Skip to main content

Table 3 Best candidate crRNAs from in silico docking with Cas13 proteins

From: In silico optimization of RNA–protein interactions for CRISPR-Cas13-based antimicrobials

Cas13 protein GT structure

and predicted ΔG

Best model

Candidate crRNA

Model

Distance (Å)

Cluster

Human expertise

Predicted ΔG (kcal/mol)

5W1H

− 14.06 kcal/mol

RNAC_5W1HvsAP019845_1_1_1

AP019845_1_1

1

15.42061

8

1

− 13.47

RNAC_5W1HvsAP019845_1_1_5

AP019845_1_1

5

15.91598

6

1

− 13.53

RNAC_5W1HvsCP002345_2_4_1

CP002345_2_4

1

18.63954

16

1

− 15.16

RNAC_5W1HvsCP002345_2_9_10

CP002345_2_9

10

8.592774

3

0

− 15.16

Rose_5W1HvsAP019834_1_1_1

AP019834_1_1

1

17.97766

3

1

− 15.09

Rose_5W1HvsAP019845_1_1_3

AP019845_1_1

3

8.767469

16

0

− 13.53

Rose_5W1HvsAP019845_1_1_7

AP019845_1_1

7

16.31799

3

1

− 13.53

Rose_5W1HvsCP002345_2_6_1

CP002345_2_6

1

10.5807

3

0

− 15.16

Rose_5W1HvsCP002345_2_7_1

CP002345_2_7

1

10.28279

3

0

− 15.16

Rose_5W1HvsCP018618_1_1_1

CP018618_1_1

1

11.36411

3

0

− 13.46

5W1I_AB

− 13.93 kcal/mol

RNAC_5W1IABvsAP019834_2_2_1

AP019834_2_2

1

15.41219

1

1

− 15.09

RNAC_5W1IABvsAP019845_1_1_1

AP019845_1_1

1

15.4393

7

1

− 13.47

RNAC_5W1IABvsAP019845_1_1_2

AP019845_1_1

2

16.81572

15

1

− 13.53

RNAC_5W1IABvsCP091244_12_2_8

CP091244_12_2

8

19.48762

9

1

− 15.09

Rose_5W1IABvsAP019834_1_1_7

AP019834_1_1

7

18.04252

9

1

− 15.09

Rose_5W1IABvsAP019845_1_1_2

AP019845_1_1

2

17.05391

9

1

− 13.53

Rose_5W1IABvsCP002345_2_5_4

CP002345_2_5

4

14.53866

1

1

− 15.16

Rose_5W1IABvsCP002345_2_6_2

CP002345_2_6

2

10.42858

1

0

− 15.16

Rose_5W1IABvsCP002345_2_6_5

CP002345_2_6

5

13.87067

1

0

− 15.16

Rose_5W1IABvsCP002345_2_7_2

CP002345_2_7

2

10.77602

1

0

− 15.16

Rose_5W1IABvsCP018618_1_1_1

CP018618_1_1

1

10.17277

1

0

− 13.46

5W1I_CD

− 13.68 kcal/mol

RNAC_5W1ICDvsAP019834_2_2_3

AP019834_2_2

3

14.82603

18

0

− 15.09

RNAC_5W1ICDvsAP019845_1_1_1

AP019845_1_1

1

15.82544

19

1

− 13.47

RNAC_5W1ICDvsAP019845_1_1_10

AP019845_1_1

10

11.31408

18

1

− 15.09

Rose_5W1ICDvsAP019834_1_1_5

AP019834_1_1

5

18.23438

2

1

− 15.09

Rose_5W1ICDvsAP019845_1_1_9

AP019845_1_1

9

18.28236

2

1

− 13.53

Rose_5W1ICDvsCP002345_2_4_4

CP002345_2_4

4

10.64548

18

0

− 15.06

Rose_5W1ICDvsCP002345_2_6_1

CP002345_2_6

1

10.06707

18

0

− 15.16

Rose_5W1ICDvsCP002345_2_6_6

CP002345_2_6

6

13.18188

18

0

− 15.16

Rose_5W1ICDvsCP002345_2_6_7

CP002345_2_6

7

10.06989

18

0

− 15.16

Rose_5W1ICDvsCP002345_2_7_1

CP002345_2_7

1

10.96614

18

0

− 15.16

Rose_5W1ICDvsCP011102_2_1_3

CP011102_2_1

3

19.27656

18

1

− 13.15

Rose_5W1ICDvsCP018618_1_1_2

CP018618_1_1

2

8.83881

18

0

− 13.46

5WLH

− 14.06 kcal/mol

RNAC_5WLHvsAP019834_2_2_2

AP019834_2_2

2

15.66461

2

1

− 15.09

RNAC_5WLHvsAP019845_1_1_1

AP019845_1_1

1

13.99831

10

1

− 13.47

RNAC_5WLHvsCP002345_2_1_4

CP002345_2_1

4

14.43221

2

1

− 15.07

RNAC_5WLHvsCP011102_2_2_4

CP011102_2_2

4

13.4716

2

0

− 13.15

Rose_5WLHvsAP019845_1_1_1

AP019845_1_1

1

16.64761

2

1

− 13.53

Rose_5WLHvsAP019845_1_1_3

AP019845_1_1

3

12.08608

2

1

− 13.53

Rose_5WLHvsAP019845_1_1_4

AP019845_1_1

4

14.27125

2

1

− 13.53

Rose_5WLHvsCP002345_2_6_1

CP002345_2_6

1

11.24522

2

0

− 15.16

Rose_5WLHvsCP002345_2_6_3

CP002345_2_6

3

14.17092

2

0

− 15.16

Rose_5WLHvsCP002345_2_7_1

CP002345_2_7

1

11.88083

2

0

− 15.16

Rose_5WLHvsCP011102_3_2_5

CP011102_3_2

5

16.4966

2

1

− 15.09

5WTK

− 11.68 kcal/mol

RNAC_5WTKvsAP019845_1_1_1

AP019845_1_1

1

23.34363

9

1

− 13.53

Rose_5WTKvsAP019845_1_1_1

AP019845_1_1

1

3.64798

5

0

− 13.53

Rose_5WTKvsAP019845_1_1_2

AP019845_1_1

2

1.859212

5

0

− 13.53

Rose_5WTKvsAP019845_1_1_3

AP019845_1_1

3

3.46364

5

0

− 13.53

Rose_5WTKvsCP002345_2_11_8

CP002345_2_11

8

4.103924

5

0

− 15.06

Rose_5WTKvsCP002345_2_5_1

CP002345_2_5

1

9.187617

5

1

− 15.16

Rose_5WTKvsCP002345_2_6_1

CP002345_2_6

1

2.796534

5

0

− 15.06

Rose_5WTKvsCP002345_2_6_2

CP002345_2_6

2

2.4628

5

0

− 15.06

Rose_5WTKvsCP002345_2_8_1

CP002345_2_8

1

5.023773

5

0

− 15.02

Rose_5WTKvsCP011102_2_2_1

CP011102_2_2

1

6.560322

5

1

− 13.15

Rose_5WTKvsCP018618_1_2_8

CP018618_1_2

8

5.777393

5

1

− 13.56

5XWY

− 14.01 kcal/mol

RNAC_5XWYvsAP019845_1_1_1

AP019845_1_1

1

10.34585

2

0

− 13.53

RNAC_5XWYvsAP019845_1_1_3

AP019845_1_1

3

14.16364

6

1

− 13.53

Rose_5XWYvsCP011102_2_1_10

CP011102_2_1

10

17.63066

2

0

− 13.15

  1. A list of crRNA candidates for each Cas13a protein with optimal in silico docking, selected using the optimized pipeline and calculating the distance to the GT crRNA. The Model column refers to the \({n}^{th}\) best model given by HDOCK in each in silico docking experiment. The Distance column shows the Euclidean distance of each docked model to the GT crRNA. The Human expertise column indicates the following 3-D visual assessment by the human expert:
  2. 0 = docked in the same region and in a similar direction as GT
  3. 1 = partially docked in the similar region and in a similar direction as GT
Back to article page

Biology Direct

ISSN: 1745-6150

Contact us