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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
 6.2 (8/17) β-Actin Hydrophobic-favoured 661 −1128.8
 6.2 (9/17) Plasminogen activator inhibitor 1 Hydrophobic-favoured 741 −1046.5
 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)