ICM

Interactive Chromatin Modeling
ICM ~ Isee 'em
details
Nucleic Acids Res. 2010 38:W254-W261.
DOI:10.1093/nar/gkq496

Bishop Lab Home Page

Sequence Input Options:

Default Sequence

Type Sequence

Upload Sequence

This option uses the default sequence.
GenBank #V01175: the GR MMTV LTR.

This option allows for sequence input.

Please insert your sequence: Type or cut-and-paste sequence here.

Try one of our samples below or search PubMed

Sample Sequence References

A. Scipioni, S. Pisano, C. Anselmi, M. Savino, P. De Santis, 2004, Biophys. Chem. v.107, p.7

This option allows a sequence selection to be uploaded.

Choose a DNA sequence to upload:

Thermal Fluctuation:
This option controls the level of thermal fluctuation.

Temperature:

Temperature

This determines the thermal fluctions in the helical parameters for the regions of free DNA. The fluctuations yeild a Gaussian distribution as determined by the chosen stiffness parameters and temperature.

Kelvin

Nucleosome Placement Options

Use Default Parameters

Use Energy Calculations

Specify Nucleosome Placement

This option will use default values for the placement parameters.

These options control automatic placement of nucleosomes in the energy landscape.

Energy Options E_nuc = ½ ∑ K(X_nuc - X_DNA)²

Energy:

The sequence specific nucleosome positioning energy.

Ref: Sereda and Bishop J. Biol. Struc. Dyn. 27(6):713-894, 2010.

K =

K: Stiffness

Is the measure of the stiffness of DNA. It accounts for six degress of freedom: Shift, Slide, Rise, Tilt, Roll, Twist. This button lets you select values of K as determined by several methods

FORCE CONSTANT

MD-B => Lankas 2003
XRAYB => Olson 1998
XRAYP => Olson 1998
IDEAL => Lankas 2003

X_nuc =

Nucleosome Geometry

X is the shape of the nucleosome. This button lets you select from any of the available x-ray structures. All parameters extracted using 3DNA.

Nucleosome Geometry

KO, KI => Bishop 2008
pdbid => See RCSB.org

X_DNA =

Free DNA Geometry

X0 is the shape of the DNA when free in solution. This button lets you define the shape of free DNA to agree with xray or MD data.

Free DNA Geometry

MDB => Lankas 2003
XRAYB => Olson 1998
XRAYP => Olson 1998
IDEAL => Lankas 2003

Occupancy Occupancy:

Occupancy Info

n > 1 : integer number of nucleosomes
n < 1 : percentage of maximum possible number of nucleosomes
n = 0 : constant spacing of "linker length" between nucleosomes
n < 0 : constant spacing with all locations shifted by n

Linker Length:

Linker Info

Minimum nucleosome-nucleosome distance in basepair.

This option places nucleosomes at the assigned starting positions. An energy landscape is provided, but is not used in determining nucleosome placements.

Energy Options E_nuc = ½ ∑ K(X_nuc - X_DNA)²

Energy:

The sequence specific nucleosome positioning energy.

Ref: Sereda and Bishop J. Biol. Struc. Dyn. 27(6):713-894, 2010.

K =

FORCE CONSTANT

MD-B => Lankas 2003
XRAYB => Olson 1998
XRAYP => Olson 1998
IDEAL => Lankas 2003

X_nuc =

Nucleosome Geometry

X is the shape of the nucleosome. This button lets you select from any of the available x-ray structures. All parameters extracted using 3DNA.

Nucleosome Geometry

KO, KI => Bishop 2008
pdbid => See RCSB.org

X_DNA =

Free DNA Geometry

X0 is the shape of the DNA when free in solution. This button lets you define the shape of free DNA to agree with xray or MD data.

Free DNA Geometry

MDB => Lankas 2003
XRAYB => Olson 1998
XRAYP => Olson 1998
IDEAL => Lankas 2003

Occupancy Occupancy:

K =

FORCE CONSTANT

MD-B => Lankas 2003
XRAYB => Olson 1998
XRAYP => Olson 1998
IDEAL => Lankas 2003

X_nuc =

Nucleosome Geometry

X is the shape of the nucleosome. This button lets you select from any of the available x-ray structures. All parameters extracted using 3DNA.

Nucleosome Geometry

KO, KI => Bishop 2008
pdbid => See RCSB.org

X_DNA =

Free DNA Geometry

X0 is the shape of the DNA when free in solution. This button lets you define the shape of free DNA to agree with xray or MD data.

Free DNA Geometry

MDB => Lankas 2003
XRAYB => Olson 1998
XRAYP => Olson 1998
IDEAL => Lankas 2003

Nucleosome Start Sites Positions:

NSS Info

To place nucleosomes at specific locations provide a list of integers corresponding to the start of each nucleosome footprint.

Click here for References

Click here for Related Sites