Why protein structure How does a protein

Why protein structure?

How does a protein fold?

The basics

The (L-)amino acid

The peptide bond

Coplanar atoms

Levels of protein structure

Levels of protein structure

Ramachandran / phi-psi plot

Levels of protein structure

Levels of protein structure

Structural classes

Structural classes

Structural information

The PDB data

PDB Header details

The data itself

Structural Families

Structure comparison facts

Structure comparison facts

Visualizing PDB information

Homologous folds

Analogous folds

Surface Properties

Mapping Functional Regions

Siblings and Cousins

Multiple Sequence Alignment

MSA Methods

Alignment Checks

Sequence Motifs & Patterns

Aligned Sequence Families

Protein Domains

Protein Architectures

Dissection into Domains

Structural Homologues

Small Proteins: Disulfide bonds

Metal-binding domains

Structure Prediction Methods

Tertiary Structure Prediction

One or many templates?

One or many templates?

Many templates

Query - Template Alignment

QTA Checks

QTA Checks

Visual Inspection of Indels

Input for Model Building

Methods Available

Methods Available

Methods Available

Methods Available

Methods Available

Methods Available

Automatic or Manual Mode?

How good is the model?

Improving ill-defined regions

Molecular Modeling Protocol

MM Protocol – Input Files

Ex 1. High Homology Case

1. SOX 9 Models

Ex 2. Low Homology Situation

2. Alignment of POC 4 & GFP

2. POC 4 Model

3. Templates for f. H SCRs 6 -7

3. Query-Templates alignment

3. hf. H 67 model

Ex 4: Protein Engineering

5. EV 71 genome structure

5. Picornaviridae

5. Template hunt

5. Fixing the VP 1 Alignment

5. VP 1 alignment to templates

5. Model building steps

5. Round 2: Pentamer Check

5. Fifth and final attempt

5. Putative antigenic sites