Prediction of Self-Interacting Proteins from Protein Sequence Information Based on Random Projection Model and Fast Fourier Transform

ACPred-FL: a sequence-based predictor using effective feature representation to improve the prediction of anti-cancer peptides

(2018) Leyi Wei et al.   BIOINFORMATICS

Improving Prediction of Self-interacting Proteins Using Stacked Sparse Auto-Encoder with PSSM profiles

(2018) Yan-Bin Wang et al.   International Journal of Biological Sciences

Machine-Learning-Based Prediction of Cell-Penetrating Peptides and Their Uptake Efficiency with Improved Accuracy

(2018) Balachandran Manavalan et al.   JOURNAL OF PROTEOME RESEARCH

PVP-SVM: Sequence-Based Prediction of Phage Virion Proteins Using a Support Vector Machine

(2018) Balachandran Manavalan et al.   Frontiers in Microbiology

AIPpred: Sequence-Based Prediction of Anti-inflammatory Peptides Using Random Forest

(2018) Balachandran Manavalan et al.   Frontiers in Pharmacology

M6APred-EL: A sequence-based predictor for identifying N6-methyladenosine sites using ensemble learning

(2018) Leyi Wei et al.   Molecular Therapy-Nucleic Acids

A Deep Learning Framework for Robust and Accurate Prediction of ncRNA-Protein Interactions Using Evolutionary Information

(2018) Hai-Cheng Yi et al.   Molecular Therapy-Nucleic Acids

Exploring sequence-based features for the improved prediction of DNA N4-methylcytosine sites in multiple species

(2018) Leyi Wei et al.   BIOINFORMATICS

PIP-EL: A New Ensemble Learning Method for Improved Proinflammatory Peptide Predictions

(2018) Balachandran Manavalan et al.   Frontiers in Immunology

iBCE-EL: A New Ensemble Learning Framework for Improved Linear B-Cell Epitope Prediction

(2018) Balachandran Manavalan et al.   Frontiers in Immunology

Set of approaches based on 3D structure and position specific-scoring matrix for predicting DNA-binding proteins

(2018) Loris Nanni et al.   BIOINFORMATICS

Identify origin of replication in Saccharomyces cerevisiae using two-step feature selection technique

(2018) Fu-Ying Dao et al.   BIOINFORMATICS

Prediction of protein self-interactions using stacked long short-term memory from protein sequences information

(2018) Yan-Bin Wang et al.   BMC Systems Biology

Prediction and Validation of Disease Genes Using HeteSim Scores

(2017) Xiangxiang Zeng et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

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

Advancing the prediction accuracy of protein-protein interactions by utilizing evolutionary information from position-specific scoring matrix and ensemble classifier

(2017) Lei Wang 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

Detection of Interactions between Proteins by Using Legendre Moments Descriptor to Extract Discriminatory Information Embedded in PSSM

(2017) Yan-Bin Wang et al.   MOLECULES

DHSpred: support-vector-machine-based human DNase I hypersensitive sites prediction using the optimal features selected by random forest

(2017) Balachandran Manavalan et al.   Oncotarget

MLACP: machine-learning-based prediction of anticancer peptides

(2017) Balachandran Manavalan et al.   Oncotarget

PBMDA: A novel and effective path-based computational model for miRNA-disease association prediction

(2017) Zhu-Hong You et al.   PLoS Computational Biology

Highly Efficient Framework for Predicting Interactions Between Proteins

(2017) Zhu-Hong You et al.   IEEE Transactions on Cybernetics

SPAR: a random forest-based predictor for self-interacting proteins with fine-grained domain information

(2016) Xuhan Liu et al.   AMINO ACIDS

Pretata: predicting TATA binding proteins with novel features and dimensionality reduction strategy

(2016) Quan Zou et al.   BMC Systems Biology

The BioGRID interaction database: 2017 update

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

Similarity computation strategies in the microRNA-disease network: a survey

(2015) Quan Zou et al.   Briefings in Functional Genomics

LocFuse: Human protein–protein interaction prediction via classifier fusion using protein localization information

(2014) Javad Zahiri et al.   GENOMICS

A Novel Feature Extraction Scheme with Ensemble Coding for Protein–Protein Interaction Prediction

(2014) Xiuquan Du et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

A set of descriptors for identifying the protein–drug interaction in cellular networking

(2014) Loris Nanni et al.   JOURNAL OF THEORETICAL BIOLOGY

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

An Empirical Study of Different Approaches for Protein Classification

(2014) Loris Nanni et al.   TheScientificWorldJOURNAL

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

(2013) Javad Zahiri et al.   GENOMICS

Proteome-wide Prediction of Self-interacting Proteins Based on Multiple Properties

(2013) Zhongyang Liu et al.   MOLECULAR & CELLULAR PROTEOMICS

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

(2013) Sandra Orchard et al.   NUCLEIC ACIDS RESEARCH

InnateDB: systems biology of innate immunity and beyond—recent updates and continuing curation

(2012) Karin Breuer et al.   NUCLEIC ACIDS RESEARCH

LIBSVM

(2012) Chih-Chung Chang et al.   ACM Transactions on Intelligent Systems and Technology

Wavelet images and Chou’s pseudo amino acid composition for protein classification

(2011) Loris Nanni et al.   AMINO ACIDS

Using manifold embedding for assessing and predicting protein interactions from high-throughput experimental data

(2010) Z.-H. You et al.   BIOINFORMATICS

Some remarks on protein attribute prediction and pseudo amino acid composition

(2010) Kuo-Chen Chou   JOURNAL OF THEORETICAL BIOLOGY

MatrixDB, the extracellular matrix interaction database

(2010) E. Chautard et al.   NUCLEIC ACIDS RESEARCH

Linking molecular affinity and cellular specificity in cadherin-mediated adhesion

(2009) P. Katsamba 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

Alteration of oligomeric state and domain architecture is essential for functional transformation between transferase and hydrolase with the same scaffold

(2009) Ryotaro Koike et al.   PROTEIN SCIENCE