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A presentation on Curves+, a program used for DNA analysis
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IntroductionHow It Works
Using Curves+: A Nucleic Acid Analysis Tool
Emily Cribas
Penn State
July 1, 2014
Emily Cribas Using Curves+: A Nucleic Acid Analysis Tool
2/16
IntroductionHow It Works
The BasicsStructureParameters
An Overview
Curves+1 Web server that analyzes the conformations ofnucleic acid structures
Note: Web server version does not work foranalyzing MD trajectories
Canal1 Accompanying program that uses data from Curves+to analyze molecular dynamics trajectories
Canion1 Accompanying program that analyzes the distributionof ions, solute atoms, or water molecules surrounding(or belonging to) a nucleic acid
1Blanchet, C. et al. Nucleic acids research July 2011, 39, W68–73.Emily Cribas Using Curves+: A Nucleic Acid Analysis Tool
2/16
IntroductionHow It Works
The BasicsStructureParameters
An Overview
Curves+1 Web server that analyzes the conformations ofnucleic acid structures
Note: Web server version does not work foranalyzing MD trajectories
Canal1 Accompanying program that uses data from Curves+to analyze molecular dynamics trajectories
Canion1 Accompanying program that analyzes the distributionof ions, solute atoms, or water molecules surrounding(or belonging to) a nucleic acid
1Blanchet, C. et al. Nucleic acids research July 2011, 39, W68–73.Emily Cribas Using Curves+: A Nucleic Acid Analysis Tool
2/16
IntroductionHow It Works
The BasicsStructureParameters
An Overview
Curves+1 Web server that analyzes the conformations ofnucleic acid structures
Note: Web server version does not work foranalyzing MD trajectories
Canal1 Accompanying program that uses data from Curves+to analyze molecular dynamics trajectories
Canion1 Accompanying program that analyzes the distributionof ions, solute atoms, or water molecules surrounding(or belonging to) a nucleic acid
1Blanchet, C. et al. Nucleic acids research July 2011, 39, W68–73.Emily Cribas Using Curves+: A Nucleic Acid Analysis Tool
3/16
IntroductionHow It Works
The BasicsStructureParameters
Features
Applicable to NA structures with up to 4 strands and witheither canonical or modified bases and backbones2
Provides helical and backbone parameters2
Full analysis of groove widths and depths2
Uses a curvilinear helical axis2
2Lavery, R. et al. Nucleic acids research Sept. 2009, 37, 5917–29.Emily Cribas Using Curves+: A Nucleic Acid Analysis Tool
4/16
IntroductionHow It Works
The BasicsStructureParameters
Parameters
There are 5 sets of parameters used in Curves+3:
Intra-base pair
BP-axis
Inter-BP
Backbone
Groove
3Lavery, R. et al. Nucleic acids research Jan. 2010, 38, 299–313.Emily Cribas Using Curves+: A Nucleic Acid Analysis Tool
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IntroductionHow It Works
The BasicsStructureParameters
General Structure
Emily Cribas Using Curves+: A Nucleic Acid Analysis Tool
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IntroductionHow It Works
The BasicsStructureParameters
Groove Parameters
Emily Cribas Using Curves+: A Nucleic Acid Analysis Tool
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IntroductionHow It Works
The BasicsStructureParameters
Groove Parameters
Emily Cribas Using Curves+: A Nucleic Acid Analysis Tool
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IntroductionHow It Works
The BasicsStructureParameters
Base Pair Parameters
Emily Cribas Using Curves+: A Nucleic Acid Analysis Tool
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IntroductionHow It Works
The BasicsStructureParameters
Base Pair Parameters
Emily Cribas Using Curves+: A Nucleic Acid Analysis Tool
10/16
IntroductionHow It Works
The BasicsStructureParameters
Backbone Parameters
Emily Cribas Using Curves+: A Nucleic Acid Analysis Tool
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IntroductionHow It Works
The BasicsStructureParameters
Backbone Parameters
Emily Cribas Using Curves+: A Nucleic Acid Analysis Tool
12/16
IntroductionHow It Works
Example
How It Works
1. Fix a reference frame for each baseCalculated starting from the glycosidic bondRequires three atoms to build the frame
2. Obtain helical parameters (intrabase pairs)Calculates rigid body transformations(RBT) that maps onebase reference frame to anotherConsists of a translation and a rotationCreates a reference frame for the base pair
3. Obtain helical parameters (interbase pairs)Starting from base pair reference frames, it calculates the RBTbetween two successive framesGenerates a new mid frameCalculates components of the rotation and translation of themid frame
4
4Lavery, R. et al. Nucleic acids research Jan. 2010, 38, 299–313.Emily Cribas Using Curves+: A Nucleic Acid Analysis Tool
12/16
IntroductionHow It Works
Example
How It Works
1. Fix a reference frame for each baseCalculated starting from the glycosidic bondRequires three atoms to build the frame
2. Obtain helical parameters (intrabase pairs)Calculates rigid body transformations(RBT) that maps onebase reference frame to anotherConsists of a translation and a rotationCreates a reference frame for the base pair
3. Obtain helical parameters (interbase pairs)Starting from base pair reference frames, it calculates the RBTbetween two successive framesGenerates a new mid frameCalculates components of the rotation and translation of themid frame
4
4Lavery, R. et al. Nucleic acids research Jan. 2010, 38, 299–313.Emily Cribas Using Curves+: A Nucleic Acid Analysis Tool
12/16
IntroductionHow It Works
Example
How It Works
1. Fix a reference frame for each baseCalculated starting from the glycosidic bondRequires three atoms to build the frame
2. Obtain helical parameters (intrabase pairs)Calculates rigid body transformations(RBT) that maps onebase reference frame to anotherConsists of a translation and a rotationCreates a reference frame for the base pair
3. Obtain helical parameters (interbase pairs)Starting from base pair reference frames, it calculates the RBTbetween two successive framesGenerates a new mid frameCalculates components of the rotation and translation of themid frame
4
4Lavery, R. et al. Nucleic acids research Jan. 2010, 38, 299–313.Emily Cribas Using Curves+: A Nucleic Acid Analysis Tool
13/16
IntroductionHow It Works
Example
How It Works
4. Calculate helical axis
Using the screw axis linking successive base pair referenceframesAverages vectors per base pair and smoothes the curve using apolynomial weighting function
5. Generate BP-axis parameters
Uses a similar rigid body transformation procedure5
5Lavery, R. et al. Nucleic acids research Jan. 2010, 38, 299–313.Emily Cribas Using Curves+: A Nucleic Acid Analysis Tool
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IntroductionHow It Works
Example
Input
Emily Cribas Using Curves+: A Nucleic Acid Analysis Tool
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IntroductionHow It Works
Example
Output
Emily Cribas Using Curves+: A Nucleic Acid Analysis Tool
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IntroductionHow It Works
Example
Visual Output
6
6Lavery, R. et al. Nucleic acids research Sept. 2009, 37, 5917–29.Emily Cribas Using Curves+: A Nucleic Acid Analysis Tool
