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Table 2 Data from the best docking model of the phage-display peptides against breast cancer biomarkers: biomarker, type of interaction, number of cluster members and lowest-energy weighted score (E)

From: Screening and characterization of novel specific peptides targeting MDA-MB-231 claudin-low breast carcinoma by computer-aided phage display methodologies

Phage clone

Best docking model

Breast cancer biomarkers

Type of interaction a

Cluster members b

Lowest energy E c

Conventional

 6.2 (8/17)

β-Actin

Hydrophobic-favoured

661

−1128.8

 6.2 (9/17)

Plasminogen activator inhibitor 1

Hydrophobic-favoured

741

−1046.5

BRASIL

 1.3 (7/52)

Metalloprotease inhibitor 1

Hydrophobic-favoured

595

−1127

 5.3 (14/45)

E-cadherin

Electrostatic-favoured

443

−1106

 5.3 (19/45)

β-Actin

Hydrophobic-favoured

600

−1696.6

  1. a Coefficient weights of E formula are adapted for Balanced, Electrostatic-favored, Hydrophobic-favored or van der Waals and Electrostatic interactions
  2. b ClusPro 2.0 ranks models by cluster size. 1000 rotation/translation combinations of lowest score are chosen from 70,000 rotations performed, and are clustered together to find the ligand position with the most “neighbors” in 9 angstroms, becoming a cluster center and the neighbors the members of the cluster. A second cluster center is obtained with the remaining rotations and so on. So the most members on the cluster, the most significant the result
  3. c Weighted score is calculated according to formula E = 0.40Erep + −0.40Eatt + 600Eelec + 1.00EDARS (Balanced), E = 0.40Erep + −0.40Eatt + 1200Eelec + 1.00EDARS (Electrostatic-favored), E = 0.40Erep + −0.40Eatt + 600Eelec + 2.00EDARS (Hydrophobic-favored), or E = 0.40Erep + −0.10Eatt + 600Eelec + 0.00EDARS (Van der Waals and Electrostatic)