Machine-learning techniques for the prediction of protein–protein interactions

Completing sparse and disconnected protein-protein network by deep learning

(2018) Lei Huang et al.   BMC BIOINFORMATICS

Improving prediction of heterodimeric protein complexes using combination with pairwise kernel

(2018) Peiying Ruan et al.   BMC BIOINFORMATICS

LMDIPred: A web-server for prediction of linear peptide sequences binding to SH3, WW and PDZ domains

(2018) Debasree Sarkar et al.   PLoS One

PCVMZM: Using the Probabilistic Classification Vector Machines Model Combined with a Zernike Moments Descriptor to Predict Protein–Protein Interactions from Protein Sequences

(2017) Yanbin Wang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

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

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

Multi-scale encoding of amino acid sequences for predicting protein interactions using gradient boosting decision tree

(2017) Chang Zhou et al.   PLoS One

Predicting physiologically relevant SH3 domain mediated protein–protein interactions in yeast

(2016) Shobhit Jain et al.   BIOINFORMATICS

Prediction of Protein–Protein Interaction via co-occurring Aligned Pattern Clusters

(2016) Antonio Sze-To et al.   METHODS

Prediction of residue-residue contact matrix for protein-protein interaction with Fisher score features and deep learning

(2016) Tianchuan Du et al.   METHODS

APID interactomes: providing proteome-based interactomes with controlled quality for multiple species and derived networks

(2016) Diego Alonso-López et al.   NUCLEIC ACIDS RESEARCH

The BioGRID interaction database: 2017 update

(2016) Andrew Chatr-aryamontri et al.   NUCLEIC ACIDS RESEARCH

SAINTq: Scoring protein-protein interactions in affinity purification - mass spectrometry experiments with fragment or peptide intensity data

(2016) Guoci Teo et al.   PROTEOMICS

Characterizing informative sequence descriptors and predicting binding affinities of heterodimeric protein complexes

(2015) Yerukala Srinivasulu et al.   BMC BIOINFORMATICS

A Cascade Random Forests Algorithm for Predicting Protein-Protein Interaction Sites

(2015) Zhi-Sen Wei et al.   IEEE TRANSACTIONS ON NANOBIOSCIENCE

Predicting Protein-Protein Interaction Sites with a Novel Membership Based Fuzzy SVM Classifier

(2015) Brijesh K. Sriwastava et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Prediction of Protein–Protein Interaction Sites with Machine-Learning-Based Data-Cleaning and Post-Filtering Procedures

(2015) Guang-Hui Liu et al.   JOURNAL OF MEMBRANE BIOLOGY

mapDIA: Preprocessing and statistical analysis of quantitative proteomics data from data independent acquisition mass spectrometry

(2015) Guoshou Teo et al.   Journal of Proteomics

Prediction of Intra-Species Protein-Protein Interactions in Enteropathogens Facilitating Systems Biology Study

(2015) Ranjan Kumar Barman et al.   PLoS One

LMPID: A manually curated database of linear motifs mediating protein–protein interactions

(2015) Debasree Sarkar et al.   Database-The Journal of Biological Databases and Curation

Predicting Protein-Protein Interactions from Primary Protein Sequences Using a Novel Multi-Scale Local Feature Representation Scheme and the Random Forest

(2015) Zhu-Hong You et al.   PLoS One

MoDPepInt: an interactive web server for prediction of modular domain–peptide interactions

(2014) Kousik Kundu et al.   BIOINFORMATICS

Prediction of protein-protein interactions from amino acid sequences using a novel multi-scale continuous and discontinuous feature set

(2014) Zhu-Hong You et al.   BMC BIOINFORMATICS

From Function to Interaction: A New Paradigm for Accurately Predicting Protein Complexes Based on Protein-to-Protein Interaction Networks

(2014) Bin Xu et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Prediction of Interactions between Viral and Host Proteins Using Supervised Machine Learning Methods

(2014) Ranjan Kumar Barman et al.   PLoS One

Feature selection and classification of protein-protein complexes based on their binding affinities using machine learning approaches

(2014) K. Yugandhar et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Predicting whole genome protein interaction networks from primary sequence data in model and non-model organisms using ENTS

(2013) Eli Rodgers-Melnick et al.   BMC GENOMICS

PPIevo : Protein–protein interaction prediction from PSSM based evolutionary information

(2013) Javad Zahiri et al.   GENOMICS

A novel method based on new adaptive LVQ neural network for predicting protein–protein interactions from protein sequences

(2013) Abdulaziz Yousef et al.   JOURNAL OF THEORETICAL BIOLOGY

Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system

(2013) Ben C Collins et al.   NATURE METHODS

The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases

(2013) Sandra Orchard et al.   NUCLEIC ACIDS RESEARCH

Probability Weighted Ensemble Transfer Learning for Predicting Interactions between HIV-1 and Human Proteins

(2013) Suyu Mei   PLoS One

Protein-protein interactions: General trends in the relationship between binding affinity and interfacial buried surface area

(2013) Jieming Chen et al.   PROTEIN SCIENCE

Characterization of Domain–Peptide Interaction Interface: Prediction of SH3 Domain-Mediated Protein–Protein Interaction Network in Yeast by Generic Structure-Based Models

(2012) Tingjun Hou et al.   JOURNAL OF PROTEOME RESEARCH

Structure-based prediction of protein–protein interactions on a genome-wide scale

(2012) Qiangfeng Cliff Zhang et al.   NATURE

Prediction of Protein-Protein Interaction Sites by Random Forest Algorithm with mRMR and IFS

(2012) Bi-Qing Li et al.   PLoS One

Combining many interaction networks to predict gene function and analyze gene lists

(2012) Sara Mostafavi et al.   PROTEOMICS

The protein interaction network mediated by human SH3 domains

(2011) Martina Carducci et al.   BIOTECHNOLOGY ADVANCES

The power of protein interaction networks for associating genes with diseases

(2010) Saket Navlakha et al.   BIOINFORMATICS

Applying the Naïve Bayes classifier with kernel density estimation to the prediction of protein–protein interaction sites

(2010) Yoichi Murakami et al.   BIOINFORMATICS

Predicting protein-protein interactions in unbalanced data using the primary structure of proteins

(2010) Chi-Yuan Yu et al.   BMC BIOINFORMATICS

Class prediction for high-dimensional class-imbalanced data

(2010) Rok Blagus et al.   BMC BIOINFORMATICS

The Bait Compatibility Index: Computational Bait Selection for Interaction Proteomics Experiments

(2010) Sudipto Saha et al.   JOURNAL OF PROTEOME RESEARCH

SAINT: probabilistic scoring of affinity purification–mass spectrometry data

(2010) Hyungwon Choi et al.   NATURE METHODS

Network medicine: a network-based approach to human disease

(2010) Albert-László Barabási et al.   NATURE REVIEWS GENETICS

Radial Basis Function Neural Network Ensemble for Predicting Protein-Protein Interaction Sites in Heterocomplexes

(2010) Bing Wang et al.   PROTEIN AND PEPTIDE LETTERS

Sequence-based prediction of protein interaction sites with an integrative method

(2009) Xue-wen Chen et al.   BIOINFORMATICS

Defining the Human Deubiquitinating Enzyme Interaction Landscape

(2009) Mathew E. Sowa et al.   CELL

Uncovering the rules for protein-protein interactions from yeast genomic data

(2009) J. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Bayesian Modeling of the Yeast SH3 Domain Interactome Predicts Spatiotemporal Dynamics of Endocytosis Proteins

(2009) Raffi Tonikian et al.   PLOS BIOLOGY

A quantitative study of the recruitment potential of all intracellular tyrosine residues on EGFR, FGFR1 and IGF1R

(2008) Alexis Kaushansky et al.   Molecular BioSystems

Integrated network analysis platform for protein-protein interactions

(2008) Jianmin Wu et al.   NATURE METHODS

An empirical framework for binary interactome mapping

(2008) Kavitha Venkatesan et al.   NATURE METHODS

HOMCOS: a server to predict interacting protein pairs and interacting sites by homology modeling of complex structures

(2008) N. Fukuhara et al.   NUCLEIC ACIDS RESEARCH

Using support vector machine combined with auto covariance to predict protein–protein interactions from protein sequences

(2008) Yanzhi Guo et al.   NUCLEIC ACIDS RESEARCH

Probabilistic assembly of human protein interaction networks from label-free quantitative proteomics

(2008) M. E. Sardiu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-Quality Binary Protein Interaction Map of the Yeast Interactome Network

(2008) H. Yu et al.   SCIENCE

Linear Motif Atlas for Phosphorylation-Dependent Signaling

(2008) M. L. Miller et al.   Science Signaling

A Specificity Map for the PDZ Domain Family

(2008) Raffi Tonikian et al.   PLOS BIOLOGY