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© Burkhard Rost (TUM Munich) /661
title: Intro domainsshort title: cb1_introstruc2
lecture: Protein Prediction 1 - Protein structure Computational Biology 1 TUM summer 2014
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Announcements
Videos: YouTube / www.rostlab.orgTHANKS : Tim Karl + Jonas ReebSpecial lectures:
• Apr 15 - Andrea Schafferhans
No lecture:• Apr 17/22 Easter• May 01 Thu May day• May 06 Tue Student assembly• May 29 Thu Ascension day• Jun 10 Tue Whitsun holidays• Jun 19 Thu Corpus Christi
LAST lecture: July 1Examen: July 3/8
• Makeup: Oct 21 - morning
CONTACT: Lothar Richter [email protected]
2
TimKarl
LotharRichter
JonasReeb
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
TOC today
LAST week (tuesday)Protein introduction• amino acids• protein structure• bonds & energiesthis lecture (thursday)• protein domainsNEXT WEEK (tuesday)• structure comparison
3Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Reality and images
4Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Marco Punta contributed the slides
5
PhD in Trieste (MD for membrane proteins)Postdoc @ Columbia Univ in the City of New York (contact predictions)Senior scientist in NYCOMPS (Target selection for membrane proteins) IAS Fellow @ TUMProject manager @ Pfam @ Sanger Inst. Hinxton (Cambridgeshire)
Shapers and Shakers
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /666slide context © Marco Punta TUM
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Georges Braque - Houses at L'Estaque
7slide context © Marco Punta TUMWednesday April 23, 2014
© Burkhard Rost (TUM Munich) /668
Where is that?
Illustration by David S. Goodsell, the Scripps Research Institute, UCSD, USA
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /669
Mycoplasma genitalium
Illustration by David S. Goodsell, the Scripps Research Institute, UCSD, USA
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /6610
Mycoplasma genitalium
Illustration by David S. Goodsell, the Scripps Research Institute, UCSD, USA
Protein synthesis (labels in black)1. DNA2. DNA polymerase3. single-stranded-DNA binding protein (protects single-stranded portions during replication)4. RNA polymerase5. messenger RNA6. ribosome7. transfer RNA (in pink) and elongation factor Tu (in blue)8. elongation factor Tu and Ts9. elongation factor G10. aminoacyl-tRNA synthetases11. topoisomerases12. Rec system for DNA repair: a) RecA, b) RecBC13. chaperonin GroEL (helps folding of new proteins)14. proteasome ClpA (destroys old proteins)
Enzymes for energy production (labels in red)15. glycolytic enymes16. pyruvate dehydrogenase complex
Membrane proteins (labels in blue)17. ATP synthase18. secretory proteins19. sodium pump20. zinc transporter21. magnesium transporter22. ABC transporter (different ABC transporters transport different types of molecules-ABC is short for "ATP-binding cassette")23. magnesium transporter24. lypoglycan (long carbohydrate chains connected to lipid in the membrane)
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /6611
Eukaryotic cell
Illustration by David S. Goodsell, the Scripps Research Institute, UCSD, USA
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /6612
Eukaryotic cell
Illustration by David S. Goodsell, the Scripps Research Institute, UCSD, USA
© Wikipedia - LadyOfHats© Wikipedia - LadyOfHats
PLANT cell ANIMAL cell
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /6613
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Doyle et al. (1998) Science 280:69-77 - The structure of the potassium channel: molecular basis of K+ conduction and selectivity
14Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /6615
http://www.proteopedia.org/wiki/images/7/7b/1htb2.png
Alcohol dehydrogenase (ADH)
PC Sanghani, H Robinson, WF Bosron, TD Hurley (2002) Biochemistry 41:10778-86
http://upload.wikimedia.org/wikipedia/commons/thumb/a/a5/Protein_ADH5_PDB_1m6h.png/800px-Protein_ADH5_PDB_1m6h.png
homodimer ADH5
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /6616slide context © Marco Punta TUM
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Umberto Boccioni - Dynamism of a soccer player
17slide context © Marco Punta TUMWednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Photograph: Filippo Monteforte/AFP/Getty Images
18slide context © Marco Punta TUMWednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Different levels of abstraction
Wu et al. unpublished
Photograph: Filippo Monteforte/AFP/Getty Images
19slide context © Marco Punta TUMWednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
“components” of protein structure:
domains
20Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Domain from introns?
21
© Wikipedia
RNA splicing
Gene product = protein
domais = introns?
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Domain merger
22
prokaryote P, protein Aprokaryote P, protein B
prokaryote P2, protein C
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /6623
Domains
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /6624
Domains
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /6625
Domains
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
3D modules
26
Multiple 3D alignment identfies consensus secondary structure
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Guessing domains from sequence
27
protein Aprotein Bprotein Cprotein Dprotein Eprotein F
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Guessing domains from sequence
28
protein Aprotein Bprotein Cprotein Dprotein Eprotein F
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Guessing domains from sequence
29
protein Aprotein Bprotein Cprotein Dprotein Eprotein F
domain 1 domain 2
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Problem: biology is not that simple
30
REALITYDREAM
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Domain length distribution
31J Liu & B Rost (2003) Current Opinion Chem Biol 7, 5-11Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
some common assumptions and
facts about proteins
32Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Some facts about proteins
33Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Some facts about proteins
33
how many in human?
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Some facts about proteins
34Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Some facts about proteins
34
how many in human?
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Some facts about proteins
34
how many in human?• 20-25K in human
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Some facts about proteins
34
how many in human?• 20-25K in humanhow long are they?
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Some facts about proteins
35Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Some facts about proteins
35
how many in human?
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Some facts about proteins
35
how many in human?• 20-25K in human
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Some facts about proteins
35
how many in human?• 20-25K in humanhow long are they?
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Some facts about proteins
35
how many in human?• 20-25K in humanhow long are they?• ~35-30k, median around 400
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Some facts about proteins
35
how many in human?• 20-25K in humanhow long are they?• ~35-30k, median around 400do they consist of units?
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
protein “units”/
domains
36Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
37
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
37
Longer proteins are rarer than shorter ones?
Prokas shorter than eukas?
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
37
Longer proteins are rarer than shorter ones?
Prokas shorter than eukas?
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
37
Longer proteins are rarer than shorter ones?
Prokas shorter than eukas?
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
37
Longer proteins are rarer than shorter ones?
Prokas shorter than eukas?
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
37
Longer proteins are rarer than shorter ones?
Prokas shorter than eukas?
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
37
Longer proteins are rarer than shorter ones?
Prokas shorter than eukas?
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
37
Longer proteins are rarer than shorter ones?
Prokas shorter than eukas?
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
37
Longer proteins are rarer than shorter ones?
Prokas shorter than eukas?
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
37
Longer proteins are rarer than shorter ones?
Prokas shorter than eukas?
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
37
Longer proteins are rarer than shorter ones?
Prokas shorter than eukas?
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
37
Longer proteins are rarer than shorter ones?
Prokas shorter than eukas?
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
37
Longer proteins are rarer than shorter ones?
Prokas shorter than eukas?
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
37
Longer proteins are rarer than shorter ones?
Prokas shorter than eukas?
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
37
Longer proteins are rarer than shorter ones?
Prokas shorter than eukas?
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
38
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
38
Longer proteins are rarer than shorter ones? yes
Prokas shorter than eukas? yes
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
38
Longer proteins are rarer than shorter ones? yes
Prokas shorter than eukas? yes
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
38
Longer proteins are rarer than shorter ones? yes
Prokas shorter than eukas? yes
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
38
Longer proteins are rarer than shorter ones? yes
Prokas shorter than eukas? yes
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
38
Longer proteins are rarer than shorter ones? yes
Prokas shorter than eukas? yes
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
38
Longer proteins are rarer than shorter ones? yes
Prokas shorter than eukas? yes
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
38
Longer proteins are rarer than shorter ones? yes
Prokas shorter than eukas? yes
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
38
Longer proteins are rarer than shorter ones? yes
Prokas shorter than eukas? yes
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
38
Longer proteins are rarer than shorter ones? yes
Prokas shorter than eukas? yes
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
38
Longer proteins are rarer than shorter ones? yes
Prokas shorter than eukas? yes
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
38
Longer proteins are rarer than shorter ones? yes
Prokas shorter than eukas? yes
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
38
Longer proteins are rarer than shorter ones? yes
Prokas shorter than eukas? yes
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
38
Longer proteins are rarer than shorter ones? yes
Prokas shorter than eukas? yes
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
38
Longer proteins are rarer than shorter ones? yes
Prokas shorter than eukas? yes
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Kingdoms similar in length
J Liu. & B Rost (2001) Prot. Sci. 10, 1970-1979.B Rost (2002) Curr Op Struct Biol, 12, 409-416 39
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Kingdoms similar in length
J Liu. & B Rost (2001) Prot. Sci. 10, 1970-1979.B Rost (2002) Curr Op Struct Biol, 12, 409-416 39
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
40
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Longer proteins are rarer than shorter ones? yes
Prokas shorter than eukas? yes
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
40
Some proteins are multi-domain, most are not
Most proteins are multi-domain?
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Longer proteins are rarer than shorter ones? yes
Prokas shorter than eukas? yes
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
40
Some proteins are multi-domain, most are not
Most proteins are multi-domain?
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Longer proteins are rarer than shorter ones? yes
Prokas shorter than eukas? yes
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
40
Some proteins are multi-domain, most are not
Most proteins are multi-domain?
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Longer proteins are rarer than shorter ones? yes
Prokas shorter than eukas? yes
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
40
Some proteins are multi-domain, most are not
Most proteins are multi-domain?
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Longer proteins are rarer than shorter ones? yes
Prokas shorter than eukas? yes
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
40
Some proteins are multi-domain, most are not
Most proteins are multi-domain?
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Longer proteins are rarer than shorter ones? yes
Prokas shorter than eukas? yes
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
40
Some proteins are multi-domain, most are not
Most proteins are multi-domain?
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Longer proteins are rarer than shorter ones? yes
Prokas shorter than eukas? yes
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
40
Some proteins are multi-domain, most are not
Most proteins are multi-domain?
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Longer proteins are rarer than shorter ones? yes
Prokas shorter than eukas? yes
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
40
Some proteins are multi-domain, most are not
Most proteins are multi-domain?
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Longer proteins are rarer than shorter ones? yes
Prokas shorter than eukas? yes
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
40
Some proteins are multi-domain, most are not
Most proteins are multi-domain?
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Longer proteins are rarer than shorter ones? yes
Prokas shorter than eukas? yes
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
40
Some proteins are multi-domain, most are not
Most proteins are multi-domain?
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Longer proteins are rarer than shorter ones? yes
Prokas shorter than eukas? yes
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
40
Some proteins are multi-domain, most are not
Most proteins are multi-domain?
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Longer proteins are rarer than shorter ones? yes
Prokas shorter than eukas? yes
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
40
Some proteins are multi-domain, most are not
Most proteins are multi-domain?
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Longer proteins are rarer than shorter ones? yes
Prokas shorter than eukas? yes
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
40
Some proteins are multi-domain, most are not
Most proteins are multi-domain?
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Longer proteins are rarer than shorter ones? yes
Prokas shorter than eukas? yes
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
40
Some proteins are multi-domain, most are not
Most proteins are multi-domain?
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Longer proteins are rarer than shorter ones? yes
Prokas shorter than eukas? yes
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Most proteins multi-domain
41Liu, Hegyi, Acton, Montelione & Rost 2003 Proteins 56:188-200Liu & Rost 2004 Proteins 55:678-686Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Most proteins multi-domain
42Liu, Hegyi, Acton, Montelione & Rost 2003 Proteins 56:188-200Liu & Rost 2004 Proteins 55:678-686Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Most proteins multi-domain
42Liu, Hegyi, Acton, Montelione & Rost 2003 Proteins 56:188-200Liu & Rost 2004 Proteins 55:678-686
Single-domain proteins:61% in PDB28% in 62 proteomes
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
43
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Longer proteins are rarer than shorter ones? yes
Prokas shorter than eukas? yes
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
43
Some proteins are multi-domain, most are not no
Most proteins are multi-domain? yes
There are more proteins with 3 domains than with 1? ?
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Longer proteins are rarer than shorter ones? yes
Prokas shorter than eukas? yes
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
43
Some proteins are multi-domain, most are not no
Most proteins are multi-domain? yes
There are more proteins with 3 domains than with 1? ?
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Longer proteins are rarer than shorter ones? yes
Prokas shorter than eukas? yes
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
43
Some proteins are multi-domain, most are not no
Most proteins are multi-domain? yes
There are more proteins with 3 domains than with 1? ?
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Longer proteins are rarer than shorter ones? yes
Prokas shorter than eukas? yes
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
43
Some proteins are multi-domain, most are not no
Most proteins are multi-domain? yes
There are more proteins with 3 domains than with 1? ?
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Longer proteins are rarer than shorter ones? yes
Prokas shorter than eukas? yes
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
43
Some proteins are multi-domain, most are not no
Most proteins are multi-domain? yes
There are more proteins with 3 domains than with 1? ?
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Longer proteins are rarer than shorter ones? yes
Prokas shorter than eukas? yes
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
43
Some proteins are multi-domain, most are not no
Most proteins are multi-domain? yes
There are more proteins with 3 domains than with 1? ?
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Longer proteins are rarer than shorter ones? yes
Prokas shorter than eukas? yes
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
43
Some proteins are multi-domain, most are not no
Most proteins are multi-domain? yes
There are more proteins with 3 domains than with 1? ?
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Longer proteins are rarer than shorter ones? yes
Prokas shorter than eukas? yes
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
43
Some proteins are multi-domain, most are not no
Most proteins are multi-domain? yes
There are more proteins with 3 domains than with 1? ?
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Longer proteins are rarer than shorter ones? yes
Prokas shorter than eukas? yes
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
43
Some proteins are multi-domain, most are not no
Most proteins are multi-domain? yes
There are more proteins with 3 domains than with 1? ?
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Longer proteins are rarer than shorter ones? yes
Prokas shorter than eukas? yes
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
43
Some proteins are multi-domain, most are not no
Most proteins are multi-domain? yes
There are more proteins with 3 domains than with 1? ?
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Longer proteins are rarer than shorter ones? yes
Prokas shorter than eukas? yes
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
43
Some proteins are multi-domain, most are not no
Most proteins are multi-domain? yes
There are more proteins with 3 domains than with 1? ?
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Longer proteins are rarer than shorter ones? yes
Prokas shorter than eukas? yes
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
43
Some proteins are multi-domain, most are not no
Most proteins are multi-domain? yes
There are more proteins with 3 domains than with 1? ?
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Longer proteins are rarer than shorter ones? yes
Prokas shorter than eukas? yes
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
43
Some proteins are multi-domain, most are not no
Most proteins are multi-domain? yes
There are more proteins with 3 domains than with 1? ?
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Longer proteins are rarer than shorter ones? yes
Prokas shorter than eukas? yes
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
43
Some proteins are multi-domain, most are not no
Most proteins are multi-domain? yes
There are more proteins with 3 domains than with 1? ?
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Longer proteins are rarer than shorter ones? yes
Prokas shorter than eukas? yes
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Facts about proteins & domains
44
Some proteins are multi-domain, most are not no
Most proteins are multi-domain? yes
There are more proteins with 3 domains than with 1? yes
Do prokas have more domains than eukas?
Do prokas have more proteins with very many domains eukas?
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Longer proteins are rarer than shorter ones? yes
Prokas shorter than eukas? yes
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Prokaryotes and eukaryotes similar
45Liu, Hegyi, Acton, Montelione & Rost 2003 Proteins 56:188-200Liu & Rost 2004 Proteins 55:678-686Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Prokaryotes and eukaryotes similar
46Liu, Hegyi, Acton, Montelione & Rost 2003 Proteins 56:188-200Liu & Rost 2004 Proteins 55:678-686Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Prokaryotes and eukaryotes similar
46Liu, Hegyi, Acton, Montelione & Rost 2003 Proteins 56:188-200Liu & Rost 2004 Proteins 55:678-686
Average domain length• in proteins ≥ 2 domains: ~100 residues• in proteins with 1 domain: 1.7-3 times longer
Wednesday April 23, 2014
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Facts about proteins & domains
47
Some proteins are multi-domain, most are not no
Most proteins are multi-domain? yes
There are more proteins with 3 domains than with 1? yes
Do prokas have more domains than eukas? no
Do prokas have more proteins with very many domains eukas? yes
prokas=prokaryotic proteins / eukas: eukaryotic proteins
Longer proteins are rarer than shorter ones? yes
Prokas shorter than eukas? yes
Wednesday April 23, 2014
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Target selection
48Wednesday April 23, 2014
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Grouping is biology
49Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Grouping is biology
49Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Grouping is biology
50Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Grouping is biology
50Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Some facts about proteins
51Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Some facts about proteins
51
how many in human?
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Some facts about proteins
51
how many in human?• 20-25K in human
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Some facts about proteins
51
how many in human?• 20-25K in humanhow long are they?
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Some facts about proteins
51
how many in human?• 20-25K in humanhow long are they?• ~35-30k, median around 400
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Some facts about proteins
51
how many in human?• 20-25K in humanhow long are they?• ~35-30k, median around 400do they consist of units?
Wednesday April 23, 2014
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Some facts about proteins
51
how many in human?• 20-25K in humanhow long are they?• ~35-30k, median around 400do they consist of units?• most proteins have more than 2 domains
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Some facts about proteins
51
how many in human?• 20-25K in humanhow long are they?• ~35-30k, median around 400do they consist of units?• most proteins have more than 2 domainshow many proteins known?
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Some facts about proteins
52Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Some facts about proteins
52
how many in human?
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Some facts about proteins
52
how many in human?• 20-25K in human
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Some facts about proteins
52
how many in human?• 20-25K in humanhow long are they?
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Some facts about proteins
52
how many in human?• 20-25K in humanhow long are they?• ~35-30k, median around 400
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Some facts about proteins
52
how many in human?• 20-25K in humanhow long are they?• ~35-30k, median around 400do they consist of units?
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Some facts about proteins
52
how many in human?• 20-25K in humanhow long are they?• ~35-30k, median around 400do they consist of units?• most proteins have more than 2 domains
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Some facts about proteins
52
how many in human?• 20-25K in humanhow long are they?• ~35-30k, median around 400do they consist of units?• most proteins have more than 2 domainshow many proteins known?
Wednesday April 23, 2014
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Databases explode!
B Rost (2004) unpublished 53Wednesday April 23, 2014
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Databases explode!
B Rost (2004) unpublished 53Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /6654
Gap sequence/annotation grows!
>52 million protein sequences known by spring 2014
© UniProt 2014
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /6655
Gap sequence/annotation grows!
>52 million protein sequences known by spring 2014
© UniProt 2014
double: 18 months
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Some facts about proteins
56Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Some facts about proteins
56
how many in human?
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Some facts about proteins
56
how many in human?• 20-25K in human
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Some facts about proteins
56
how many in human?• 20-25K in humanhow long are they?
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Some facts about proteins
56
how many in human?• 20-25K in humanhow long are they?• ~35-30k, median around 400
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Some facts about proteins
56
how many in human?• 20-25K in humanhow long are they?• ~35-30k, median around 400do they consist of units?
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Some facts about proteins
56
how many in human?• 20-25K in humanhow long are they?• ~35-30k, median around 400do they consist of units?• most proteins have more than 2 domains
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Some facts about proteins
56
how many in human?• 20-25K in humanhow long are they?• ~35-30k, median around 400do they consist of units?• most proteins have more than 2 domainshow many proteins known?
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Some facts about proteins
56
how many in human?• 20-25K in humanhow long are they?• ~35-30k, median around 400do they consist of units?• most proteins have more than 2 domainshow many proteins known?• over 50 million (109 !! doubling every 18 months!)
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Some facts about proteins
56
how many in human?• 20-25K in humanhow long are they?• ~35-30k, median around 400do they consist of units?• most proteins have more than 2 domainshow many proteins known?• over 50 million (109 !! doubling every 18 months!)prokaryotes and eukaryotes use same amino acids?
Wednesday April 23, 2014
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Kingdoms similar in amino acids usage
J Liu. & B Rost (2001) Prot Sci 10, 1970-1979.B Rost (2002) Curr Op Struct Biol, 12, 409-416 57
Wednesday April 23, 2014
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Some facts about proteins
58
S
Wednesday April 23, 2014
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Some facts about proteins
58
how many in human?
S
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Some facts about proteins
58
how many in human?• 20-25K in human
S
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Some facts about proteins
58
how many in human?• 20-25K in humanhow long are they?
S
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Some facts about proteins
58
how many in human?• 20-25K in humanhow long are they?• ~35-30k, median around 400
S
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Some facts about proteins
58
how many in human?• 20-25K in humanhow long are they?• ~35-30k, median around 400do they consist of units?
S
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Some facts about proteins
58
how many in human?• 20-25K in humanhow long are they?• ~35-30k, median around 400do they consist of units?• most proteins have more than 2 domains
S
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Some facts about proteins
58
how many in human?• 20-25K in humanhow long are they?• ~35-30k, median around 400do they consist of units?• most proteins have more than 2 domainshow many proteins known?
S
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Some facts about proteins
58
how many in human?• 20-25K in humanhow long are they?• ~35-30k, median around 400do they consist of units?• most proteins have more than 2 domainshow many proteins known?• over 50 million (109 !! doubling every 18 months!)
S
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Some facts about proteins
58
how many in human?• 20-25K in humanhow long are they?• ~35-30k, median around 400do they consist of units?• most proteins have more than 2 domainshow many proteins known?• over 50 million (109 !! doubling every 18 months!)prokaryotes and eukaryotes use same amino acids?
S
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Some facts about proteins
58
how many in human?• 20-25K in humanhow long are they?• ~35-30k, median around 400do they consist of units?• most proteins have more than 2 domainshow many proteins known?• over 50 million (109 !! doubling every 18 months!)prokaryotes and eukaryotes use same amino acids?• yes, except for Selenocysteine cysteine
S
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Some facts about proteins
58
how many in human?• 20-25K in humanhow long are they?• ~35-30k, median around 400do they consist of units?• most proteins have more than 2 domainshow many proteins known?• over 50 million (109 !! doubling every 18 months!)prokaryotes and eukaryotes use same amino acids?• yes, except for Selenocysteine cysteine... but you can predict organism from AAs
S
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
short insert:CHOP - domain
guessing
59Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /6660
CHOP proteins into structural domains
J Liu & Rost 2004 Proteins 55:678-686
CUT 1:3D domains
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /6660
CHOP proteins into structural domains
J Liu & Rost 2004 Proteins 55:678-686
CUT 1:3D domains
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /6660
CHOP proteins into structural domains
J Liu & Rost 2004 Proteins 55:678-686
CUT 1:3D domains
CUT 2:Pfam regions
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /6660
CHOP proteins into structural domains
J Liu & Rost 2004 Proteins 55:678-686
CUT 1:3D domains
CUT 2:Pfam regions
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /6660
CHOP proteins into structural domains
J Liu & Rost 2004 Proteins 55:678-686
CUT 1:3D domains
CUT 2:Pfam regions
CUT 3: SWISS-PROT
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /6660
CHOP proteins into structural domains
J Liu & Rost 2004 Proteins 55:678-686
CUT 1:3D domains
CUT 2:Pfam regions
CUT 3: SWISS-PROT
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /6660
CHOP proteins into structural domains
J Liu & Rost 2004 Proteins 55:678-686
CUT 1:3D domains
CUT 2:Pfam regions
CUT 3: SWISS-PROT
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /6660
CHOP proteins into structural domains
J Liu & Rost 2004 Proteins 55:678-686
CUT 1:3D domains
CUT 2:Pfam regions
CUT 3: SWISS-PROT
Final 3D done
3 target domains
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /6661
CHOP proteins into structural domains
J Liu & Rost 2004 Proteins 55:678-686
CUT 1:3D domains
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /6661
CHOP proteins into structural domains
J Liu & Rost 2004 Proteins 55:678-686
CUT 1:3D domains
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /6661
CHOP proteins into structural domains
J Liu & Rost 2004 Proteins 55:678-686
CUT 1:3D domains
CUT 2:Pfam regions
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /6661
CHOP proteins into structural domains
J Liu & Rost 2004 Proteins 55:678-686
CUT 1:3D domains
CUT 2:Pfam regions
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /6661
CHOP proteins into structural domains
J Liu & Rost 2004 Proteins 55:678-686
CUT 1:3D domains
CUT 2:Pfam regions
CUT 3: SWISS-PROT
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /6661
CHOP proteins into structural domains
J Liu & Rost 2004 Proteins 55:678-686
CUT 1:3D domains
CUT 2:Pfam regions
CUT 3: SWISS-PROT
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /6661
CHOP proteins into structural domains
J Liu & Rost 2004 Proteins 55:678-686
CUT 1:3D domains
CUT 2:Pfam regions
CUT 3: SWISS-PROT
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /6661
CHOP proteins into structural domains
J Liu & Rost 2004 Proteins 55:678-686
CUT 1:3D domains
CUT 2:Pfam regions
CUT 3: SWISS-PROT
Final 3D done
3 target domains
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /6661
CHOP proteins into structural domains
J Liu & Rost 2004 Proteins 55:678-686
CUT 1:3D domains
CUT 2:Pfam regions
CUT 3: SWISS-PROT
Final 3D done
3 target domains
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /6661
CHOP proteins into structural domains
J Liu & Rost 2004 Proteins 55:678-686
CUT 1:3D domains
CUT 2:Pfam regions
CUT 3: SWISS-PROT
Final 3D done
3 target domains
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /6662
CHOP proteins into structural domains
J Liu & Rost 2004 Proteins 55:678-686
CUT 1:3D domains
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /6662
CHOP proteins into structural domains
J Liu & Rost 2004 Proteins 55:678-686
CUT 1:3D domains
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /6662
CHOP proteins into structural domains
J Liu & Rost 2004 Proteins 55:678-686
CUT 1:3D domains
CUT 2:Pfam regions
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /6662
CHOP proteins into structural domains
J Liu & Rost 2004 Proteins 55:678-686
CUT 1:3D domains
CUT 2:Pfam regions
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /6662
CHOP proteins into structural domains
J Liu & Rost 2004 Proteins 55:678-686
CUT 1:3D domains
CUT 2:Pfam regions
CUT 3: SWISS-PROT
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /6662
CHOP proteins into structural domains
J Liu & Rost 2004 Proteins 55:678-686
CUT 1:3D domains
CUT 2:Pfam regions
Final 3D done
4 target domains
CUT 3: SWISS-PROT
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /6663
CHOP proteins into structural domains
J Liu & Rost 2004 Proteins 55:678-686
CUT 1:3D domains
Final5 domains “today”
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /6663
CHOP proteins into structural domains
J Liu & Rost 2004 Proteins 55:678-686
CUT 1:3D domains
Final5 domains “today”
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /6663
CHOP proteins into structural domains
J Liu & Rost 2004 Proteins 55:678-686
CUT 1:3D domains
CUT 2:Pfam regions
Final5 domains “today”
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /6663
CHOP proteins into structural domains
J Liu & Rost 2004 Proteins 55:678-686
CUT 1:3D domains
CUT 2:Pfam regions
Final5 domains “today”
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /6663
CHOP proteins into structural domains
J Liu & Rost 2004 Proteins 55:678-686
CUT 1:3D domains
CUT 2:Pfam regions
Final5 domains “today”
CUT 3: SWISS-PROT
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /6663
CHOP proteins into structural domains
J Liu & Rost 2004 Proteins 55:678-686
CUT 1:3D domains
CUT 2:Pfam regions
Final5 domains “today”
CUT 3: SWISS-PROT
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /6664
CHOP proteins into structural domains
J Liu & Rost 2004 Proteins 55:678-686
CUT 1:3D domains
Final5 domains “today”
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /6664
CHOP proteins into structural domains
J Liu & Rost 2004 Proteins 55:678-686
CUT 1:3D domains
Final5 domains “today”
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /6664
CHOP proteins into structural domains
J Liu & Rost 2004 Proteins 55:678-686
CUT 1:3D domains
CUT 2:Pfam regions
Final5 domains “today”
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /6664
CHOP proteins into structural domains
J Liu & Rost 2004 Proteins 55:678-686
CUT 1:3D domains
CUT 2:Pfam regions
Final5 domains “today”
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /6664
CHOP proteins into structural domains
J Liu & Rost 2004 Proteins 55:678-686
CUT 1:3D domains
CUT 2:Pfam regions
Final5 domains “today”
CUT 3: SWISS-PROT
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /6664
CHOP proteins into structural domains
J Liu & Rost 2004 Proteins 55:678-686
CUT 1:3D domains
CUT 2:Pfam regions
Final5 domains “today”
CUT 3: SWISS-PROT
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /6664
CHOP proteins into structural domains
J Liu & Rost 2004 Proteins 55:678-686
CUT 1:3D domains
CUT 2:Pfam regions
Final5 domains “today”
CUT 3: SWISS-PROT
Wednesday April 23, 2014
© Burkhard Rost (TUM Munich) /66
Lecture plan (CB1: Structure)-generic01: 2014/04/08 Tue: sorry02: 2014/04/10 Thu: welcome: who we are03: 2014/04/15 Tue: Intro 1 - acids/structure (Andrea Schafferhans)04: 2014/04/17 Thu: SKIP: Easter vacation05: 2014/04/22 Tue: SKIP: Easter vacation06: 2014/04/24 Thu: Intro 2 - domains07: 2014/04/29 Tue: Intro 3 - 3D comparisons 08: 2014/05/01 Thu: SKIP: “May day” - (NOT to be confused with “m’aidez”)09: 2014/05/06 Tue: SKIP: student assembly (SVV)10: 2014/05/08 Thu: Alignment11: 2014/05/13 Tue: Comparative modeling 112: 2014/05/15 Thu: Comparative modeling 213: 2014/05/20 Tue: Experimental structure determination14: 2014/05/22 Thu: 3D -> 1D: Secondary structure assignment15: 2014/05/27 Tue: 1D: Secondary structure prediction 116: 2014/05/29 Thu: SKIP: holiday (Ascension Day)17: 2014/06/03 Tue: Normal mode analysis (Edda Kloppmann)18: 2014/06/05 Thu: 1D: Secondary structure prediction 219: 2014/06/10 Tue: SKIP: Whitsun holidays20: 2014/06/12 Thu: 1D: Transmembrane helix prediction21: 2014/06/17 Tue: Nobel prize symposium22: 2014/06/19 Thu: SKIP: Corpus Christi (Fronleichnam)23: 2014/06/24 Tue: 1D: Transmembrane strand prediction, solvent accessibility24: 2014/06/26 Thu: 2D prediction25: 2014/07/01 Tue: 3D prediction/wrap up26: 2014/07/03 Thu: examen, no lecture27: 2014/07/08 Tue: examen, no lecture28: 2014/07/10 Thu: no lecture
65Wednesday April 23, 2014
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