# fourfinger-circ

### Scaffold Selector Results
11 March 2024 09:50:51

# Results

## Top Scoring Origamis (on Pareto Front)

## SAW Top 5

SAW Rank | Origami Id | Scaffold Name | Rotation Offset | G Quad Staples | Metric 1 | Metric 3 | Metric 4 | Origami Contact Map | Origami Sequences
1 | 653 | original scaffold | 653 | 1 | 152.92 ↓-41.7% ↓-34.4% | 8.65 ↓-16.3% ↓-21.5% | 1.15 ↓-44.1% ↑+8.5% | CSV | FASTA
2 | 335 | original scaffold | 335 | 2 | 187.70 ↓-28.5% ↓-19.5% | 7.91 ↓-23.4% ↓-28.2% | 1.32 ↓-35.6% ↑+24.9% | CSV | FASTA
3 | 126 | original scaffold | 126 | 2 | 186.44 ↓-28.9% ↓-20.1% | 7.99 ↓-22.7% ↓-27.5% | 1.29 ↓-36.9% ↑+22.4% | CSV | FASTA
4 | 47 | original scaffold | 47 | 3 | 196.44 ↓-25.1% ↓-15.8% | 9.39 ↓-9.1% ↓-14.8% | 0.04 ↓-98.2% ↓-96.5% | CSV | FASTA
5 | 37 | original scaffold | 37 | 3 | 229.50 ↓-12.5% ↓-1.6% | 8.47 ↓-18.0% ↓-23.1% | 0.11 ↓-94.6% ↓-89.5% | CSV | FASTA

## KNEE Top 5

KNEE Rank | Origami Id | Scaffold Name | Rotation Offset | G Quad Staples | Metric 1 | Metric 3 | Metric 4 | Origami Contact Map | Origami Sequences
1 | 653 | original scaffold | 653 | 1 | 152.92 ↓-41.7% ↓-34.4% | 8.65 ↓-16.3% ↓-21.5% | 1.15 ↓-44.1% ↑+8.5% | CSV | FASTA
2 | 126 | original scaffold | 126 | 2 | 186.44 ↓-28.9% ↓-20.1% | 7.99 ↓-22.7% ↓-27.5% | 1.29 ↓-36.9% ↑+22.4% | CSV | FASTA
3 | 335 | original scaffold | 335 | 2 | 187.70 ↓-28.5% ↓-19.5% | 7.91 ↓-23.4% ↓-28.2% | 1.32 ↓-35.6% ↑+24.9% | CSV | FASTA
4 | 588 | original scaffold | 588 | 3 | 206.44 ↓-21.3% ↓-11.5% | 8.42 ↓-18.5% ↓-23.6% | 0.94 ↓-54.3% ↓-11.3% | CSV | FASTA
5 | 47 | original scaffold | 47 | 3 | 196.44 ↓-25.1% ↓-15.8% | 9.39 ↓-9.1% ↓-14.8% | 0.04 ↓-98.2% ↓-96.5% | CSV | FASTA

## TOPSIS Top 5

TOPSIS Rank | Origami Id | Scaffold Name | Rotation Offset | G Quad Staples | Metric 1 | Metric 3 | Metric 4 | Origami Contact Map | Origami Sequences
1 | 653 | original scaffold | 653 | 1 | 152.92 ↓-41.7% ↓-34.4% | 8.65 ↓-16.3% ↓-21.5% | 1.15 ↓-44.1% ↑+8.5% | CSV | FASTA
2 | 126 | original scaffold | 126 | 2 | 186.44 ↓-28.9% ↓-20.1% | 7.99 ↓-22.7% ↓-27.5% | 1.29 ↓-36.9% ↑+22.4% | CSV | FASTA
3 | 335 | original scaffold | 335 | 2 | 187.70 ↓-28.5% ↓-19.5% | 7.91 ↓-23.4% ↓-28.2% | 1.32 ↓-35.6% ↑+24.9% | CSV | FASTA
4 | 588 | original scaffold | 588 | 3 | 206.44 ↓-21.3% ↓-11.5% | 8.42 ↓-18.5% ↓-23.6% | 0.94 ↓-54.3% ↓-11.3% | CSV | FASTA
5 | 47 | original scaffold | 47 | 3 | 196.44 ↓-25.1% ↓-15.8% | 9.39 ↓-9.1% ↓-14.8% | 0.04 ↓-98.2% ↓-96.5% | CSV | FASTA

# Settings Used

## Origami

Origami | Scaffold-Staples Material | Energy Model | Scaffold | Num Staples
fourfinger-circ | DNA-DNA | DNA | 704 nt, CIRCULAR | 24

## Selection Mode & Metrics Used

MODE 1 - Score all rotations of a fixed scaffold sequence Run on local machine NUPACK v4.0.1.8

| Used | Description | Unit | Weight
Metric 1 | ✔ | Staple-Scaffold: Total energy of off-target staple binding sites | kcal/mol Absolute Value | 0.33
Metric 2 | ❌ | Intra Scaffold: Total energy of scaffold-scaffold binding sites | kcal/mol Absolute Value | 0
Metric 3 | ✔ | Staple-Staple: Worst binding energy between two staples | kcal/mol Absolute Value | 0.33
Metric 4 | ✔ | Intra Staple: Worst secondary structure energy of a single staple | kcal/mol Absolute Value | 0.33

## Scaffold Pool

Original origami scaffold sequence [ CSV ]

## Final Origami Pool Selected From

Origami Rotation Number, R | x Scaffold Pool Size | = Total Origami Pool Size | Origamis Scored | % Total Pool Coverage
704 | 1 | 704 | 704 | 100

# Other Information

## Objective Space (3 Dimensional)

Origamis Scored | Number on Pareto Front | % Origamis on Pareto Front | Total Number Dominated | ..of which on Reverse Front | % Origamis on Reverse Front | Objective Space Data
704 | 30 | 4.26 | 674 | 19 | 2.70 | CSV

Open Objective Space plot below in a new window

## Metric Distributions in Objective Space

Distributions | Mean | Standard Dev. | Min | Max | Pareto Centroid | Reverse Pareto Centroid | Histogram Raw Data
Metric 1 | 262.41 | 37.57 | 138.92 | 379.69 | 225.10 | 315.76 | CSV
Metric 3 | 10.33 | 1.51 | 7.10 | 14.39 | 8.60 | 11.93 | CSV
Metric 4 | 2.05 | 1.23 | 0 | 7.96 | 1.23 | 4.11 | CSV

Relative Changes | Max → Min Value | Pop Centroid → Pareto Centroid | Pop Centroid → Reverse Pareto Centroid | Reverse Pareto Centroid → Pareto Centroid
Metric 1 | ↓-63.4% | ↓-14.2% | ↑+20.3% | ↓-28.7%
Metric 3 | ↓-50.6% | ↓-16.7% | ↑+15.4% | ↓-27.9%
Metric 4 | ↓-100.0% | ↓-39.7% | ↑+100.9% | ↓-70.0%

## Origamis Minimising and Maximising Individual Metrics

Origami Description | Origami Id | Scaffold Name | Rotation Offset | G Quad Staples | Metric 1 | Metric 3 | Metric 4 | Origami Contact Map | Origami Sequences
Original Origami | 703 | original scaffold | 703 | 2 | 233.27 ↓-11.1% 0.0% | 11.02 ↑+6.6% 0.0% | 1.06 ↓-48.5% 0.0% | CSV | FASTA
M1 Min Origami | 221 | original scaffold | 221 | 2 | 138.92 ↓-47.1% ↓-40.4% | 11.80 ↑+14.2% ↑+7.1% | 2.10 ↑+2.5% ↑+98.8% | CSV | FASTA
M1 Max Origami | 187 | original scaffold | 187 | 2 | 379.69 ↑+44.7% ↑+62.8% | 11.80 ↑+14.2% ↑+7.1% | 1.55 ↓-24.2% ↑+47.0% | CSV | FASTA
M3 Min Origami | 688 | original scaffold | 688 | 3 | 274.24 ↑+4.5% ↑+17.6% | 7.10 ↓-31.3% ↓-35.5% | 1.85 ↓-9.6% ↑+75.5% | CSV | FASTA
M3 Max Origami | 662 | original scaffold | 662 | 3 | 287.20 ↑+9.5% ↑+23.1% | 14.39 ↑+39.2% ↑+30.6% | 1.15 ↓-44.1% ↑+8.5% | CSV | FASTA
M4 Min Origami | 179 | original scaffold | 179 | 3 | 246.54 ↓-6.0% ↑+5.7% | 10.28 ↓-0.5% ↓-6.7% | 0.00 ↓-100.0% ↓-100.0% | CSV | FASTA
M4 Max Origami | 117 | original scaffold | 117 | 2 | 271.41 ↑+3.4% ↑+16.4% | 8.02 ↓-22.4% ↓-27.2% | 7.96 ↑+288.6% ↑+654.0% | CSV | FASTA

## Worst Scoring Origamis (on Reverse Pareto Front)

## SAW Top 5

SAW Rank | Origami Id | Scaffold Name | Rotation Offset | Metric 1 | Metric 3 | Metric 4 | Origami Contact Map | Origami Sequences
1 | 53 | original scaffold | 53 | 279.56 ↑+6.5% ↑+19.8% | 13.96 ↑+35.1% ↑+26.7% | 7.19 ↑+251.0% ↑+581.1% | CSV | FASTA
2 | 54 | original scaffold | 54 | 261.80 ↓-0.2% ↑+12.2% | 14.39 ↑+39.2% ↑+30.6% | 7.19 ↑+251.0% ↑+581.1% | CSV | FASTA
3 | 464 | original scaffold | 464 | 313.24 ↑+19.4% ↑+34.3% | 11.80 ↑+14.2% ↑+7.1% | 6.69 ↑+226.9% ↑+534.3% | CSV | FASTA
4 | 369 | original scaffold | 369 | 310.73 ↑+18.4% ↑+33.2% | 11.80 ↑+14.2% ↑+7.1% | 5.82 ↑+184.4% ↑+451.9% | CSV | FASTA
5 | 370 | original scaffold | 370 | 328.98 ↑+25.4% ↑+41.0% | 11.80 ↑+14.2% ↑+7.1% | 4.45 ↑+117.1% ↑+321.4% | CSV | FASTA

## KNEE Top 5

KNEE Rank | Origami Id | Scaffold Name | Rotation Offset | Metric 1 | Metric 3 | Metric 4 | Origami Contact Map | Origami Sequences
1 | 53 | original scaffold | 53 | 279.56 ↑+6.5% ↑+19.8% | 13.96 ↑+35.1% ↑+26.7% | 7.19 ↑+251.0% ↑+581.1% | CSV | FASTA
2 | 464 | original scaffold | 464 | 313.24 ↑+19.4% ↑+34.3% | 11.80 ↑+14.2% ↑+7.1% | 6.69 ↑+226.9% ↑+534.3% | CSV | FASTA
3 | 54 | original scaffold | 54 | 261.80 ↓-0.2% ↑+12.2% | 14.39 ↑+39.2% ↑+30.6% | 7.19 ↑+251.0% ↑+581.1% | CSV | FASTA
4 | 369 | original scaffold | 369 | 310.73 ↑+18.4% ↑+33.2% | 11.80 ↑+14.2% ↑+7.1% | 5.82 ↑+184.4% ↑+451.9% | CSV | FASTA
5 | 370 | original scaffold | 370 | 328.98 ↑+25.4% ↑+41.0% | 11.80 ↑+14.2% ↑+7.1% | 4.45 ↑+117.1% ↑+321.4% | CSV | FASTA

## TOPSIS Top 5

TOPSIS Rank | Origami Id | Scaffold Name | Rotation Offset | Metric 1 | Metric 3 | Metric 4 | Origami Contact Map | Origami Sequences
1 | 53 | original scaffold | 53 | 279.56 ↑+6.5% ↑+19.8% | 13.96 ↑+35.1% ↑+26.7% | 7.19 ↑+251.0% ↑+581.1% | CSV | FASTA
2 | 54 | original scaffold | 54 | 261.80 ↓-0.2% ↑+12.2% | 14.39 ↑+39.2% ↑+30.6% | 7.19 ↑+251.0% ↑+581.1% | CSV | FASTA
3 | 464 | original scaffold | 464 | 313.24 ↑+19.4% ↑+34.3% | 11.80 ↑+14.2% ↑+7.1% | 6.69 ↑+226.9% ↑+534.3% | CSV | FASTA
4 | 369 | original scaffold | 369 | 310.73 ↑+18.4% ↑+33.2% | 11.80 ↑+14.2% ↑+7.1% | 5.82 ↑+184.4% ↑+451.9% | CSV | FASTA
5 | 370 | original scaffold | 370 | 328.98 ↑+25.4% ↑+41.0% | 11.80 ↑+14.2% ↑+7.1% | 4.45 ↑+117.1% ↑+321.4% | CSV | FASTA

## Metric Score Pairwise Correlations

| Pearson's r | Metric 1 | Metric 3 | Metric 4
Metric 1 | 1.00 | 0.05 | -0.00
Metric 3 | 0.05 | 1 | 0.00
Metric 4 | -0.00 | 0.00 | 1

| Spearman's r | Metric 1 | Metric 3 | Metric 4
Metric 1 | 1 | 0.10 | 0.01
Metric 3 | 0.10 | 1.00 | 0.04
Metric 4 | 0.01 | 0.04 | 1

## Metric Individual Execution Times

| Mean Execution Time (s) | Min Execution Time (s) | Max Execution Time (s)
Metric 1 | 0.2362 | 0.2276 | 0.3001
Metric 3 | 0.3018 | 0.2561 | 0.3576
Metric 4 | 0.0104 | 0.0089 | 0.0175

## Whole Job Estimated Run Time on Single CPU

00:06:26