Natural Science

Volume 1, Issue 2 (September 2009)

ISSN Print: 2150-4091   ISSN Online: 2150-4105

Google-based Impact Factor: 1.08  Citations  

REVIEW : Recent advances in developing web-servers for predicting protein attributes

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DOI: 10.4236/ns.2009.12011    9,258 Downloads   18,827 Views  Citations

Affiliation(s)

.

ABSTRACT

Recent advance in large-scale genome se-quencing has generated a huge volume of pro-tein sequences. In order to timely utilize the in-formation hidden in these newly discovered sequences, it is highly desired to develop com- putational methods for efficiently identifying their various attributes because the information thus obtained will be very useful for both basic research and drug development. Particularly, it would be even more useful and welcome if a user-friendly web-server could be provided for each of these methods. In this minireview, a sy- stematic introduction is presented to highlight the development of these web-servers by our group during the last three years.

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Chou, K. and Shen, H. (2009) REVIEW : Recent advances in developing web-servers for predicting protein attributes. Natural Science, 1, 63-92. doi: 10.4236/ns.2009.12011.

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[223] Prediction of interface residue based on the features of residue interaction network
Journal of Theoretical Biology, 2017
[224] iRSpotH-TNCPseAAC: Identifying Recombination Spots in Human by Using Pseudo Trinucleotide Composition With an Ensemble of Support Vector Machine …
Letters in Organic Chemistry, 2017
[225] Sequence-based discrimination of protein-RNA interacting residues using a probabilistic approach
Journal of Theoretical Biology, 2017
[226] Extracting features from protein sequences to improve deep extreme learning machine for protein fold recognition
Journal of Theoretical Biology, 2017
[227] DrugECs: An ensemble system with feature subspaces for accurate drug-target interaction prediction
BioMed Research International, 2017
[228] Prediction subcellular localization of Gram-negative bacterial proteins by support vector machine using wavelet denoising and Chou's pseudo amino acid composition
Chemometrics and Intelligent Laboratory Systems, 2017
[229] An effective fault diagnosis approach based on optimal weighted least squares support vector machine
The Canadian Journal of Chemical Engineering, 2017
[230] 2L-piRNA: A Two-Layer Ensemble Classifier for Identifying Piwi-Interacting RNAs and Their Function
Molecular Therapy - Nucleic Acids, 2017
[231] Sequence based predictor for discrimination of Enhancer and their Types by applying general form of Chou's Trinucleotide Composition
Computer Methods and Programs in Biomedicine, 2017
[232] Pse-in-One 2.0: An Improved Package of Web Servers for Generating Various Modes of Pseudo Components of DNA, RNA, and Protein Sequences
2017
[233] Multi-label classifier based on histogram of gradients for predicting the anatomical therapeutic chemical class/classes of a given compound
Bioinformatics, 2017
[234] Prediction of metastasis in advanced colorectal carcinomas using CGH data
Journal of Theoretical Biology, 2017
[235] iRNA-2methyl: Identify RNA 2'-O-methylation Sites by Incorporating Sequence-Coupled Effects into General PseKNC and Ensemble Classifier
Medicinal Chemistry, 2017
[236] pLoc-mAnimal: predict subcellular localization of animal proteins with both single and multiple sites
Bioinformatics, 2017
[237] 2L-PCA: a two-level principal component analyzer for quantitative drug design and its applications
Oncotarget, 2017
[238] iPromoter-2L: a two-layer predictor for identifying promoters and their types by multi-window-based PseKNC
Bioinformatics, 2017
[239] pLoc-mGneg: Predict subcellular localization of Gram-negative bacterial proteins by deep gene ontology learning via general PseAAC
Genomics, 2017
[240] Prediction of lysine propionylation sites using biased SVM and incorporating four different sequence features into Chou's PseAAC
Journal of Molecular Graphics and Modelling, 2017
[241] Small molecular floribundiquinone B derived from medicinal plants inhibits acetylcholinesterase activity
Oncotarget, 2017
[242] Prediction of presynaptic and postsynaptic neurotoxins by combining various Chou's pseudo components
Scientific Reports, 2017
[243] Ikcr-pseens: Identify lysine crotonylation sites in histone proteins with pseudo components and ensemble classifier
Genomics, 2017
[244] Predict protein structural class by incorporating two different modes of evolutionary information into chou's general pseudo amino acid composition
Journal of Molecular Graphics and Modelling, 2017
[245] pLoc-mHum: predict subcellular localization of multi-location human proteins via general PseAAC to winnow out the crucial GO information
Bioinformatics, 2017
[246] Bi-PSSM: Position specific scoring matrix based intelligent computational model for identification of mycobacterial membrane proteins
Journal of Theoretical Biology, 2017
[247] Computational prediction of therapeutic peptides based on graph index
Journal of Biomedical Informatics, 2017
[248] Predicting lysine glycation sites using bi-profile bayes feature extraction
Computational Biology and Chemistry, 2017
[249] Ensemble Architecture for Prediction of Enzyme‐ligand Binding Residues Using Evolutionary Information
Molecular Informatics, 2017
[250] Recognition of long-range enhancer-promoter interactions by adding genomic signatures of segmented regulatory regions
Genomics, 2017
[251] mRNA 序列中回文密度对蛋白质折叠速率的影响
内蒙古师范大学学报：自然科学汉文版, 2016
[252] Protein fold recognition using HMM-HMM alignment and Dynamic Programming
Journal of Theoretical Biology, 2016
[253] Predicting lysine phosphoglycerylation with fuzzy SVM by incorporating k-spaced amino acid pairs into Chou׳ s general PseAAC
Journal of Theoretical Biology, 2016
[254] An In Silico Approach to Investigation of the Source of Controversial Interpretations about Phenotypic Results of Human AhR-gene G1661A Polymorphism
Journal of theoretical biology, 2016
[255] A soft sensor for industrial melt index prediction based on evolutionary extreme learning machine
Chinese Journal of Chemical Engineering, 2016
[256] Identification of S-glutathionylation sites in species-specific proteins by incorporating five sequence-derived features into the general pseudo-amino acid composition
Journal of theoretical biology, 2016
[257] Identification of glucose-binding pockets in human serum albumin using support vector machine and molecular dynamics simulations
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2016
[258] QSPR-Perturbation Models for the Prediction of B-Epitopes from Immune Epitope Database: A Potentially Valuable Route for Predicting “In Silico” New Optimal Peptide Sequences and/or Boundary Conditions for Vaccine Development
International Journal of Peptide Research and Therapeutics, 2016
[259] Identification of DNA binding proteins using evolutionary profiles position specific scoring matrix
Neurocomputing, 2016
[260] Improving the Prediction of Protein Structural Class for Low-Similarity Sequences by Incorporating Evolutionaryand Structural Information
2016
[261] Identification of thermophilic proteins by incorporating evolutionary and acid dissociation information into Chou's general pseudo amino acid composition
Journal of Theoretical Biology, 2016
[262] Predicting protein-protein interactions by weighted pseudo amino acid composition
International Journal of Data Mining and Bioinformatics, 2016
[263] Classify vertebrate hemoglobin proteins by incorporating the evolutionary information into the general PseAAC with the hybrid approach
Journal of Theoretical Biology, 2016
[264] DrugRPE: Random projection ensemble approach to drug-target interaction prediction
Neurocomputing, 2016
[265] Predicting Protein–Protein Interaction Sites Using Sequence Descriptors and Site Propensity of Neighboring Amino Acids
International Journal of Molecular Sciences, 2016
[266] iAFP-Ense: An Ensemble Classifier for Identifying Antifreeze Protein by Incorporating Grey Model and PSSM into PseAAC
The Journal of Membrane Biology, 2016
[267] iACP: a sequence-based tool for identifying anticancer peptides
Oncotarget, 2016
[268] Improving the prediction of protein structural class for low-similarity sequences by incorporating evolutionary and structural information
Journal of Advanced Computational Intelligence and Intelligent Informatics, 2016
[269] Identification of signal peptide sequences based on mean value matrix image
2016
[270] Probabilistic expression of spatially varied amino acid dimers into general form of Chou׳ s pseudo amino acid composition for protein fold recognition
Journal of Theoretical Biology, 2015
[271] Hologram QSAR models of a series of 6-arylquinazolin-4-amine inhibitors of a new Alzheimer's disease target: dual specificity tyrosine-phosphorylation-regulated …
2015
[272] 基于序列的 G 蛋白偶联受体一药物相互作用预测研究
2015
[273] Molecular Structures and Structural Dynamics of Prion Proteins and Prions: Mechanism Underlying the Resistance to Prion Diseases
2015
[274] 基于序列的 G 蛋白偶联受体-药物相互作用预测研究
计算机科学, 2015
[275] Some applications of nonlinear science methods and support vector machine methods to protein problems
Mini-Reviews in Organic Chemistry, 2015
[276] Recent Advances on Prediction of Protein Subcellular Localization
Mini-Reviews in Organic Chemistry, 2015
[277] iSuc-PseAAC: predicting lysine succinylation in proteins by incorporating peptide position-specific propensity
Scientific Reports, 2015
[278] PGlcS: Prediction of protein O-GlcNAcylation sites with multiple features and analysis
Journal of Theoretical Biology, 2015
[279] MOWGLI: prediction of protein–MannOse interacting residues With ensemble classifiers usinG evoLutionary Information
Journal of Biomolecular Structure and Dynamics, 2015
[280] In silico screening for identification of novel anti-malarial inhibitors by molecular docking, pharmacophore modeling and virtual screening
Medicinal Chemistry, 2015
[281] Protein Subcellular Location Prediction Based on Pseudo Amino Acid Composition and PSI-Blast Profile
Journal of Computational and Theoretical Nanoscience, 2015
[282] Characterization of proteins in S. cerevisiae with subcellular localizations
Molecular BioSystems, 2015
[283] Using Chou's Pseudo Amino Acid Composition and Machine Learning Method to Predict the Antiviral Peptides
Open Bioinformatics Journal, 2015
[284] Molecular structures and structural dynamics of prion proteins and prions
Focus on Structural Biology book series, 2015
[285] Advancing the Accuracy of Protein Fold Recognition by Utilizing Profiles from Hidden Markov Models
2015
[286] A Novel Canonical Dual Global Optimization Computational Approach
Molecular Structures and Structural Dynamics of Prion Proteins and Prions, 2015
[287] Association analysis between the distributions of histone modifications and gene expression in the human embryonic stem cell
Gene, 2015
[288] A highly accurate protein structural class prediction approach using auto cross covariance transformation and recursive feature elimination
Computational Biology and Chemistry, 2015
[289] Hologram QSAR Models of a Series of 6-Arylquinazolin-4-Amine Inhibitors of a New Alzheimer’s Disease Target: Dual Specificity Tyrosine-Phosphorylation-Regulated Kinase-1A Enzyme
International Journal of Molecular Sciences, 2015
[290] Using temperature effects to predict the interactions between two RNAs
Journal of Theoretical Biology, 2015
[291] A new technique for generating pathogenic barcodes in breast cancer susceptibility analysis
Journal of theoretical biology, 2015
[292] Identifying new targets in leukemogenesis using computational approaches
Saudi Journal of Biological Sciences, 2015
[293] iMiRNA-PseDPC: microRNA precursor identification with a pseudo distance-pair composition approach
Journal of Biomolecular Structure and Dynamics, 2015
[294] miRNA-dis: microRNA precursor identification based on distance structure status pairs
Molecular BioSystems, 2015
[295] Analysis of the multi-copied genes and the impact of the redundant protein coding sequences on gene annotation in prokaryotic genomes
Journal of theoretical biology, 2015
[296] Hologram QSAR Models of a Series of 6-Arylquinazolin-4-Amine Inhibitors of a New Alzheimer’s Disease Target: Dual Specificity Tyrosine-Phosphorylation-Regulated Kinase-1A Enzyme
International journal of molecular sciences, 2015
[297] A New Multi-label Classifier in Identifying the Functional Types of Human Membrane Proteins
The Journal of membrane biology, 2014
[298] iNitro-Tyr: Prediction of nitrotyrosine sites in proteins with general pseudo amino acid composition
PloS one, 2014
[299] iDNA-Prot| dis: Identifying DNA-binding proteins by incorporating amino acid distance-pairs and reduced alphabet profile into the general pseudo amino acid composition
PloS one, 2014
[300] R3P-Loc: A compact multi-label predictor using ridge regression and random projection for protein subcellular localization
Journal of theoretical biology, 2014
[301] Identification of DNA-binding proteins by incorporating evolutionary information into pseudo amino acid composition via the top-n-gram approach
Journal of Biomolecular Structure and Dynamics, 2014
[302] RETRACTED: Identifying halophilic proteins based on random forests with preprocessing of the pseudo-amino acid composition
Journal of theoretical biology, 2014
[303] Identification of cytokine via an improved genetic algorithm
Frontiers of Computer Science, 2014
[304] Prediction of Vanillin and Glutamate Productions in Yeast Using a Hybrid of Continuous Bees Algorithm and Flux Balance Analysis (CBAFBA)
Current Bioinformatics, 2014
[305] Pseudo amino acid composition improves antifreeze protein prediction
2014
[306] Prediction of Protein Secondary Structure Using Feature Selection and Analysis Approach
Acta biotheoretica, 2014
[307] An effective haplotype assembly algorithm based on hypergraph partitioning
Journal of Theoretical Biology, 2014
[308] PseDNA‐Pro: DNA‐Binding Protein Identification by Combining Chou's PseAAC and Physicochemical Distance Transformation
Molecular Informatics, 2014
[309] Protein fold recognition by alignment of amino acid residues using kernelized dynamic time warping
Journal of theoretical biology, 2014
[310] iCTX-Type: A Sequence-Based Predictor for Identifying the Types of Conotoxins in Targeting Ion Channels
BioMed Research International, 2014
[311] Sequence-specific flexibility organization of splicing flanking sequence and prediction of splice sites in the human genome
Chromosome Research, 2014
[312] Potential non homologous protein targets of mycobacterium tuberculosis H37Rv identified from protein–protein interaction network
Journal of theoretical biology, 2014
[313] Predicting peroxidase subcellular location by hybridizing different descriptors of Chou'pseudo amino acid patterns
Analytical biochemistry, 2014
[314] Prediction of posttranslational modification sites from amino acid sequences with kernel methods
Journal of theoretical biology , 2014
[315] Neural network and SVM classifiers accurately predict lipid binding proteins, irrespective of sequence homology
Journal of theoretical biology, 2014
[316] Screening drug target proteins based on sequence information
Journal of biomedical informatics, 2014
[317] Differential Bees Flux Balance Analysis with OptKnock for In Silico Microbial Strains Optimization
PloS one, 2014
[318] Human proteins characterization with subcellular localizations
Journal of theoretical biology, 2014
[319] iMethyl-PseAAC: Identification of Protein Methylation Sites via a Pseudo Amino Acid Composition Approach
BioMed Research International, 2014
[320] A protein structural classes prediction method based on PSI-BLAST profile
Journal of theoretical biology, 2014
[321] Predict protein structural class for low-similarity sequences by evolutionary difference information into the general form of Chou's pseudo amino acid composition
Journal of theoretical biology, 2014
[322] Multi-Label Learning With Fuzzy Hypergraph Regularizition for Protein Subcellular Location Prediction
2014
[323] Signal peptide discrimination and cleavage site identification using SVM and NN
Computers in biology and medicine, 2014
[324] A QSPR-like model for multilocus genotype networks of Fasciola hepatica in Northwest Spain
Journal of theoretical biology, 2014
[325] TIBS: A web database to browse gene expression in irritable bowel syndrome
Journal of theoretical biology , 2014
[326] Statistical approach for lysosomal membrane proteins (LMPs) identification
Systems and Synthetic Biology, 2014
[327] iSS-PseDNC: Identifying Splicing Sites Using Pseudo Dinucleotide Composition
BioMed Research International, 2014
[328] Time series clustering by a robust autoregressive metric with application to air pollution
Chemometrics and Intelligent Laboratory Systems, 2014
[329] LECTINPred: web Server that Uses Complex Networks of Protein Structure for Prediction of Lectins with Potential Use as Cancer Biomarkers or in Parasite Vaccine Design
Molecular Informatics, 2014
[330] Toward a better understanding of structural divergences in proteins using different secondary structure assignment methods
Journal of Molecular Structure, 2014
[331] Prediction of Signal Peptide Cleavage Sites with Subsite‐Coupled and Template Matching Fusion Algorithm
Molecular Informatics , 2014
[332] Human Dopamine Receptors Interaction Network (DRIN): A systems biology perspective on topology, stability and functionality of the network
Journal of theoretical biology, 2014
[333] Gram-positive and Gram-negative Protein Subcellular Localization by Incorporating Evolutionary-based Descriptors into Chou's General PseAAC
Journal of theoretical biology , 2014
[334] Constructing a linear QSAR for some metabolizable drugs by human or pig flavin-containing monooxygenases using some molecular features selected by a genetic algorithm trained SVM
Journal of theoretical biology, 2014
[335] A two-layer classification framework for protein fold recognition
Journal of theoretical biology, 2014
[336] A Computational Algorithm for Functional Clustering of Proteome Dynamics During Development
Current genomics , 2014
[337] Discriminating protein structure classes by incorporating Pseudo Average Chemical Shift to Chou's general PseAAC and Support Vector Machine
Computer methods and programs in biomedicine, 2014
[338] Prediction of protein structure classes by incorporating different protein descriptors into general Chou's pseudo amino acid composition
Journal of theoretical biology, 2014
[339] A two-stage SVM method to predict membrane protein types by incorporating amino acid classifications and physicochemical properties into a general form of Chou's PseAAC
Journal of theoretical biology, 2014
[340] Accurate prediction of protein structural classes by incorporating predicted secondary structure information into the general form of Chou's pseudo amino acid composition
Journal of theoretical biology, 2014
[341] iHyd-PseAAC: predicting hydroxyproline and hydroxylysine in proteins by incorporating dipeptide position-specific propensity into pseudo amino acid composition
International journal of molecular sciences , 2014
[342] k-Partite cliques of protein interactions: A novel subgraph topology for functional coherence analysis on PPI networks
Journal of theoretical biology, 2014
[343] Chou? s pseudo amino acid composition improves sequence-based antifreeze protein prediction
Journal of theoretical biology, 2014
[344] Predicting the protein solubility by integrating chaos games representation and entropy in information theory
Expert Systems with Applications, 2014
[345] A set of descriptors for identifying the protein–drug interaction in cellular networking
Journal of theoretical biology, 2014
[346] Predicting DNA binding proteins using support vector machine with hybrid fractal features
Journal of theoretical biology, 2014
[347] Transmission of intra-cellular genetic information: A system proposal
Journal of theoretical biology, 2014
[348] Predicting anticancer peptides with Chou′ s pseudo amino acid composition and investigating their mutagenicity via Ames test
Journal of theoretical biology, 2014
[349] iTIS-PseTNC: a sequence-based predictor for identifying translation initiation site in human genes using pseudo trinucleotide composition
Analytical biochemistry, 2014
[350] iNR-Drug: predicting the interaction of drugs with nuclear receptors in cellular networking
International journal of molecular sciences , 2014
[351] Prediction of bacterial protein subcellular localization by incorporating various features into Chou's PseAAC and a backward feature selection approach
Biochimie, 2014
[352] Graphic mapping of protein-coding DNA sequence in four-dimensional space and its application
Journal of Computational and Theoretical Nanoscience, 2014
[353] k-Partite cliques of protein interactions: A novel subgraph topology for functional coherence analysis on PPI networks
Journal of Theoretical Biology, 2014
[354] iDNA-Prot| dis: Identifying DNA-Binding Proteins by Incorporating Amino Acid Distance-Pairs and Reduced
2014
[355] iNitro-Tyr: Prediction of Nitrotyrosine Sites in Proteins with General Pseudo Amino Acid
2014
[356] Differential Bees Flux Balance Analysis with OptKnock for In Silico Microbial Strains
2014
[357] iDNA-Prot| dis: Identifying DNA-binding proteins by incorporating amino acid distance-pairs and reduced alphabet profile into the general pseudo amino acid composition
PloS one, 2014
[358] Enhancement Predicting Accuracy for Elastin-Like Polypeptides Temperature Transition by Back Propagation Neural Network
Protein and peptide letters, 2014
[359] mRNA 的二级结构对蛋白质折叠速率的影响
生物物理学报, 2014
[360] Identifying ion channel genes related to cardiomyopathy using a novel decision forest strategy
Molecular BioSystems, 2014
[361] iHyd-PseAAC: predicting hydroxyproline and hydroxylysine in proteins by incorporating dipeptide position-specific propensity into pseudo amino acid …
International journal of …, 2014
[362] Prediction of Lysosomal Membrane Proteins Using Machine Learning Techniques
2014
[363] Na\ve Bayes Classifier with Feature Selection to Identify Phage Virion Proteins
2013
[364] Theoretical and experimental biology in one—A symposium in honour of Professor Kuo-Chen Chou’s 50th anniversary and Professor Richard Giegé’s 40th anniversary of their scientific careers
Journal of Biomedical Science and Engineering, 2013
[365] Virus-ECC-mPLoc: a multi-label predictor for predicting the subcellular localization of virus proteins with both single and multiple sites based on a general form of Chou's pseudo amino acid composition
Protein and peptide letters, 2013
[366] Protein sequence comparison based on K-string dictionary
Gene, 2013
[367] Técnicas de ingeniería informática e inteligencia artificial para clasificación: aplicaciones para el descubrimiento de fármacos y dianas moleculares
2013
[368] Theoretical and experimental biology in one
2013
[369] A simple k-word interval method for phylogenetic analysis of DNA sequences
Journal of Theoretical Biology, 2013
[370] Alignment free comparison: k word voting model and its applications
Journal of Theoretical Biology, 2013
[371] Multilabel learning via random label selection for protein subcellular multilocations prediction
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 2013
[372] Predicting acidic and alkaline enzymes by incorporating the average chemical shift and gene ontology informations into the general form of Chou's PseAAC
Process Biochemistry, 2013
[373] HIV-1 protease cleavage site prediction based on two-stage feature selection method
Protein and peptide letters , 2013
[374] Recent advances in predicting protein classification and their applications to drug development
Current topics in medicinal chemistry, 2013
[375] Predict drug-protein interaction in cellular networking
Current topics in medicinal chemistry , 2013
[376] Recent progresses in identifying nuclear receptors and their families
Current topics in medicinal chemistry , 2013
[377] A novel statistical measure for sequence comparison on the basis of k-word counts
Journal of theoretical biology, 2013
[378] A novel ensemble and composite approach for classifying proteins based on Chou's pseudo amino acid composition
African Journal of Biotechnology, 2013
[379] An alignment-free method to find similarity among protein sequences via the general form of Chou's pseudo amino acid composition
SAR and QSAR in Environmental Research , 2013
[380] Use of fast conformational sampling to improve the characterization of VEGF A–peptide interactions
Journal of theoretical biology, 2013
[381] Protein motifs retrieval by SS terns occurrences
Pattern Recognition Letters, 2013
[382] Naive Bayes classifier with feature selection to identify phage virion proteins
Computational and mathematical methods in medicine , 2013
[383] A soft sensor based on adaptive fuzzy neural network and support vector regression for industrial melt index prediction
Chemometrics and Intelligent Laboratory Systems, 2013
[384] Predicting subchloroplast locations of proteins based on the general form of Chou's pseudo amino acid composition: approached from optimal tripeptide composition
International Journal of Biomathematics , 2013
[385] A Multilabel Model Based on Chou's Pseudo–Amino Acid Composition for Identifying Membrane Proteins with Both Single and Multiple Functional Types
The Journal of membrane biology, 2013
[386] Protein Remote Homology Detection by Combining Chou's Pseudo Amino Acid Composition and Profile‐Based Protein Representation
Molecular Informatics, 2013
[387] Prediction of metabolic pathway using graph property, chemical functional group and chemical structural set
Current Bioinformatics, 2013
[388] Characterization of structure–antioxidant activity relationship of peptides in free radical systems using QSAR models: Key sequence positions and their amino acid properties
Journal of theoretical biology, 2013
[389] A simple k-word interval method for phylogenetic analysis of DNA sequences
Journal of theoretical biology, 2013
[390] Using radial basis function on the general form of Chou's pseudo amino acid composition and PSSM to predict subcellular locations of proteins with both single and multiple sites
Biosystems, 2013
[391] Predicting protein subchloroplast locations with both single and multiple sites via three different modes of Chou's pseudo amino acid compositions
Journal of theoretical biology, 2013
[392] A feature extraction technique using bi-gram probabilities of position specific scoring matrix for protein fold recognition
Journal of theoretical biology, 2013
[393] GOASVM: A subcellular location predictor by incorporating term-frequency gene ontology into the general form of Chou's pseudo-amino acid composition
Journal of Theoretical Biology, 2013
[394] iSNO-AAPair: incorporating amino acid pairwise coupling into PseAAC for predicting cysteine S-nitrosylation sites in proteins
PeerJ, 2013
[395] Predicting membrane protein types by incorporating protein topology, domains, signal peptides, and physicochemical properties into the general form of Chou’s pseudo amino acid composition
Journal of Theoretical Biology, 2013
[396] Prediction of Substrate-Enzyme-Product Interaction Based on Molecular Descriptors and Physicochemical Properties
BioMed research international , 2013
[397] Comparison between the Repression Potency of siRNA Targeting the Coding Region and the 3′-Untranslated Region of mRNA
BioMed research international, 2013
[398] Sucrose Hydrolytic Enzymes: Old Enzymes for New Uses as Biocatalysts for Medical Applications
Current topics in medicinal chemistry , 2013
[399] Support vector machine with a Pearson VII function kernel for discriminating halophilic and non-halophilic proteins
Computational biology and chemistry, 2013
[400] Predicting the Activity of Antimicrobial Peptides with Amino Acid Topological Information
Medicinal Chemistry, 2013
[401] Interconnection between the protein solubility and amino acid and dipeptide compositions
Protein and peptide letters, 2013
[402] Locating apoptosis proteins by incorporating the signal peptide cleavage sites into the general form of Chou's Pseudo amino acid composition
International Journal of Quantum Chemistry , 2013
[403] A Two-step Similarity-based Method for Prediction of Drug's Target Group
Protein and peptide letters, 2013
[404] Predict Subcellular Locations of Singleplex and Multiplex Proteins by Semi-Supervised Learning and Dimension-Reducing General Mode of Chou's PseAAC
2013
[405] A hybrid computational model for the effects of maspin on cancer cell dynamics
Journal of theoretical biology , 2013
[406] Use of multivariate chemometric algorithms on 1 H NMR data to assess a soluble fiber ( Plantago ovata husk) nutritional intervention
Chemometrics and Intelligent Laboratory Systems , 2013
[407] Prediction of Methylation Sites Using the Composition of K-Spaced Amino Acid Pairs
Protein and peptide letters, 2013
[408] Linear regression model of short k-word: a similarity distance suitable for biological sequences with various lengths
Journal of theoretical biology, 2013
[409] Predicting the heats of combustion of polynitro arene, polynitro heteroarene, acyclic and cyclic nitramine, nitrate ester and nitroaliphatic compounds using bee algorithm and adaptive neuro-fuzzy inference system
Chemometrics and Intelligent Laboratory Systems , 2013
[410] Metallo-β-lactamases: structural features, antibiotic recognition, inhibition, and inhibitor design
Current topics in medicinal chemistry, 2013
[411] Prediction of essential proteins in prokaryotes by incorporating various physico-chemical features into the general form of Chou's pseudo amino acid composition
Protein and peptide letters, 2013
[412] Analysis of codon use features of stearoyl-acyl carrier protein desaturase gene in Camellia sinensis
Journal of theoretical biology, 2013
[413] Identification of antioxidants from sequence information using Naive Bayes
Computational and mathematical methods in medicine, 2013
[414] Predicting ion channel-drug interactions based on sequence-derived features and functional groups
Journal of Bionanoscience, 2013
[415] Using the concept of Chou's pseudo amino acid composition to predict protein solubility: An approach with entropies in information theory
Journal of theoretical biology, 2013
[416] A challenge for medicinal chemistry by the 17β-hydroxysteroid dehydrogenase superfamily: an integrated biological function and inhibition study
Current topics in medicinal chemistry , 2013
[417] Protein space: a natural method for realizing the nature of protein universe
Journal of theoretical biology , 2013
[418] Stability of halophilic proteins: from dipeptide attributes to discrimination classifier
International journal of biological macromolecules, 2013
[419] Alignment free comparison: k word voting model and its applications
Journal of theoretical biology, 2013
[420] Efficacy of function specific 3D-motifs in enzyme classification according to their EC-numbers
Journal of theoretical biology, 2013
[421] Unconventional Interaction Forces in Protein and Protein-ligand Systems and their Impacts to Drug Design
Current topics in medicinal chemistry , 2013
[422] The Prediction of Calpain Cleavage Sites with the mRMR and IFS Approaches
Mathematical Problems in Engineering , 2013
[423] Discriminating lysosomal membrane protein types using dynamic neural network
Journal of Biomolecular Structure and Dynamics ahead-of-print, 2013
[424] Recent Advances on QSAR-Based Profiling of Agonist and Antagonist A3 Adenosine Receptor Ligands
Current topics in medicinal chemistry , 2013
[425] Characterizing the Functional Similarity of Enzymes with High Co-Citation in Interaction Networks
Protein and peptide letters, 2013
[426] Metagenome Assembly Validation: Which Metagenome Contigs are Bona Fide?
Current Bioinformatics, 2013
[427] Investigation Binding Patterns of Human Carboxylesterase I (hCES I) with Broad Substrates by MD Simulations
Current topics in medicinal chemistry, 2013
[428] TRAINER: A General-Purpose Trainable Short Biosequence Classifer
Protein and peptide letters, 2013
[429] Predicting Protein Model Quality from Sequence Alignments by Support Vector Machines
J Proteomics Bioinform S, 2013
[430] Prediction of Protein Methylation Sites Using Conditional Random Field
Protein and peptide letters, 2013
[431] Engineering and analysis of protease fine specificity via site-directed mutagenesis
2013
[432] Using Cheminformatics for the Identification of Biological Functions of Small Molecules in Metabolic Pathway
Current topics in medicinal chemistry, 2013
[433] Theoretical and experimental biology in one—A symposium in honour of Professor Kuo-Chen Chou’s 50th anniversary and Professor Richard Giegé’s 40th anniversary of their scientific careers
Journal of Biomedical Science and Engineering, 2013
[434] Target network analysis of adiponectin, a multifaceted adipokine
Journal of cellular biochemistry, 2013
[435] PFP-RFSM: Protein fold prediction by using random forests and sequence motifs
Journal of Biomedical Science and Engineering, 2013
[436] New Markov–Shannon Entropy models to assess connectivity quality in complex networks: from molecular to cellular pathway, parasite–host, neural, industry, and legal–social networks
Journal of theoretical biology, 2012
[437] Identify GPCRs and their types with Chou’s pseudo amino acid composition: an approach from multi-scale energy representation and position specific scoring matrix
Protein and Peptide Letters, 2012
[438] Using the improved position specific scoring matrix and ensemble learning method to predict drug-binding residues from protein sequences
Natural Science, 2012
[439] Interrogating noise in protein sequences from the perspective of protein–protein interactions prediction
Journal of theoretical biology, 2012
[440] A Large-Scale Comparison of Computational Models on the Residue Flexibility for NMR-derived Proteins
Protein and peptide letters, 2012
[441] 人类β 珠蛋白基因HBB 及其突变体的mRNA-蛋白质二级结构分析
科学通报, 2012
[442] Relationships of mRNA-protein secondary structures in the human β-globin gene HBB and four variants
Chinese Science Bulletin , 2012
[443] Enhancing membrane protein subcellular localization prediction by parallel fusion of multi-view features
NanoBioscience, IEEE Transactions on, 2012
[444] Elman RNN based classification of proteins sequences on account of their mutual information
Journal of theoretical biology, 2012
[445] Differential Phosphoproteome Analysis of K562 Cells Exposed to 3'-Azido-3'-Deoxythymidine (AZT)
Current Proteomics, 2012
[446] Predicting gram-positive bacterial protein subcellular localization based on localization motifs
Journal of theoretical biology, 2012
[447] RFCRYS: Sequence-based protein crystallization propensity prediction by means of random forest
Journal of theoretical biology, 2012
[448] Predicting the metabolic pathways of small molecules based on their physicochemical properties
Protein and peptide letters, 2012
[449] SOMEViz: a web service for site of metabolism estimating and visualizing
Protein and peptide letters, 2012
[450] Prediction of human major histocompatibility complex class II binding peptides by continuous kernel discrimination method
Artificial intelligence in medicine, 2012
[451] SVM prediction of ligand-binding sites in bacterial lipoproteins employing shape and physio-chemical descriptors
Protein and peptide letters , 2012
[452] Predicting deleterious non-synonymous single nucleotide polymorphisms in signal peptides based on hybrid sequence attributes
Computational biology and chemistry, 2012
[453] Predicting the Classification of Transcription Factors by Incorporating their Binding Site Properties into a Novel Mode of Chou's Pseudo Amino Acid Composition
Protein and peptide letters, 2012
[454] Proteome-wide inference of human endophilin 1-binding peptides
Protein and peptide letters, 2012
[455] Machine learning study of Classifiers trained with Biophysiochemical properties of amino acids to predict fibril forming peptide motifs
Protein and peptide letters, 2012
[456] Annotating the protein-RNA interaction sites in proteins using evolutionary information and protein backbone structure
Journal of theoretical biology, 2012
[457] Prediction of nicotinamide adenine dinucleotide interacting sites based on ensemble support vector machine
Protein and peptide letters, 2012
[458] A new hybrid fractal algorithm for predicting thermophilic nucleotide sequences
Journal of theoretical biology, 2012
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