Predicting DNA-Binding using 3D structures and PWMs
Predicting DNA-Binding using 3D structures and PWMs
by: shawnyost
|
January 9, 2009
Shawn Yost presents his hypothesis that given a database of position-weight matrices created from 3-D models of DNA,...
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Tags
- acid
- acknowledgements
- Alexandre Morozov
- alignment
- all-atom 3-D structures
- amino acids
- atomic reactions
- backbone
- bases
- Binding Sites
- CE method
- combinations
- conclusion
- conserved base
- coordinates
- crystallized 3-D structure
- cut-off
- cut-off score
- Database
- deleted base
- DNA segments
- domain
- down regulate
- electrophoresis mobility shift
- enhancers
- Eric Siggia
- ETL
- ETO
- experiments
- false positives
- frequency data set
- GC percent
- generates structure
- genome
- human genes
- hypothesis
- identity
- impact
- interactions
- list
- maximum
- model
- motif
- mRNA
- mutation
- non-specific base
- nucleus zone
- Orientation
- overlapping
- papers
- PDPD
- Phillip Bourne
- position change
- position-weight matrix
- PPGDS
- predicting
- predicting DNA protein binding
- Predicting Protein Given a DNA Sequence
- prediction
- procedures
- program
- Protein DNA Position-Weight Matrix Database
- pwm
- ranking
- redundancy
- region
- regulate
- regulation
- RMSD value
- rocks
- rolls
- sensitivity
- sequence
- sets
- Shawn Yost
- shifts
- size
- slides
- specificity
- superimposition
- tilts
- time
- transcribe
- transcription factors
- twists
- UCSD
- University of California San Diego
- unknown DNA binding sites
- X-ray crystallography
