Cell membrane Voltage-gated Ion Channels voltage-gated because they open and close depending on the electrical potential across the membrane.

Protein structure (Part 2 of 2).

Bioinformatics on Proteomics Hsueh-Fen Juan April 24, 2003 NTNU.

Integration of Bioinformatics into Inquiry Based Learning by Kathleen Gabric.

The Protein Data Bank (PDB)

Determination of Sites of CYP1B1 Mutations in Aligned Sequences of Cytochrome P450 Family Members and 3D-Structural Model by: Betsabeh Khoramian Tusi.

Sequence Analysis. Today How to retrieve a DNA sequence? How to search for other related DNA sequences? How to search for its protein sequence? How to.

BLOSUM Information Resources Algorithms in Computational Biology Spring 2006 Created by Itai Sharon.

Bioinformatics (3 lectures) Why bother about proteins/prediction What is bioinformatics Protein databases Making use of database information –Predictions.

Detecting the Domain Structure of Proteins from Sequence Information Niranjan Nagarajan and Golan Yona Department of Computer Science Cornell University.

Chemical mechanism is dominant Nature selects the protein for divergent evolution from a pool of enzymes whose mechanism provide a partial mechanism, or.

Arabidopsis Gene Project GK-12 April Workshop Karolyn Giang and Dr. Mulligan.

3DM: Protein engineering Super-family platforms 1.Find the best starting enzyme 2.Find the hotspots 3.Select the best mutations at these hotspots.

Abstract Visualization of protein structural data is an important aspect of protein research. Incorporation of genomic annotations into a protein structural.

y-sa/2.0/. Integrating the Data Prof:Rui Alves Dept Ciencies Mediques Basiques, 1st.

Fast Search Protein Structure Prediction Algorithm for Almost Perfect Matches1 By Jayakumar Rudhrasenan S Primary Supervisor: Prof. Heiko Schroder.

Biology 224 Instructor: Tom Peavy Feb 21 & 26, Protein Structure & Analysis.

 Four levels of protein structure  Linear  Sub-Structure  3D Structure  Complex Structure.

Multiple Alignment and Phylogenetic Trees Csc 487/687 Computing for Bioinformatics.

CATH – a hierarchic classification of protein domain structures Rui Kuang.

Biological Databases Biology outside the lab. Why do we need Bioinfomatics? Over the past few decades, major advances in the field of molecular biology,

Construction of Substitution Matrices

Protein Structure & Modeling Biology 224 Instructor: Tom Peavy Nov 18 & 23, 2009

Python + PyMOL Arbitrary Python code possible within python scripts PyMOL functionality available by importing PyMOL's modules cmd, cgo, stored etc. Call.

Protein Modeling Protein Structure Prediction. 3D Protein Structure ALA CαCα LEU CαCαCαCαCαCαCαCα PRO VALVAL ARG …… ??? backbone sidechain.

PROTEIN PATTERN DATABASES. PROTEIN SEQUENCES SUPERFAMILY FAMILY DOMAIN MOTIF SITE RESIDUE.

Alignment & Secondary Structure You have learned about: Data & databases Tools Amino Acids Protein Structure Today we will discuss: Aligning sequences.

3DM: Protein engineering Super-family platforms Bio-Prodict DM super-family systems Henk-Jan Joosten Remko Kuipers Tom v/d Bergh Bas Vroling.

Construction of Substitution matrices

Polish Infrastructure for Supporting Computational Science in the European Research Space EUROPEAN UNION Examining Protein Folding Process Simulation and.

Structural classification of Proteins SCOP Classification: consists of a database Family Evolutionarily related with a significant sequence identity Superfamily.

An Efficient Index-based Protein Structure Database Searching Method 陳冠宇.

 What is MSA (Multiple Sequence Alignment)? What is it good for? How do I use it?  Software and algorithms The programs How they work? Which to use?

Bioinformatics A Summary seminar (with many hints for exam questions)

Genetic Code and Interrupted Gene Chapter 4. Genetic Code and Interrupted Gene Aala A. Abulfaraj.

Sequence: PFAM Used example: Database of protein domain families. It is based on manually curated alignments.

Bio/Chem-informatics

Alignment table: group 4

Archives and Information Retrieval

Have (y)Our Protein Explained

Acetylcholine Receptor Binding Toxins

Relationship between Genotype and Phenotype

Amino‐acid sequence of the heterogeneous nuclear RNP G protein family and RNA‐binding SELEX consensus sequence obtained for human RBMY. (A) Sequence alignment.

Strategies for annotation of a genome

Searching the NCBI Databases

Prediction of protein structure

Growth Hormone Receptor

The future of protein secondary structure prediction accuracy

By Stitziel, Tseng, Pervouchine, Goddeau, Kasif, Liang

Phosphopeptides identified harboring minimal binding motifs

Regulation of AMPA Receptor Gating by Ligand Binding Core Dimers

Protein domains Jasmin sutkovic

AKAP15 coimmunoprecipitates with CaV1

Figure 1 Pedigree and genetic findings

The family of bone morphogenetic proteins

Alignment of the deduced amino acid sequences of the myosin light chain 2 (MLC2) proteins. Alignment of the deduced amino acid sequences of the myosin.

(A) Segregation of mutations in TMEM231 in JBTS families.

Phosphopeptides identified harboring minimal binding motifs

Figure 2 Compound heterozygous mutations in ADAM22

SUBMITTED BY: DEEPTI SHARMA BIOLOGICAL DATABASE AND SEQUENCE ANALYSIS.

Alignment of the Amino Acid Sequences of NCS and Other PR10/Bet v1 Proteins from Various Plant Species.Deduced amino acid sequences were aligned using.

Presentation transcript:

3DM: Protein Super-family Platforms 3DM Protein super-family data integration Tom van den Bergh Bio-Prodict

3DM: Protein Super-family Platforms Superimposing family structures 69 P450 structures These structures are sequentially all different: <80%

3DM: Protein Super-family Platforms Structure based alignments Structural conserved residues get the same 3D- number because these residues have a similar role in the proteins

3DM: Protein Super-family Platforms 3D number: the alignment structure link

3DM: Protein Super-family Platforms

Amino acid data Mutation data literature, Swiss-Prot, OMIM, … > mutations searchable for effects!!!! Structure data PPI, ligand contacts, bridges, solvent accessibility, flexibility/RMSD, … Alignment data Conservation, correlated mutations, family specific residues, … SNP data SNP databases, genome sequencing projects Data integration All data are stored connected to the 3D numbering scheme and thus to the alignment, to the structures and each other

3DM: Protein Super-family Platforms