A feature extraction technique using bi-gram probabilities of position specific scoring matrix for protein fold recognition.

No abstract is available for this paper.

• Publication year

  2013

• Venue

  Journal of Theoretical Biology

• Publication date

  2013-03-07

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1016/j.jtbi.2012.12.008PMID 23246717
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Prediction of protein-protein interaction sites using patch-based residue characterization.

  2012cited by this paper
• A method to distinguish between lysine acetylation and lysine methylation from protein sequences.

  2012cited by this paper
• A hybrid discriminative/generative approach to protein fold recognition

  2012cited by this paper
• MemHyb: predicting membrane protein types by hybridizing SAAC and PSSM.

  2012cited by this paper
• Fold prediction problem: the application of new physical and physicochemical-based features.

  2011cited by this paper
• Solving protein fold prediction problem using fusion of heterogeneous classifiers

  2011cited by this paper
• LIBSVM: A library for support vector machines

  2011cited by this paper
• A protein fold classifier formed by fusing different modes of pseudo amino acid composition via PSSM

  2011cited by this paper
• Predicting membrane protein types by fusing composite protein sequence features into pseudo amino acid composition.

  2011cited by this paper
• Margin-based ensemble classifier for protein fold recognition

  2011cited by this paper
• AFP-Pred: A random forest approach for predicting antifreeze proteins from sequence-derived properties.

  2011cited by this paper
• Accurate prediction of protein structural class using auto covariance transformation of PSI-BLAST profiles

  2011cited by this paper
• Prediction of cyclin proteins using Chou's pseudo amino acid composition.

  2010cited by this paper
• Cell-PLoc 2.0: an improved package of web-servers for predicting subcellular localization of proteins in various organisms

  2010cited by this paper
• A comparative study of multi-classification methods for protein fold recognition

  2010cited by this paper
• Determination of protein folding kinetic types using sequence and predicted secondary structure and solvent accessibility

  2010cited by this paper
• Using the concept of Chou's pseudo amino acid composition for risk type prediction of human papillomaviruses.

  2010cited by this paper
• Some remarks on protein attribute prediction and pseudo amino acid composition

  2010cited by this paper
• A novel feature representation method based on Chou's pseudo amino acid composition for protein structural class prediction

  2010cited by this paper
• Enhanced protein fold recognition through a novel data integration approach

  2009cited by this paper
• Predicting protein fold pattern with functional domain and sequential evolution information.

  2009cited by this paper
• Protein fold recognition with adaptive local hyperplane algorithm

  2009cited by this paper
• Enhanced protein fold recognition using a structural alphabet

  2009cited by this paper
• Prediction of Protein Folds: Extraction of New Features, Dimensionality Reduction, and Fusion of Heterogeneous Classifiers

  2009cited by this paper
• Enhancing Protein Fold Prediction Accuracy Using an Ensemble of Different Classifiers

  2009cited by this paper
• REVIEW : Recent advances in developing web-servers for predicting protein attributes

  2009cited by this paper
• Protein Fold Prediction Problem Using Ensemble of Classifiers

  2009cited by this paper
• Using Chou's pseudo amino acid composition to predict subcellular localization of apoptosis proteins: An approach with immune genetic algorithm-based ensemble classifier

  2008cited by this paper
• Boosting Methods for Protein Fold Recognition: An Empirical Comparison

  2008cited by this paper
• Prediction protein structural classes with pseudo-amino acid composition: approximate entropy and hydrophobicity pattern.

  2008cited by this paper
• Secondary structure-based assignment of the protein structural classes

  2008cited by this paper
• Application of amino acid occurrence for discriminating different folding types of globular proteins

  2007cited by this paper
• Ensemble of Probabilistic Neural Networks for Protein Fold Recognition

  2007cited by this paper
• Support Vector Machine-based classification of protein folds using the structural properties of amino acid residues and amino acid residue pairs

  2007cited by this paper
• Amino acid sequence predicts folding rate for middle‐size two‐state proteins

  2006cited by this paper
• Protein Fold Recognition using a Structural Hidden Markov Model

  2006cited by this paper
• Ensemble classifier for protein fold pattern recognition

  2006cited by this paper
• Pattern Recognition and Machine Learning

  2006cited by this paper
• Recent Developments in Multilayer Perceptron Neural Networks

  2005cited by this paper
• Protein Structure and Fold Prediction Using Tree-augmented Naïve Bayesian Classifier

  2005cited by this paper
• Protein structure and fold prediction using tree-augmented naive Bayesian classifier.

  2003cited by this paper
• Multi-class protein fold recognition using support vector machines and neural networks

  2001cited by this paper
• Improvements to Platt's SMO Algorithm for SVM Classifier Design

  2001cited by this paper
• Prediction of protein cellular attributes using pseudo‐amino acid composition

  2001cited by this paper
• Side‐chain flexibility in proteins upon ligand binding

  2000cited by this paper
• The Nature of Statistical Learning Theory

  2000cited by this paper
• Fast Training of Support Vector Machines using Sequential Minimal Optimization

  2000cited by this paper
• How good is prediction of protein structural class by the component‐coupled method?

  2000cited by this paper
• Advances in kernel methods: support vector learning

  1999cited by this paper
• Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

  1997cited by this paper
• Protein Folding Class Predictor for SCOP: Approach Based on Global Descriptors

  1997cited by this paper
• Predicting Protein Folding Classes without Overly Relying on Homology

  1995cited by this paper
• SCOP: a structural classification of proteins database for the investigation of sequences and structures.

  1995cited by this paper
• Prediction of protein structural class by discriminant analysis.

  1986cited by this paper

• Prediction of protein-carbohydrate binding sites from protein primary sequence

  2026cites this paper
• Predicting protein–carbohydrate binding sites: a deep learning approach integrating protein language model embeddings and structural features

  2026cites this paper
• Predicting C- and S-linked Glycosylation sites from protein sequences using protein language models

  2025cites this paper
• Sensing Compound Substructures Combined with Molecular Fingerprinting to Predict Drug-Target Interactions

  2025cites this paper
• Integrating system calls and position-specific scoring for enhanced anomaly detection in Internet of Things environments

  2025cites this paper
• Recent Advances, Challenges, and Functional Applications of Protein Chemical Modification in the Food Industry

  2025cites this paper
• Evolving techniques in sentiment analysis: a comprehensive review

  2025cites this paper
• Role of Machine and Deep Learning in Predicting Protein Modification Sites: Review and Future Directions

  2025cites this paper
• ProtCB-bind: Protein-carbohydrate binding site prediction using an ensemble of classifiers.

  2025cites this paper
• PRFold-TNN: Protein Fold Recognition With an Ensemble Feature Selection Method Using PageRank Algorithm Based on Transformer

  2024cites this paper
• Predicting Phosphoglycerylation with Transformer Features and Deep Learning

  2023cites this paper
• Transformer-based deep learning for predicting protein properties in the life sciences

  2023cites this paper
• An Analysis of Sentiment: Methods, Applications, and Challenges

  2023cites this paper
• A Biological Feature and Heterogeneous Network Representation Learning-Based Framework for Drug–Target Interaction Prediction

  2023cites this paper
• Feature Selection using Particle Swarm Optimization for Sentiment Analysis of Drug Reviews

  2023cites this paper
• DRPBind: prediction of DNA, RNA and protein binding residues in intrinsically disordered protein sequences

  2023cites this paper
• DaDL-SChlo: protein subchloroplast localization prediction based on generative adversarial networks and pre-trained protein language model

  2023cites this paper
• Computational Methods and Deep Learning for Elucidating Protein Interaction Networks.

  2023cites this paper
• Prediction of protein-protein interaction sites in intrinsically disordered proteins

  2022cites this paper
• CNN-Pred: Prediction of single-stranded and double-stranded DNA-binding protein using convolutional neural networks.

  2022cites this paper
• Accurately predicting microbial phosphorylation sites using evolutionary and structural features.

  2022cites this paper
• MethEvo: an accurate evolutionary information-based methylation site predictor

  2022cites this paper
• PredAoDP: Accurate identification of antioxidant proteins by fusing different descriptors based on evolutionary information with support vector machine

  2022cites this paper
• ACCURATELY PREDICTING PROTEIN ACETYLATION SITE USING CONVOLUTIONAL NEURAL NETWORK

  2022cites this paper
• Target-DBPPred: An intelligent model for prediction of DNA-binding proteins using discrete wavelet transform based compression and light eXtreme gradient boosting

  2022cites this paper
• DeepDNAbP: A deep learning-based hybrid approach to improve the identification of deoxyribonucleic acid-binding proteins

  2022cites this paper
• Predicting Protein-Protein Interactions via Random Ferns with Evolutionary Matrix Representation

  2022cites this paper
• An effective machine learning-based model for the prediction of protein–protein interaction sites in health systems

  2022cites this paper
• A survey on sentiment analysis methods, applications, and challenges

  2022cites this paper
• An end-to-end heterogeneous graph representation learning-based framework for drug-target interaction prediction

  2021cites this paper
• Targeting GPCRs Via Multi-Platforms Arrays and AI

  2021cites this paper
• ASFold-DNN: Protein Fold Recognition Based on Evolutionary Features With Variable Parameters Using Full Connected Neural Network

  2021cites this paper
• An Enhanced Protein Fold Recognition for Low Similarity Datasets Using Convolutional and Skip-Gram Features With Deep Neural Network

  2020influential citation
• Accurately Predicting Glutarylation Sites Using Sequential Bi-Peptide-Based Evolutionary Features

  2020cites this paper
• Pred-BVP-Unb: Fast prediction of bacteriophage Virion proteins using un-biased multi-perspective properties with recursive feature elimination.

  2020cites this paper
• CWLy-SVM: A support vector machine-based tool for identifying cell wall lytic enzymes

  2020cites this paper
• Mal-Light: Enhancing Lysine Malonylation Sites Prediction Problem Using Evolutionary-based Features

  2020cites this paper
• A Feature Extraction Method in Large Scale Prediction of Human Protein-Protein Interactions using Physicochemical Properties into Bi-gram

  2020cites this paper
• Machine learning approaches and databases for prediction of drug–target interaction: a survey paper

  2020cites this paper
• Enhanced Prediction of Lysine Propionylation Sites using Bi-peptide Evolutionary Features Resolving Data Imbalance

  2020cites this paper
• An Effective Multi-Label Protein Sub-Chloroplast Localization Prediction by Skipped-Grams of Evolutionary Profiles Using Deep Neural Network

  2020cites this paper
• SEMal: Accurate protein malonylation site predictor using structural and evolutionary information

  2020cites this paper
• Single-stranded and double-stranded DNA-binding protein prediction using HMM profiles.

  2020cites this paper
• Protein fold recognition based on multi-view modeling

  2019cites this paper
• SDBP-Pred: Prediction of single-stranded and double-stranded DNA-binding proteins by extending consensus sequence and K-segmentation strategies into PSSM.

  2019cites this paper
• Protein tertiary structure prediction using hidden Markov model based on lattice

  2019cites this paper
• HseSUMO: Sumoylation site prediction using half-sphere exposures of amino acids residues

  2019cites this paper
• Relevance of Machine Learning Techniques and Various Protein Features in Protein Fold Classification: A Review

  2019cites this paper
• Computational Prediction of Lysine Pupylation Sites in Prokaryotic Proteins Using Position Specific Scoring Matrix into Bigram for Feature Extraction

  2019cites this paper
• LipoFNT: Lipoylation Sites Identification with Flexible Neural Tree

  2019cites this paper
• Protein fold recognition using Deep Kernelized Extreme Learning Machine and linear discriminant analysis

  2019cites this paper
• An Efficient LightGBM Model to Predict Protein Self-interacting Using Chebyshev Moments and Bi-gram

  2019cites this paper
• Sequence-based Prediction of Protein-Protein Interactions Using Gray Wolf Optimizer–Based Relevance Vector Machine

  2019cites this paper
• iDTi-CSsmoteB: Identification of Drug–Target Interaction Based on Drug Chemical Structure and Protein Sequence Using XGBoost With Over-Sampling Technique SMOTE

  2019cites this paper
• EvolStruct-Phogly: incorporating structural properties and evolutionary information from profile bigrams for the phosphoglycerylation prediction

  2019cites this paper
• Computational Pipelines and Workflows in Bioinformatics

  2019cites this paper
• StackSSSPred: A Stacking-Based Prediction of Supersecondary Structure from Sequence.

  2019cites this paper
• A novel fusion based on the evolutionary features for protein fold recognition using support vector machines

  2019cites this paper
• Systematic Analysis and Identification of Substrates Secreted by Gram-negative Bacteria

  2019cites this paper
• Performance of rotation forest ensemble classifier and feature extractor in predicting protein interactions using amino acid sequences

  2019cites this paper
• Accurate classification of membrane protein types based on sequence and evolutionary information using deep learning

  2019cites this paper
• Bigram-PGK: phosphoglycerylation prediction using the technique of bigram probabilities of position specific scoring matrix

  2019cites this paper
• Predicting structural class for protein sequences of 40% identity based on features of primary and secondary structure using Random Forest algorithm

  2019cites this paper
• Prediction of drug-target interaction based on protein features using undersampling and feature selection techniques with boosting.

  2019cites this paper
• StackCBPred: A stacking based prediction of protein-carbohydrate binding sites from sequence.

  2019cites this paper
• Computational analysis and prediction of lysine malonylation sites by exploiting informative features in an integrative machine-learning framework

  2018cites this paper
• EvoStruct-Sub: An accurate Gram-positive protein subcellular localization predictor using evolutionary and structural features.

  2018cites this paper
• Improving succinylation prediction accuracy by incorporating the secondary structure via helix, strand and coil, and evolutionary information from profile bigrams

  2018cites this paper
• OPAL: prediction of MoRF regions in intrinsically disordered protein sequences

  2018cites this paper
• Success: evolutionary and structural properties of amino acids prove effective for succinylation site prediction

  2018influential citation
• PBRpredict-Suite: a suite of models to predict peptide-recognition domain residues from protein sequence

  2018cites this paper
• Prediction of Protein-Protein Interactions Using An Effective Sequence Based Combined Method

  2018cites this paper
• MoRFPred-plus: Computational Identification of MoRFs in Protein Sequences using Physicochemical Properties and HMM profiles.

  2018cites this paper
• Detecting Succinylation sites from protein sequences using ensemble support vector machine

  2018cites this paper
• StackDPPred: a stacking based prediction of DNA‐binding protein from sequence

  2018cites this paper
• PADME: A Deep Learning-based Framework for Drug-Target Interaction Prediction

  2018cites this paper
• Accurate Prediction of ncRNA-Protein Interactions From the Integration of Sequence and Evolutionary Information

  2018cites this paper
• Set of approaches based on 3D structure and position specific-scoring matrix for predicting DNA-binding proteins

  2018cites this paper
• OPAL+: Length‐Specific MoRF Prediction in Intrinsically Disordered Protein Sequences

  2018cites this paper
• SumSec: Accurate Prediction of Sumoylation Sites Using Predicted Secondary Structure

  2018cites this paper
• Machine Learning Methods for the Protein Fold Recognition Problem

  2018cites this paper
• Subcellular Localization of Multi-class Proteins Using Label Power-set Encoding

  2018cites this paper
• Enhanced Artificial Neural Network for Protein Fold Recognition and Structural Class Prediction

  2018influential citation
• Intelligent computational method for discrimination of anticancer peptides by incorporating sequential and evolutionary profiles information

  2018cites this paper
• Prediction of DNA-Binding Proteins and their Binding Sites

  2018cites this paper
• PSSM-PROREP: A Flexible Web Server for Generating Various Position Specific Score Matrix-derived Protein Representations*

  2018cites this paper
• Hidden Markov model and Chapman Kolmogrov for protein structures prediction from images

  2017cites this paper
• Prediction of Drug–Target Interaction Networks from the Integration of Protein Sequences and Drug Chemical Structures

  2017cites this paper
• SucStruct: Prediction of succinylated lysine residues by using structural properties of amino acids.

  2017cites this paper
• iDNAProt-ES: Identification of DNA-binding Proteins Using Evolutionary and Structural Features

  2017cites this paper
• PSSM-Suc: Accurately predicting succinylation using position specific scoring matrix into bigram for feature extraction.

  2017cites this paper
• HMMBinder: DNA-Binding Protein Prediction Using HMM Profile Based Features

  2017cites this paper
• Machine Learning based Protein Sequence to (un)Structure Mapping and Interaction Prediction

  2017influential citation
• EFFECT OF SALVIA EGYPTICAE AND FOENICULUM VULGARA EXTRACTS ON QUORUM SENSING AND BIOFILM FORMATION OF METHICILLIN RESISTANT/SENSITIVE STAPHYLOCOCCUS AUREUS ISOLATES

  2017cites this paper
• iPHLoc-ES: Identification of bacteriophage protein locations using evolutionary and structural features.

  2017cites this paper
• Screening drug-target interactions with positive-unlabeled learning

  2017cites this paper
• Intelligent computational model for classification of sub-Golgi protein using oversampling and fisher feature selection methods

  2017cites this paper
• An improved method for predicting interactions between virus and human proteins

  2017cites this paper
• Protein fold recognition based on sparse representation based classification

  2017cites this paper
• Feature Selection Method for DNA-Binding Protein Identification

  2017cites this paper