Encodings and models for antimicrobial peptide classification for multi-resistant pathogens

SCOTCH: subtype A coreceptor tropism classification in HIV-1

(2018) Hannah F Löchel et al.   BIOINFORMATICS

DeepEfflux: a 2D convolutional neural network model for identifying families of efflux proteins in transporters

(2018) Semmy Wellem Taju et al.   BIOINFORMATICS

DeepFam: deep learning based alignment-free method for protein family modeling and prediction

(2018) Seokjun Seo et al.   BIOINFORMATICS

iFeature: a Python package and web server for features extraction and selection from protein and peptide sequences

(2018) Zhen Chen et al.   BIOINFORMATICS

Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation

(2018) Tathiane M. Malta et al.   CELL

Machine learning in chemoinformatics and drug discovery

(2018) Yu-Chen Lo et al.   DRUG DISCOVERY TODAY

Deep learning of genomic variation and regulatory network data

(2018) Amalio Telenti et al.   HUMAN MOLECULAR GENETICS

PREvaIL, an integrative approach for inferring catalytic residues using sequence, structural, and network features in a machine-learning framework

(2018) Jiangning Song et al.   JOURNAL OF THEORETICAL BIOLOGY

Computer-aided prediction of antigen presenting cell modulators for designing peptide-based vaccine adjuvants

(2018) Gandharva Nagpal et al.   Journal of Translational Medicine

Antimicrobial resistance among migrants in Europe: a systematic review and meta-analysis

(2018) Laura B Nellums et al.   LANCET INFECTIOUS DISEASES

PyBioMed: a python library for various molecular representations of chemicals, proteins and DNAs and their interactions

(2018) Jie Dong et al.   Journal of Cheminformatics

AmPEP: Sequence-based prediction of antimicrobial peptides using distribution patterns of amino acid properties and random forest

(2018) Pratiti Bhadra et al.   Scientific Reports

EnzyNet: enzyme classification using 3D convolutional neural networks on spatial representation

(2018) Afshine Amidi et al.   PeerJ

Prediction of Antitubercular Peptides From Sequence Information Using Ensemble Classifier and Hybrid Features

(2018) Salman Sadullah Usmani et al.   Frontiers in Pharmacology

SENSE: Siamese neural network for sequence embedding and alignment-free comparison

(2018) Wei Zheng et al.   BIOINFORMATICS

Antimicrobial peptide similarity and classification through rough set theory using physicochemical boundaries

(2018) Kyle Boone et al.   BMC BIOINFORMATICS

Identifying anticancer peptides by using a generalized chaos game representation

(2018) Li Ge et al.   JOURNAL OF MATHEMATICAL BIOLOGY

iPPI-PseAAC(CGR): Identify protein-protein interactions by incorporating chaos game representation into PseAAC

(2018) Jianhua Jia et al.   JOURNAL OF THEORETICAL BIOLOGY

Decoding HIV resistance: from genotype to therapy

(2017) Irene T Weber et al.   Future Medicinal Chemistry

Improving Recognition of Antimicrobial Peptides and Target Selectivity through Machine Learning and Genetic Programming

(2017) Daniel Veltri et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Antimicrobial potency of cationic antimicrobial peptides can be predicted from their amino acid composition: Application to the detection of “cryptic” antimicrobial peptides

(2017) Katia Pane et al.   JOURNAL OF THEORETICAL BIOLOGY

Predicting protein–protein interactions from protein sequences by a stacked sparse autoencoder deep neural network

(2017) Yan-Bin Wang et al.   Molecular BioSystems

A novel numerical mapping method based on entropy for digitizing DNA sequences

(2017) Bihter Das et al.   NEURAL COMPUTING & APPLICATIONS

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

(2017) Ernest Y. Lee et al.   Interface Focus

Predicting antimicrobial peptides with improved accuracy by incorporating the compositional, physico-chemical and structural features into Chou’s general PseAAC

(2017) Prabina Kumar Meher et al.   Scientific Reports

A generalization of CGR representation for analyzing and comparing protein sequences

(2016) Ping-An He et al.   INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY

DBAASP v.2: an enhanced database of structure and antimicrobial/cytotoxic activity of natural and synthetic peptides

(2016) Malak Pirtskhalava et al.   NUCLEIC ACIDS RESEARCH

Enabling the Discovery and Virtual Screening of Potent and Safe Antimicrobial Peptides. Simultaneous Prediction of Antibacterial Activity and Cytotoxicity

(2016) Valeria V. Kleandrova et al.   ACS Combinatorial Science

Antimicrobial Peptides: An Emerging Category of Therapeutic Agents

(2016) Margit Mahlapuu et al.   Frontiers in Cellular and Infection Microbiology

DRAMP: a comprehensive data repository of antimicrobial peptides

(2016) Linlin Fan et al.   Scientific Reports

ProFET: Feature engineering captures high-level protein functions

(2015) Dan Ofer et al.   BIOINFORMATICS

protr/ProtrWeb: R package and web server for generating various numerical representation schemes of protein sequences

(2015) Nan Xiao et al.   BIOINFORMATICS

Identifying DNA-binding proteins by combining support vector machine and PSSM distance transformation

(2015) Ruifeng Xu et al.   BMC Systems Biology

Deep learning

(2015) Yann LeCun et al.   NATURE

CAMPR3: a database on sequences, structures and signatures of antimicrobial peptides: Table 1.

(2015) Faiza Hanif Waghu et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Guangshun Wang et al.   NUCLEIC ACIDS RESEARCH

Machine Learning Assisted Design of Highly Active Peptides for Drug Discovery

(2015) Sébastien Giguère et al.   PLoS Computational Biology

Continuous Distributed Representation of Biological Sequences for Deep Proteomics and Genomics

(2015) Ehsaneddin Asgari et al.   PLoS One

Bacterial multidrug efflux pumps: Mechanisms, physiology and pharmacological exploitations

(2014) Jingjing Sun et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Antimicrobial Peptides: Promising Compounds Against Pathogenic Microorganisms

(2014) J. Cruz et al.   CURRENT MEDICINAL CHEMISTRY

Identification of bacteriophage virion proteins by the ANOVA feature selection and analysis

(2014) Hui Ding et al.   Molecular BioSystems

A simple structure-based model for the prediction of HIV-1 co-receptor tropism

(2014) Dominik Heider et al.   BioData Mining

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

(2013) Xuan Xiao et al.   ANALYTICAL BIOCHEMISTRY

Prediction of Antimicrobial Activity of Synthetic Peptides by a Decision Tree Model

(2013) Felipe Lira et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2013) Dong-Sheng Cao et al.   BIOINFORMATICS

Learning a peptide-protein binding affinity predictor with kernel ridge regression

(2013) Sébastien Giguère et al.   BMC BIOINFORMATICS

QSAR Modeling: Where Have You Been? Where Are You Going To?

(2013) Artem Cherkasov et al.   JOURNAL OF MEDICINAL CHEMISTRY

CAMP: Collection of sequences and structures of antimicrobial peptides

(2013) Faiza Hanif Waghu et al.   NUCLEIC ACIDS RESEARCH

Antimicrobial Peptides Design by Evolutionary Multiobjective Optimization

(2013) Giuseppe Maccari et al.   PLoS Computational Biology

Analysis of Physicochemical and Structural Properties Determining HIV-1 Coreceptor Usage

(2013) Katarzyna Bozek et al.   PLoS Computational Biology

Antibiotic development challenges: the various mechanisms of action of antimicrobial peptides and of bacterial resistance

(2013) Fernanda Guilhelmelli et al.   Frontiers in Microbiology

ClassAMP: A Prediction Tool for Classification of Antimicrobial Peptides

(2012) Shaini Joseph et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

YADAMP: yet another database of antimicrobial peptides

(2012) Stefano P. Piotto et al.   INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS

Predicting the Activity of Antimicrobial Peptides with Amino Acid Topological Information

(2012) Mao Shu et al.   Medicinal Chemistry

AVPpred: collection and prediction of highly effective antiviral peptides

(2012) Nishant Thakur et al.   NUCLEIC ACIDS RESEARCH

Overview on the recent study of antimicrobial peptides: Origins, functions, relative mechanisms and application

(2012) Yanmei Li et al.   PEPTIDES

AMPA: an automated web server for prediction of protein antimicrobial regions

(2011) Marc Torrent et al.   BIOINFORMATICS

Identifying Bacterial Virulent Proteins by Fusing a Set of Classifiers Based on Variants of Chou's Pseudo Amino Acid Composition and on Evolutionary Information

(2011) Loris Nanni et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Designing antimicrobial peptides: form follows function

(2011) Christopher D. Fjell et al.   NATURE REVIEWS DRUG DISCOVERY

Connecting Peptide Physicochemical and Antimicrobial Properties by a Rational Prediction Model

(2011) Marc Torrent et al.   PLoS One

Improved Bevirimat resistance prediction by combination of structural and sequence-based classifiers

(2011) J Nikolaj Dybowski et al.   BioData Mining

Interpol: An R package for preprocessing of protein sequences

(2011) Dominik Heider et al.   BioData Mining

Predicting Bevirimat resistance of HIV-1 from genotype

(2010) Dominik Heider et al.   BMC BIOINFORMATICS

Exploiting physico-chemical properties in string kernels

(2010) Nora C Toussaint et al.   BMC BIOINFORMATICS

Prediction of Co-Receptor Usage of HIV-1 from Genotype

(2010) J. Nikolaj Dybowski et al.   PLoS Computational Biology

Prediction of mitochondrial proteins of malaria parasite using split amino acid composition and PSSM profile

(2009) Ruchi Verma et al.   AMINO ACIDS

Computational Design of Highly Selective Antimicrobial Peptides

(2009) Davor Juretić et al.   Journal of Chemical Information and Modeling

Classification of antimicrobial peptide using diversity measure with quadratic discriminant analysis

(2009) Wei Chen et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Systems biology evaluation of immune responses induced by human host defence peptide LL-37 in mononuclear cells

(2009) Neeloffer Mookherjee et al.   Molecular BioSystems

Sequence-Based Prediction of Protein-Protein Interactions by Means of Rotation Forest and Autocorrelation Descriptor

(2009) Jun-Feng Xia et al.   PROTEIN AND PEPTIDE LETTERS

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

Computational prediction of human proteins that can be secreted into the bloodstream

(2008) Juan Cui et al.   BIOINFORMATICS

Predicting linear B‐cell epitopes using string kernels

(2008) Yasser EL‐Manzalawy et al.   JOURNAL OF MOLECULAR RECOGNITION

Using genetic algorithms to select most predictive protein features

(2008) Andrew Kernytsky et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

HIV-1 coreceptor usage prediction without multiple alignments: an application of string kernels

(2008) Sébastien Boisvert et al.   Retrovirology

Predicting cell-penetrating peptides

(2007) Mats Hansen et al.   ADVANCED DRUG DELIVERY REVIEWS

Prediction of RNA binding sites in a protein using SVM and PSSM profile

(2007) Manish Kumar et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

MAMMOTH (Matching molecular models obtained from theory): An automated method for model comparison

(2002) Angel R. Ortiz et al.   PROTEIN SCIENCE