What can machine learning do for antimicrobial peptides, and what can antimicrobial peptides do for machine learning?

Machine learning-enabled discovery and design of membrane-active peptides

(2018) Ernest Y. Lee et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Antimicrobial peptides

(2016) Ling-juan Zhang et al.   CURRENT BIOLOGY

Hybrid Network Model for “Deep Learning” of Chemical Data: Application to Antimicrobial Peptides

(2016) Petra Schneider et al.   Molecular Informatics

Mastering the game of Go with deep neural networks and tree search

(2016) David Silver et al.   NATURE

Mapping membrane activity in undiscovered peptide sequence space using machine learning

(2016) Ernest Y. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fluid lipid membranes: From differential geometry to curvature stresses

(2015) Markus Deserno   CHEMISTRY AND PHYSICS OF LIPIDS

APD3: the antimicrobial peptide database as a tool for research and education

(2015) Guangshun Wang et al.   NUCLEIC ACIDS RESEARCH

Helical antimicrobial polypeptides with radial amphiphilicity

(2015) Menghua Xiong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Viral fusion protein transmembrane domain adopts β-strand structure to facilitate membrane topological changes for virus–cell fusion

(2015) Hongwei Yao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Machine Learning Assisted Design of Highly Active Peptides for Drug Discovery

(2015) Sébastien Giguère et al.   PLoS Computational Biology

Two interdependent mechanisms of antimicrobial activity allow for efficient killing in nylon-3-based polymeric mimics of innate immunity peptides

(2014) Michelle W. Lee et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

The role of spontaneous lipid curvature in the interaction of interfacially active peptides with membranes

(2014) Daniel Koller et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Machine learning methods in chemoinformatics

(2014) John B. O. Mitchell   Wiley Interdisciplinary Reviews-Computational Molecular Science

iAMP-2L: A two-level multi-label classifier for identifying antimicrobial peptides and their functional types

(2013) Xuan Xiao et al.   ANALYTICAL BIOCHEMISTRY

propy: a tool to generate various modes of Chou’s PseAAC

(2013) Dong-Sheng Cao et al.   BIOINFORMATICS

Generation and sensing of membrane curvature: Where materials science and biophysics meet

(2013) Qiang Cui et al.   CURRENT OPINION IN SOLID STATE & MATERIALS SCIENCE

Antimicrobial peptides and induced membrane curvature: Geometry, coordination chemistry, and molecular engineering

(2013) Nathan W. Schmidt et al.   CURRENT OPINION IN SOLID STATE & MATERIALS SCIENCE

Why Do Arginine and Lysine Organize Lipids Differently? Insights from Coarse-Grained and Atomistic Simulations

(2013) Zhe Wu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Influenza Virus A M2 Protein Generates Negative Gaussian Membrane Curvature Necessary for Budding and Scission

(2013) Nathan W. Schmidt et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A Critical Evaluation of Random Copolymer Mimesis of Homogeneous Antimicrobial Peptides

(2013) Kan Hu et al.   MACROMOLECULES

Antimicrobial Peptides Design by Evolutionary Multiobjective Optimization

(2013) Giuseppe Maccari et al.   PLoS Computational Biology

Arginine in α-Defensins

(2012) Nathan W. Schmidt et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Molecular Basis for Nanoscopic Membrane Curvature Generation from Quantum Mechanical Models and Synthetic Transporter Sequences

(2012) Nathan W. Schmidt et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

α-Synuclein Induces Both Positive Mean Curvature and Negative Gaussian Curvature in Membranes

(2012) Anthony R. Braun et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Membrane bending by protein–protein crowding

(2012) Jeanne C. Stachowiak et al.   NATURE CELL BIOLOGY

PDBTM: Protein Data Bank of transmembrane proteins after 8 years

(2012) Dániel Kozma et al.   NUCLEIC ACIDS RESEARCH

CS-AMPPred: An Updated SVM Model for Antimicrobial Activity Prediction in Cysteine-Stabilized Peptides

(2012) William F. Porto et al.   PLoS One

Evolutionary Trade-Offs, Pareto Optimality, and the Geometry of Phenotype Space

(2012) O. Shoval et al.   SCIENCE

Mechanisms of Membrane Curvature Sensing

(2011) Bruno Antonny   Annual Review of Biochemistry

Thermodynamics and Mechanics of Membrane Curvature Generation and Sensing by Proteins and Lipids

(2011) Tobias Baumgart et al.   Annual Review of Physical Chemistry

Criterion for Amino Acid Composition of Defensins and Antimicrobial Peptides Based on Geometry of Membrane Destabilization

(2011) Nathan W. Schmidt et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Connecting Peptide Physicochemical and Antimicrobial Properties by a Rational Prediction Model

(2011) Marc Torrent et al.   PLoS One

Prediction of Antimicrobial Peptides Based on Sequence Alignment and Feature Selection Methods

(2011) Ping Wang et al.   PLoS One

HIV Fusion Peptide Penetrates, Disorders, and Softens T-Cell Membrane Mimics

(2010) Stephanie Tristram-Nagle et al.   JOURNAL OF MOLECULAR BIOLOGY

Bacterial membrane lipids in the action of antimicrobial agents

(2010) Richard M. Epand et al.   JOURNAL OF PEPTIDE SCIENCE

Steric confinement of proteins on lipid membranes can drive curvature and tubulation

(2010) Jeanne C. Stachowiak et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rationalizing the membrane interactions of cationic amphipathic antimicrobial peptides by their molecular shape

(2009) Burkhard Bechinger   CURRENT OPINION IN COLLOID & INTERFACE SCIENCE

Pseudo Amino Acid Composition and its Applications in Bioinformatics, Proteomics and System Biology

(2009) Kuo-Chen Chou   Current Proteomics

Amphipathic helices and membrane curvature

(2009) Guillaume Drin et al.   FEBS LETTERS

Arginine-rich cell-penetrating peptides

(2009) Nathan Schmidt et al.   FEBS LETTERS

A Novel Connectionist System for Unconstrained Handwriting Recognition

(2009) A. Graves et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Neural network approach to quantum-chemistry data: Accurate prediction of density functional theory energies

(2009) Roman M. Balabin et al.   JOURNAL OF CHEMICAL PHYSICS

Identification of Novel Antibacterial Peptides by Chemoinformatics and Machine Learning†

(2009) Christopher D. Fjell et al.   JOURNAL OF MEDICINAL CHEMISTRY

Divalent Metal Ion Triggered Activity of a Synthetic Antimicrobial in Cardiolipin Membranes

(2009) Abhigyan Som et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Vesicle Budding Induced by a Pore-Forming Peptide

(2009) Yan Yu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Use of Artificial Intelligence in the Design of Small Peptide Antibiotics Effective against a Broad Spectrum of Highly Antibiotic-Resistant Superbugs

(2008) Artem Cherkasov et al.   ACS Chemical Biology

HIV TAT Forms Pores in Membranes by Inducing Saddle-Splay Curvature: Potential Role of Bidentate Hydrogen Bonding

(2008) Abhijit Mishra et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Structures of Human Host Defense Cathelicidin LL-37 and Its Smallest Antimicrobial Peptide KR-12 in Lipid Micelles

(2008) Guangshun Wang   JOURNAL OF BIOLOGICAL CHEMISTRY

Modulation of the Spontaneous Curvature and Bending Rigidity of Lipid Membranes by Interfacially Adsorbed Amphipathic Peptides

(2008) Assaf Zemel et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Membrane lipids: where they are and how they behave

(2008) Gerrit van Meer et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

APD2: the updated antimicrobial peptide database and its application in peptide design

(2008) Guangshun Wang et al.   NUCLEIC ACIDS RESEARCH

Mechanism of a prototypical synthetic membrane-active antimicrobial: Efficient hole-punching via interaction with negative intrinsic curvature lipids

(2008) L. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of novel host defense peptides and the absence of α-defensins in the bovine genome

(2008) Christopher D. Fjell et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS