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Artificial Intelligence tools to address challenges of Antimicrobial Resistance in pathogenic Biofilm systems

https://doi.org/10.2139/ssrn.4970499
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Will new generations of modified antimicrobial peptides improve their potential as pharmaceuticals?
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YADAMP: yet another database of antimicrobial peptides
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Deep-AmPEP30: Improve Short Antimicrobial Peptides Prediction with Deep Learning
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EMBOSS: The European Molecular Biology Open Software Suite
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Protein–Ligand Scoring with Convolutional Neural Networks
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Recurrent Neural Network Model for Constructive Peptide Design
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The Potential of Antimicrobial Peptides as an Antiviral Therapy against COVID-19
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Use of Artificial Intelligence in the Design of Small Peptide Antibiotics Effective against a Broad Spectrum of Highly Antibiotic-Resistant Superbugs
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Antibacterial resistance worldwide: causes, challenges and responses
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The biofilm matrix
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Bacteriocins — a viable alternative to antibiotics?
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Antimicrobial host defence peptides: functions and clinical potential
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DRAMP 2.0, an updated data repository of antimicrobial peptides
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AmPEP: Sequence-based prediction of antimicrobial peptides using distribution patterns of amino acid properties and random forest
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Accelerating antibiotic discovery through artificial intelligence
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Feedback GAN for DNA optimizes protein functions
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Improving prediction of secondary structure, local backbone angles and solvent accessible surface area of proteins by iterative deep learning
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dPABBs: A Novel in silico Approach for Predicting and Designing Anti-biofilm Peptides
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Predicting antimicrobial peptides with improved accuracy by incorporating the compositional, physico-chemical and structural features into Chou’s general PseAAC
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Deep generative models for peptide design
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Strategies for combating bacterial biofilms: A focus on anti-biofilm agents and their mechanisms of action
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LAMP2: a major update of the database linking antimicrobial peptides
inferredcites →https://doi.org/10.1093/nar/gkaa991openalex-snapshot
DBAASP v3: database of antimicrobial/cytotoxic activity and structure of peptides as a resource for development of new therapeutics
inferredcites →https://doi.org/10.1093/nar/gkab1080openalex-snapshot
dbAMP 2.0: updated resource for antimicrobial peptides with an enhanced scanning method for genomic and proteomic data
inferredcites →https://doi.org/10.1093/nar/gkac933openalex-snapshot
CAMPR4: a database of natural and synthetic antimicrobial peptides
inferredcites →https://doi.org/10.1093/nar/gkt1191openalex-snapshot
AVPdb: a database of experimentally validated antiviral peptides targeting medically important viruses
inferredcites →https://doi.org/10.1093/nar/gkv1278openalex-snapshot
APD3: the antimicrobial peptide database as a tool for research and education
inferredcites →https://doi.org/10.1101/2024.01.02.573846openalex-snapshot
De novo multi-mechanism antimicrobial peptide design via multimodal deep learning
inferredcites →https://doi.org/10.1109/bibm52615.2021.9669452openalex-snapshot
Multi-AMP: detecting the antimicrobial peptides and their activities using the multi-task learning
inferredcites →https://doi.org/10.1109/tcbb.2015.2462364openalex-snapshot
Improving Recognition of Antimicrobial Peptides and Target Selectivity through Machine Learning and Genetic Programming
inferredcites →https://doi.org/10.1111/apm.12099openalex-snapshot
The role of bacterial biofilms in chronic infections
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The Pel and Psl polysaccharides provide Pseudomonas aeruginosa structural redundancy within the biofilm matrix
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Rosmarinic acid is a homoserine lactone mimic produced by plants that activates a bacterial quorum-sensing regulator
inferredcites →https://doi.org/10.1128/cmr.00181-19openalex-snapshot
Antimicrobial Resistance in ESKAPE Pathogens
inferredcites →https://doi.org/10.1128/microbiolspec.mb-0011-2014openalex-snapshot
Bacterial Extracellular Polysaccharides in Biofilm Formation and Function
inferredcites →https://doi.org/10.1128/mmbr.00013-14openalex-snapshot
Biofilm-Related Infections: Bridging the Gap between Clinical Management and Fundamental Aspects of Recalcitrance toward Antibiotics
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Molecular Basis of Bacterial Outer Membrane Permeability Revisited
inferredcites →https://doi.org/10.1146/annurev-bioeng-010220-095711openalex-snapshot
Engineering Selectively Targeting Antimicrobial Peptides
inferredcites →https://doi.org/10.1155/2015/475062openalex-snapshot
A Large-Scale Structural Classification of Antimicrobial Peptides
inferredcites →https://doi.org/10.1186/s12934-016-0569-5openalex-snapshot
Living together in biofilms: the microbial cell factory and its biotechnological implications
inferredcites →https://doi.org/10.1371/journal.ppat.1003526openalex-snapshot
The Extracellular Matrix Component Psl Provides Fast-Acting Antibiotic Defense in Pseudomonas aeruginosa Biofilms
inferredcites →https://doi.org/10.3389/fbinf.2023.1216362openalex-snapshot
Geometric deep learning as a potential tool for antimicrobial peptide prediction
inferredcites →https://doi.org/10.3389/fcimb.2024.1352273openalex-snapshot
Strategies for combating antibiotic resistance in bacterial biofilms
inferredcites →https://doi.org/10.3389/fmicb.2017.00727openalex-snapshot
Leaf Extracts of Mangifera indica L. Inhibit Quorum Sensing – Regulated Production of Virulence Factors and Biofilm in Test Bacteria
inferredcites →https://doi.org/10.3389/fmicb.2020.582779openalex-snapshot
Antimicrobial Peptides: Classification, Design, Application and Research Progress in Multiple Fields
inferredcites →https://doi.org/10.3389/fmicb.2021.783284openalex-snapshot
Identification of Distinct Characteristics of Antibiofilm Peptides and Prospection of Diverse Sources for Efficacious Sequences
inferredcites →https://doi.org/10.3390/antibiotics9020059openalex-snapshot
Bacterial Biofilm and its Role in the Pathogenesis of Disease
inferredcites →https://doi.org/10.3390/biom10040652openalex-snapshot
Antimicrobial and Antibiofilm Peptides
inferredcites →https://doi.org/10.3390/genes12020137openalex-snapshot
Ensemble-AMPPred: Robust AMP Prediction and Recognition Using the Ensemble Learning Method with a New Hybrid Feature for Differentiating AMPs
inferredcites →https://doi.org/10.3390/ijms150814531openalex-snapshot
New Milk Protein-Derived Peptides with Potential Antimicrobial Activity: An Approach Based on Bioinformatic Studies
inferredcites →https://doi.org/10.3390/ma11122468openalex-snapshot
Action of Antimicrobial Peptides against Bacterial Biofilms
inferredcites →https://doi.org/10.3390/molecules25133048openalex-snapshot
Towards Robust Delivery of Antimicrobial Peptides to Combat Bacterial Resistance
inferredcites →https://doi.org/10.3390/ph16091259openalex-snapshot
Revolutionizing Medicinal Chemistry: The Application of Artificial Intelligence (AI) in Early Drug Discovery
inferredcites →https://doi.org/10.4103/jmau.jmau_10_18openalex-snapshot
Anti-quorum sensing natural compounds
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Prediction of Antimicrobial Peptides Using Deep Neural Networks
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