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High-throughput
structural bioinformatics
using
Python & p3d
Dr. C. Fufezan
Institute for Biochemistry and Biotechnology of Plants (IBBP)
Overview
Background
p3d overview
example ATP binding site
Fufezan, C. and Specht M. (2009) BMC Bioinformatics 10, 258
http://p3d.fufezan.net
http://github.com/fu/p3d
Dr. C. Fufezan
Institute for Biochemistry and Biotechnology of Plants (IBBP)

clone us - fork us!
Background

Dr. C. Fufezan
Institute for Biochemistry and Biotechnology of Plants (IBBP)
Background
carbon
nitrogen

oxygen

chain(s) of amino acids ...
N D R P A

I

M K

... form proteins

Dr. C. Fufezan
Institute for Biochemistry and Biotechnology of Plants (IBBP)
Background
carbon
nitrogen

oxygen

chain(s) of amino acids ...
N D R P A

I

M K

... form proteins

Dr. C. Fufezan
Institute for Biochemistry and Biotechnology of Plants (IBBP)
Background
carbon
nitrogen

oxygen

chain(s) of amino acids ...
N D R P A

I

M K

... form proteins
and some bind cofactors
e.g. ATP
Adenosin-tri-phosphate
Dr. C. Fufezan
Institute for Biochemistry and Biotechnology of Plants (IBBP)
Background
knowledge based approaches to elucidate
structural factors that are essential for co-factor
binding
- protein engineering
proteins
- protein folding
- co-factor tuning
Proteins_c1_sp_Ob.qxp

9/11/08

4:14 PM

Page 1

proteins

STRUCTURE O FUNCTION O BIOINFORMATICS
V O LU M E

7 3 ,

N U M B E R

3 ,

N OV E M B E R

1 5 ,

V O LU M E
7 3 ,
N U M B E R
3 ,
N OV E M B E R
1 5 ,
2 0 0 8

PAG E S

Morozov et al. (2004) PNAS, 101, 6946Huang et al.(2004) PNAS, 101, 5536Fufezan et al. (2008) Proteins, 73, 690Negron et al. (2009) Proteins, 74, 400Fufezan (2010) Proteins, in press

5 2 7 – 7 9 4

Dr. C. Fufezan
Institute for Biochemistry and Biotechnology of Plants (IBBP)

A PDB Survey of Heme Ligands in Proteins

2 0 0 8
p3d

Dr. C. Fufezan
Institute for Biochemistry and Biotechnology of Plants (IBBP)
p3d overview

Fufezan, C. and Specht M. (2009) BMC Bioinformatics 10, 258
http://p3d.fufezan.net

Python module that allows
to access and manipulate protein structure files
rapid development of new screening tools
easily incorporate complex queries

Dr. C. Fufezan
Institute for Biochemistry and Biotechnology of Plants (IBBP)
chain
atom
AA
resid
type
x y z user
idx

ATOM Object
idx
atype
aa
chain
x
y
z
user
beta
protein-object
Dr. C. Fufezan
Institute for Biochemistry and Biotechnology of Plants (IBBP)

beta
or
temperature
factor
O

C

N

CA
CB
CG1

CG2
Protein Object

ATOM Object
idx
atype
aa
chain
x
y
z
user
beta
protein-object
Dr. C. Fufezan
Institute for Biochemistry and Biotechnology of Plants (IBBP)

protein
... not-proteinogenic
hash
chain['A']
...
oxygen
nitrogen
backbone
atype['CA']
...

oxygen

backbone
alpha
residues
protein

not protein
Protein Object

ATOM Object
idx
atype
aa
chain
x
y
z
user
beta
protein-object
Dr. C. Fufezan
Institute for Biochemistry and Biotechnology of Plants (IBBP)

protein
... not-proteinogenic
hash
chain['A']
...
oxygen
nitrogen
backbone
atype['CA']
...

oxygen

backbone
alpha
residues
protein

not protein
Protein Object

ATOM Object
idx
atype
aa
chain
x
y
z
user
beta
protein-object
Dr. C. Fufezan
Institute for Biochemistry and Biotechnology of Plants (IBBP)

protein
... not-proteinogenic
hash
chain['A']
...
oxygen
nitrogen
backbone
atype['CA']
...

oxygen

backbone
alpha
residues
protein

not protein
Protein Object

ATOM Object
idx
atype
aa
chain
x
y
z
user
beta
protein-object
Dr. C. Fufezan
Institute for Biochemistry and Biotechnology of Plants (IBBP)

protein
... not-proteinogenic
hash
chain['A']
...
oxygen
nitrogen
backbone
atype['CA']
...

oxygen

backbone
alpha
residues
protein

not protein
Protein Object

ATOM Object
idx
atype
aa
chain
x
y
z
user
beta
protein-object
Dr. C. Fufezan
Institute for Biochemistry and Biotechnology of Plants (IBBP)

protein
... not-proteinogenic
hash
chain['A']
...
oxygen
nitrogen
backbone
atype['CA']
...

oxygen

backbone
alpha
residues
protein

not protein
Tree Object

ATOM Object
idx
atype
aa
chain
x
y
z
user
beta
protein-object
Dr. C. Fufezan
Institute for Biochemistry and Biotechnology of Plants (IBBP)
Tree Object

ATOM Object
idx
atype
aa
chain
x
y
z
user
beta
protein-object
Dr. C. Fufezan
Institute for Biochemistry and Biotechnology of Plants (IBBP)
Tree Object
query( Vector1, radius )

ATOM Object
idx
atype
aa
chain
x
y
z
user
beta
protein-object
Dr. C. Fufezan
Institute for Biochemistry and Biotechnology of Plants (IBBP)
Tree Object
query( Vector1, radius )

ATOM Object
idx
atype
aa
chain
x
y
z
user
beta
protein-object
Dr. C. Fufezan
Institute for Biochemistry and Biotechnology of Plants (IBBP)

Vectors
do not have to
be atoms!!
Protein class

List of atom
objects (vectors)

sets (hashes)
oxygen

BSP Tree
O1

FME A

1

CA

PHE A

2

backbone
alpha
residues
protein

not protein
Protein class

List of atom
objects (vectors)

sets (hashes)
oxygen

BSP Tree
O1

FME A

1

CA

PHE A

2

backbone
alpha
residues
protein

not protein

Query function using human readable syntax
e.g.: pdb.query(‘backbone and resid 5..12 and within 5 of resname FME’)
Protein class

List of atom
objects (vectors)

sets (hashes)
oxygen

BSP Tree
O1

FME A

1

CA

PHE A

2

backbone

Query function using human readable syntax
alpha
e.g.: pdb.query(‘backbone and resid 5..12 and within 5 of resname FME’)
residues
protein

not protein
Protein class

List of atom
objects (vectors)

sets (hashes)
oxygen

BSP Tree
O1

FME A

1

CA

PHE A

2

backbone

Query function using human readable syntax
alpha
e.g.: pdb.query(‘backbone and resid 5..12 and within 5 of resname FME’)
pdb.query(‘resname HOH and within 4 of resname ASP’)

residues
protein

not protein
Protein class

List of atom
objects (vectors)

sets (hashes)
oxygen

BSP Tree
O1

FME A

1

CA

PHE A

2

backbone

Query function using human readable syntax
alpha
e.g.: pdb.query(‘backbone and resid 5..12 and within 5 of resname FME’)
pdb.query(‘resname HOH and within 4 of resname ASP’)
pdb.query(‘oxygen and not protein’)

residues

protein

not protein
Protein class

List of atom
objects (vectors)

sets (hashes)
oxygen

BSP Tree
O1

FME A

1

CA

PHE A

2

backbone

Query function using human readable syntax
alpha
e.g.: pdb.query(‘backbone and resid 5..12 and within 5 of resname FME’)
pdb.query(‘resname HOH and within 4 of resname ASP’)
pdb.query(‘oxygen and not protein’)

residues

pdb.query(‘ protein and within 4 of ’, p3d.vector.Vector(x,y,z) )

protein

not protein
Protein class

List of atom
objects (vectors)

sets (hashes)
oxygen

BSP Tree
O1

FME A

1

CA

PHE A

2

backbone

Query function using human readable syntax
alpha
e.g.: pdb.query(‘backbone and resid 5..12 and within 5 of resname FME’)
pdb.query(‘resname HOH and within 4 of resname ASP’)
pdb.query(‘oxygen and not protein’)

residues

pdb.query(‘ protein and within 4 of ’, p3d.vector.Vector(x,y,z) )

protein

not protein

for residueName in pdb.hash[non-aa-resname]:
Protein class

List of atom
objects (vectors)

sets (hashes)
oxygen

BSP Tree
O1

FME A

1

CA

PHE A

2

backbone

Query function using human readable syntax
alpha
e.g.: pdb.query(‘backbone and resid 5..12 and within 5 of resname FME’)
pdb.query(‘resname HOH and within 4 of resname ASP’)
pdb.query(‘oxygen and not protein’)

residues

pdb.query(‘ protein and within 4 of ’, p3d.vector.Vector(x,y,z) )

protein

not protein

for residueName in pdb.hash[non-aa-resname]:
targets = pdb.query(' protein and within 4 of
Protein class

List of atom
objects (vectors)

sets (hashes)
oxygen

BSP Tree
O1

FME A

1

CA

PHE A

2

backbone

Query function using human readable syntax
alpha
e.g.: pdb.query(‘backbone and resid 5..12 and within 5 of resname FME’)
pdb.query(‘resname HOH and within 4 of resname ASP’)
pdb.query(‘oxygen and not protein’)

residues

pdb.query(‘ protein and within 4 of ’, p3d.vector.Vector(x,y,z) )

protein

not protein

for residueName in pdb.hash[non-aa-resname]:
targets = pdb.query(' protein and within 4 of 
( resname 'residueName' and oxygen )' )
Example ATP binding

Dr. C. Fufezan
Institute for Biochemistry and Biotechnology of Plants (IBBP)
The ATP binding sites
Adenosine-tri-phosphate

ΔG˚' = -30 kJ mol-1
40 kg / day
Dr. C. Fufezan
Institute for Biochemistry and Biotechnology of Plants (IBBP)
The ATP binding sites

non. redundant set of proteins
24 binding sites
Dr. C. Fufezan
Institute for Biochemistry and Biotechnology of Plants (IBBP)
The ATP binding sites

non. redundant set of proteins
24 binding sites
Dr. C. Fufezan
Institute for Biochemistry and Biotechnology of Plants (IBBP)
The ATP binding sites

non. redundant set of proteins
24 binding sites
Dr. C. Fufezan
Institute for Biochemistry and Biotechnology of Plants (IBBP)
The ATP binding sites

non. redundant set of proteins
24 binding sites
Dr. C. Fufezan
Institute for Biochemistry and Biotechnology of Plants (IBBP)
Dr. C. Fufezan
Institute for Biochemistry and Biotechnology of Plants (IBBP)
The ATP binding site

Dr. C. Fufezan
Institute for Biochemistry and Biotechnology of Plants (IBBP)
The ATP binding site

Dr. C. Fufezan
Institute for Biochemistry and Biotechnology of Plants (IBBP)
The ATP binding site
+4.5

hydropathy
index

Observations

10

0

1

-4.5

Dr. C. Fufezan
Institute for Biochemistry and Biotechnology of Plants (IBBP)

non. redundant set of proteins
24 binding sites
Summary
p3d allows to develop quickly Python
scripts to screen Protein structures
combines Vectors, sets and BSPTree
p3d allows flexible and complex queries
using human readable language

Dr. C. Fufezan
Institute for Biochemistry and Biotechnology of Plants (IBBP)
Acknowledgements

M. Specht
Prof. Dr. M. Hippler

founding by the DFG and
Alexander von Humboldt Stiftung
Dr. C. Fufezan
Institute for Biochemistry and Biotechnology of Plants (IBBP)

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p3d @EuroSciPy2010 by C. Fufezan

  • 1. High-throughput structural bioinformatics using Python & p3d Dr. C. Fufezan Institute for Biochemistry and Biotechnology of Plants (IBBP)
  • 2. Overview Background p3d overview example ATP binding site Fufezan, C. and Specht M. (2009) BMC Bioinformatics 10, 258 http://p3d.fufezan.net http://github.com/fu/p3d Dr. C. Fufezan Institute for Biochemistry and Biotechnology of Plants (IBBP) clone us - fork us!
  • 3. Background Dr. C. Fufezan Institute for Biochemistry and Biotechnology of Plants (IBBP)
  • 4. Background carbon nitrogen oxygen chain(s) of amino acids ... N D R P A I M K ... form proteins Dr. C. Fufezan Institute for Biochemistry and Biotechnology of Plants (IBBP)
  • 5. Background carbon nitrogen oxygen chain(s) of amino acids ... N D R P A I M K ... form proteins Dr. C. Fufezan Institute for Biochemistry and Biotechnology of Plants (IBBP)
  • 6. Background carbon nitrogen oxygen chain(s) of amino acids ... N D R P A I M K ... form proteins and some bind cofactors e.g. ATP Adenosin-tri-phosphate Dr. C. Fufezan Institute for Biochemistry and Biotechnology of Plants (IBBP)
  • 7. Background knowledge based approaches to elucidate structural factors that are essential for co-factor binding - protein engineering proteins - protein folding - co-factor tuning Proteins_c1_sp_Ob.qxp 9/11/08 4:14 PM Page 1 proteins STRUCTURE O FUNCTION O BIOINFORMATICS V O LU M E 7 3 , N U M B E R 3 , N OV E M B E R 1 5 , V O LU M E 7 3 , N U M B E R 3 , N OV E M B E R 1 5 , 2 0 0 8 PAG E S Morozov et al. (2004) PNAS, 101, 6946Huang et al.(2004) PNAS, 101, 5536Fufezan et al. (2008) Proteins, 73, 690Negron et al. (2009) Proteins, 74, 400Fufezan (2010) Proteins, in press 5 2 7 – 7 9 4 Dr. C. Fufezan Institute for Biochemistry and Biotechnology of Plants (IBBP) A PDB Survey of Heme Ligands in Proteins 2 0 0 8
  • 8. p3d Dr. C. Fufezan Institute for Biochemistry and Biotechnology of Plants (IBBP)
  • 9. p3d overview Fufezan, C. and Specht M. (2009) BMC Bioinformatics 10, 258 http://p3d.fufezan.net Python module that allows to access and manipulate protein structure files rapid development of new screening tools easily incorporate complex queries Dr. C. Fufezan Institute for Biochemistry and Biotechnology of Plants (IBBP)
  • 10. chain atom AA resid type x y z user idx ATOM Object idx atype aa chain x y z user beta protein-object Dr. C. Fufezan Institute for Biochemistry and Biotechnology of Plants (IBBP) beta or temperature factor O C N CA CB CG1 CG2
  • 11. Protein Object ATOM Object idx atype aa chain x y z user beta protein-object Dr. C. Fufezan Institute for Biochemistry and Biotechnology of Plants (IBBP) protein ... not-proteinogenic hash chain['A'] ... oxygen nitrogen backbone atype['CA'] ... oxygen backbone alpha residues protein not protein
  • 12. Protein Object ATOM Object idx atype aa chain x y z user beta protein-object Dr. C. Fufezan Institute for Biochemistry and Biotechnology of Plants (IBBP) protein ... not-proteinogenic hash chain['A'] ... oxygen nitrogen backbone atype['CA'] ... oxygen backbone alpha residues protein not protein
  • 13. Protein Object ATOM Object idx atype aa chain x y z user beta protein-object Dr. C. Fufezan Institute for Biochemistry and Biotechnology of Plants (IBBP) protein ... not-proteinogenic hash chain['A'] ... oxygen nitrogen backbone atype['CA'] ... oxygen backbone alpha residues protein not protein
  • 14. Protein Object ATOM Object idx atype aa chain x y z user beta protein-object Dr. C. Fufezan Institute for Biochemistry and Biotechnology of Plants (IBBP) protein ... not-proteinogenic hash chain['A'] ... oxygen nitrogen backbone atype['CA'] ... oxygen backbone alpha residues protein not protein
  • 15. Protein Object ATOM Object idx atype aa chain x y z user beta protein-object Dr. C. Fufezan Institute for Biochemistry and Biotechnology of Plants (IBBP) protein ... not-proteinogenic hash chain['A'] ... oxygen nitrogen backbone atype['CA'] ... oxygen backbone alpha residues protein not protein
  • 16. Tree Object ATOM Object idx atype aa chain x y z user beta protein-object Dr. C. Fufezan Institute for Biochemistry and Biotechnology of Plants (IBBP)
  • 17. Tree Object ATOM Object idx atype aa chain x y z user beta protein-object Dr. C. Fufezan Institute for Biochemistry and Biotechnology of Plants (IBBP)
  • 18. Tree Object query( Vector1, radius ) ATOM Object idx atype aa chain x y z user beta protein-object Dr. C. Fufezan Institute for Biochemistry and Biotechnology of Plants (IBBP)
  • 19. Tree Object query( Vector1, radius ) ATOM Object idx atype aa chain x y z user beta protein-object Dr. C. Fufezan Institute for Biochemistry and Biotechnology of Plants (IBBP) Vectors do not have to be atoms!!
  • 20. Protein class List of atom objects (vectors) sets (hashes) oxygen BSP Tree O1 FME A 1 CA PHE A 2 backbone alpha residues protein not protein
  • 21. Protein class List of atom objects (vectors) sets (hashes) oxygen BSP Tree O1 FME A 1 CA PHE A 2 backbone alpha residues protein not protein Query function using human readable syntax e.g.: pdb.query(‘backbone and resid 5..12 and within 5 of resname FME’)
  • 22. Protein class List of atom objects (vectors) sets (hashes) oxygen BSP Tree O1 FME A 1 CA PHE A 2 backbone Query function using human readable syntax alpha e.g.: pdb.query(‘backbone and resid 5..12 and within 5 of resname FME’) residues protein not protein
  • 23. Protein class List of atom objects (vectors) sets (hashes) oxygen BSP Tree O1 FME A 1 CA PHE A 2 backbone Query function using human readable syntax alpha e.g.: pdb.query(‘backbone and resid 5..12 and within 5 of resname FME’) pdb.query(‘resname HOH and within 4 of resname ASP’) residues protein not protein
  • 24. Protein class List of atom objects (vectors) sets (hashes) oxygen BSP Tree O1 FME A 1 CA PHE A 2 backbone Query function using human readable syntax alpha e.g.: pdb.query(‘backbone and resid 5..12 and within 5 of resname FME’) pdb.query(‘resname HOH and within 4 of resname ASP’) pdb.query(‘oxygen and not protein’) residues protein not protein
  • 25. Protein class List of atom objects (vectors) sets (hashes) oxygen BSP Tree O1 FME A 1 CA PHE A 2 backbone Query function using human readable syntax alpha e.g.: pdb.query(‘backbone and resid 5..12 and within 5 of resname FME’) pdb.query(‘resname HOH and within 4 of resname ASP’) pdb.query(‘oxygen and not protein’) residues pdb.query(‘ protein and within 4 of ’, p3d.vector.Vector(x,y,z) ) protein not protein
  • 26. Protein class List of atom objects (vectors) sets (hashes) oxygen BSP Tree O1 FME A 1 CA PHE A 2 backbone Query function using human readable syntax alpha e.g.: pdb.query(‘backbone and resid 5..12 and within 5 of resname FME’) pdb.query(‘resname HOH and within 4 of resname ASP’) pdb.query(‘oxygen and not protein’) residues pdb.query(‘ protein and within 4 of ’, p3d.vector.Vector(x,y,z) ) protein not protein for residueName in pdb.hash[non-aa-resname]:
  • 27. Protein class List of atom objects (vectors) sets (hashes) oxygen BSP Tree O1 FME A 1 CA PHE A 2 backbone Query function using human readable syntax alpha e.g.: pdb.query(‘backbone and resid 5..12 and within 5 of resname FME’) pdb.query(‘resname HOH and within 4 of resname ASP’) pdb.query(‘oxygen and not protein’) residues pdb.query(‘ protein and within 4 of ’, p3d.vector.Vector(x,y,z) ) protein not protein for residueName in pdb.hash[non-aa-resname]: targets = pdb.query(' protein and within 4 of
  • 28. Protein class List of atom objects (vectors) sets (hashes) oxygen BSP Tree O1 FME A 1 CA PHE A 2 backbone Query function using human readable syntax alpha e.g.: pdb.query(‘backbone and resid 5..12 and within 5 of resname FME’) pdb.query(‘resname HOH and within 4 of resname ASP’) pdb.query(‘oxygen and not protein’) residues pdb.query(‘ protein and within 4 of ’, p3d.vector.Vector(x,y,z) ) protein not protein for residueName in pdb.hash[non-aa-resname]: targets = pdb.query(' protein and within 4 of ( resname 'residueName' and oxygen )' )
  • 29. Example ATP binding Dr. C. Fufezan Institute for Biochemistry and Biotechnology of Plants (IBBP)
  • 30. The ATP binding sites Adenosine-tri-phosphate ΔG˚' = -30 kJ mol-1 40 kg / day Dr. C. Fufezan Institute for Biochemistry and Biotechnology of Plants (IBBP)
  • 31. The ATP binding sites non. redundant set of proteins 24 binding sites Dr. C. Fufezan Institute for Biochemistry and Biotechnology of Plants (IBBP)
  • 32. The ATP binding sites non. redundant set of proteins 24 binding sites Dr. C. Fufezan Institute for Biochemistry and Biotechnology of Plants (IBBP)
  • 33. The ATP binding sites non. redundant set of proteins 24 binding sites Dr. C. Fufezan Institute for Biochemistry and Biotechnology of Plants (IBBP)
  • 34. The ATP binding sites non. redundant set of proteins 24 binding sites Dr. C. Fufezan Institute for Biochemistry and Biotechnology of Plants (IBBP)
  • 35. Dr. C. Fufezan Institute for Biochemistry and Biotechnology of Plants (IBBP)
  • 36. The ATP binding site Dr. C. Fufezan Institute for Biochemistry and Biotechnology of Plants (IBBP)
  • 37. The ATP binding site Dr. C. Fufezan Institute for Biochemistry and Biotechnology of Plants (IBBP)
  • 38. The ATP binding site +4.5 hydropathy index Observations 10 0 1 -4.5 Dr. C. Fufezan Institute for Biochemistry and Biotechnology of Plants (IBBP) non. redundant set of proteins 24 binding sites
  • 39. Summary p3d allows to develop quickly Python scripts to screen Protein structures combines Vectors, sets and BSPTree p3d allows flexible and complex queries using human readable language Dr. C. Fufezan Institute for Biochemistry and Biotechnology of Plants (IBBP)
  • 40. Acknowledgements M. Specht Prof. Dr. M. Hippler founding by the DFG and Alexander von Humboldt Stiftung Dr. C. Fufezan Institute for Biochemistry and Biotechnology of Plants (IBBP)