RNA Folding Simulation by Giff Ransom RNA Folding Simulation.

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RNA Folding Simulation by Giff Ransom RNA Folding Simulation

Transcript of RNA Folding Simulation by Giff Ransom RNA Folding Simulation.

Page 1: RNA Folding Simulation by Giff Ransom RNA Folding Simulation.

RNA FoldingSimulation

by Giff Ransom

RNA FoldingSimulation

Page 2: RNA Folding Simulation by Giff Ransom RNA Folding Simulation.

Scientific Background

• RNA molecules are single stranded copies of a segment of a gene in the DNA.

• Though a DNA strand is locked in a double helix with its partner, making their three dimensional structure predictable and stable, RNA molecules have no such complementary strand.

• Rather than staying stretched out in a line, RNA molecules tend to fold back on themselves, and the three-dimensional shape formed by a given strand is important for studying its interaction with other molecules.

Page 3: RNA Folding Simulation by Giff Ransom RNA Folding Simulation.

Scientific Background

• As an RNA molecule folds, its bases bond with other complementary bases in the strand, similar to DNA. However, since the sequence isn't symmetrical, it will not match perfectly and form a double helix. Exactly which bases line up with their pair determines the most stable structure of the RNA molecule.

• Most biologists use two-dimensional simulations when they need to find the ideal configuration for a given RNA molecule. However, these do not provide an accurate representation of the three-dimensional dynamics and emerging structure.

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3D Simulation

• Three-dimensional molecular dynamic simulations give a much better glimpse of the RNA molecule's structure, as well as a more accurate prediction of the actual shape.

• Ideally, each atom of the molecule would be modeled, but this limits the size and scope of the simulation.

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Kurt Grunberger, 2002

The molecular structure can be simplified while still fairly accurately predicting the RNA tertiary structure

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My Model

• I intend to create a 3D RNA folding simulation accurate enough to reproduce experimental configurations for small RNA molecules.

• Rather than implementing an atomic-level molecular dynamics engine, my model will operate on the higher level of bases and sugars. I aim to achieve computational simplicity while retaining the basic forces and angles between key elements.

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So Far…

• Created a basic simulation using the DNA double helix structure as the resting point for my spring constants

• Implemented bond length and bond angle springs

• Verlet integration• Electrostatic attraction

and repulsion in bases• Very basic rigid body (i.e.

angular forces) dynamics on bases

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Yet to Do…

• It just doesn’t look right yet – needs a good bit of tweaking

• Use constraints rather than springs on the bond-lengths

• Implement torsional potential if necessary


GIFF 2012 Program Guide

GIFF 2012 Program Guide

Current Topics RNA and Protein Folding: Common Themes and …biotheory.umd.edu/v1.0/PDF/biochemistry.pdf · 2006. 9. 21. · Current Topics RNA and Protein Folding: Common Themes

Current Topics RNA and Protein Folding: Common Themes and …biotheory.umd.edu/v1.0/PDF/biochemistry.pdf · 2006. 9. 21. · Current Topics RNA and Protein Folding: Common Themes

Protein-DNA Interactions · Transcription of DNA sequence into RNA sequence RNA 1 RNA 2 RNA 3 Translation (on the ribosome) of RNA sequence into protein sequence and folding of protein

Protein-DNA Interactions · Transcription of DNA sequence into RNA sequence RNA 1 RNA 2 RNA 3 Translation (on the ribosome) of RNA sequence into protein sequence and folding of protein

Improving Free Energy Functions for RNA Folding RNA Secondary Structure Prediction.

Improving Free Energy Functions for RNA Folding RNA Secondary Structure Prediction.

RNA-DNA Hybrid Origami: Folding a Long RNA … · RNA-DNA Hybrid Origami: Folding a Long RNA Single Strands into Complex Nanostructures ... Forward primer (P1): 5'-ttctaatacgactcactataggtctgacagttaccaat-3'

RNA-DNA Hybrid Origami: Folding a Long RNA … · RNA-DNA Hybrid Origami: Folding a Long RNA Single Strands into Complex Nanostructures ... Forward primer (P1): 5'-ttctaatacgactcactataggtctgacagttaccaat-3'

RNA Foldingckingsf/bioinfo-lectures/rnafold.pdf · RNA Folding Rules RNA folding rules: 1. If two bases are closer than 4 bases apart, they cannot pair 2. Each base is matched to

RNA Foldingckingsf/bioinfo-lectures/rnafold.pdf · RNA Folding Rules RNA folding rules: 1. If two bases are closer than 4 bases apart, they cannot pair 2. Each base is matched to

Folding and Finding RNA Secondary Structurequantum.phys.unm.edu › biophysics-16 › cshperspect-RNA... · Folding and Finding RNA Secondary Structure David H. Mathews1, Walter N.

Folding and Finding RNA Secondary Structurequantum.phys.unm.edu › biophysics-16 › cshperspect-RNA... · Folding and Finding RNA Secondary Structure David H. Mathews1, Walter N.

RNA Folding Xinyu Tang Bonnie Kirkpatrick. Overview Introduction to RNA Previous Work Problem Hofacker ’ s Paper Chen and Dill ’ s Paper Modeling RNA.

RNA Folding Xinyu Tang Bonnie Kirkpatrick. Overview Introduction to RNA Previous Work Problem Hofacker ’ s Paper Chen and Dill ’ s Paper Modeling RNA.

RNA Folding. RNA Folding Algorithms Intuitively: given a sequence, find the structure with the maximal number of base pairs For nested structures, four.

RNA Folding. RNA Folding Algorithms Intuitively: given a sequence, find the structure with the maximal number of base pairs For nested structures, four.

GIFF - Guwahati International Film Festival

GIFF - Guwahati International Film Festival

doi:10.1093/nar/gkl1036 Encoding folding paths of RNA switches · Encoding folding paths of RNA switches A. Xayaphoummine1, V. Viasnoff2, S. Harlepp1 and H. Isambert1,2,* 1Laboratoire

doi:10.1093/nar/gkl1036 Encoding folding paths of RNA switches · Encoding folding paths of RNA switches A. Xayaphoummine1, V. Viasnoff2, S. Harlepp1 and H. Isambert1,2,* 1Laboratoire

Feynman diagrams, RNA folding, and the transition polynomial · Feynman diagrams, RNA folding, and the transition polynomial Yongwu Rong Department of Mathematics George Washington

Feynman diagrams, RNA folding, and the transition polynomial · Feynman diagrams, RNA folding, and the transition polynomial Yongwu Rong Department of Mathematics George Washington

Reinforcement learning techniques in RNA inverse folding › Lehre › Theses › MA_Parastou_Kohvaei.pdf · Reinforcement learning techniques in RNA inverse folding Parastou Kohvaei

Reinforcement learning techniques in RNA inverse folding › Lehre › Theses › MA_Parastou_Kohvaei.pdf · Reinforcement learning techniques in RNA inverse folding Parastou Kohvaei

RNA folding & ncRNA discovery

RNA folding & ncRNA discovery

RNA Folding during Transcription by T7 RNA Polymerase … · 2008. 1. 6. · RNA Folding during Transcription by T7 RNA Polymerase Analyzed Using the Self-cleaving Transcript Assay+

RNA Folding during Transcription by T7 RNA Polymerase … · 2008. 1. 6. · RNA Folding during Transcription by T7 RNA Polymerase Analyzed Using the Self-cleaving Transcript Assay+

Brochure giff 2016

Brochure giff 2016

Mesoscopic Modeling of RNA Structure and Dynamics Hin Hark Gan A. Fundamentals of RNA structure 1. Hierarchical folding 2. Folding timescales B. Issues.

Mesoscopic Modeling of RNA Structure and Dynamics Hin Hark Gan A. Fundamentals of RNA structure 1. Hierarchical folding 2. Folding timescales B. Issues.

Real-time multidimensional NMR follows RNA folding with second resolution

Real-time multidimensional NMR follows RNA folding with second resolution

RNA folding with soft constraints: reconciliation of probing data …compbio.mit.edu/publications/65_Washietl_NAR_12.pdf · 2012-02-05 · RNA folding with soft constraints: reconciliation

RNA folding with soft constraints: reconciliation of probing data …compbio.mit.edu/publications/65_Washietl_NAR_12.pdf · 2012-02-05 · RNA folding with soft constraints: reconciliation

Folding of riboswitches during RNA transcription Background information What are riboswitches? Folding of riboswitch terminators Efficient folding of hairpins.

Folding of riboswitches during RNA transcription Background information What are riboswitches? Folding of riboswitch terminators Efficient folding of hairpins.