title: dPABBs: A Novel in silico Approach for Predicting and Designing Anti-biofilm Peptides.
abstract: Increasingly, biofilms are being recognised for their causative role in persistent infections (like cystic fibrosis, otitis media, diabetic foot ulcers) and nosocomial diseases (biofilm-infected vascular catheters, implants and prosthetics). Given the clinical relevance of biofilms and their recalcitrance to conventional antibiotics, it is imperative that alternative therapeutics are proactively sought. We have developed dPABBs, a web server that facilitates the prediction and design of anti-biofilm peptides. The six SVM and Weka models implemented on dPABBs were observed to identify anti-biofilm peptides on the basis of their whole amino acid composition, selected residue features and the positional preference of the residues (maximum accuracy, sensitivity, specificity and MCC of 95.24%, 92.50%, 97.73% and 0.91, respectively, on the training datasets). On the N-terminus, it was seen that either of the cationic polar residues, R and K, is present at all five positions in case of the anti-biofilm peptides, whereas in the QS peptides, the uncharged polar residue S is preponderant at the first (also anionic polar residues D, E), third and fifth positions. Positive predictions were also obtained for 29 FDA-approved peptide drugs and ten antimicrobial peptides in clinical development, indicating at their possible repurposing for anti-biofilm therapy. dPABBs is freely accessible on: http://ab-openlab.csir.res.in/abp/antibiofilm/.
authors.affiliation: Open Source Drug Discovery (OSDD) Unit, Council of Scientific and Industrial Research (CSIR), New Delhi, India.|Academy of Scientific and Innovative Research (AcSIR), CSIR-OSDD Unit, CSIR-HQ, New Delhi, India.
authors.forename: Arun
authors.initials: A
authors.lastname: Sharma
authors.affiliation: Open Source Drug Discovery (OSDD) Unit, Council of Scientific and Industrial Research (CSIR), New Delhi, India.|Bhaskaracharya College of Applied Sciences, University of Delhi, New Delhi, India.
authors.forename: Pooja
authors.initials: P
authors.lastname: Gupta
authors.affiliation: Open Source Drug Discovery (OSDD) Unit, Council of Scientific and Industrial Research (CSIR), New Delhi, India.|Academy of Scientific and Innovative Research (AcSIR), CSIR-OSDD Unit, CSIR-HQ, New Delhi, India.
authors.forename: Rakesh
authors.initials: R
authors.lastname: Kumar
authors.affiliation: Open Source Drug Discovery (OSDD) Unit, Council of Scientific and Industrial Research (CSIR), New Delhi, India.|Academy of Scientific and Innovative Research (AcSIR), CSIR-OSDD Unit, CSIR-HQ, New Delhi, India.
authors.forename: Anshu
authors.initials: A
authors.lastname: Bhardwaj
mesh_terms: D023181:Antimicrobial Cationic Peptides / Q000737:chemistry* / Q000494:pharmacology; D019540:Area Under Curve; D018441:Biofilms / Q000187:drug effects; D016208:Databases, Factual; D015195:Drug Design; D020407:Internet; D053038:Quorum Sensing / Q000187:drug effects; D012372:ROC Curve; D060388:Support Vector Machine; D014584:User-Computer Interface
chemical_list: D023181:Antimicrobial Cationic Peptides