Published in Comput Chem on March 01, 1996
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Prediction of ubiquitination sites by using the composition of k-spaced amino acid pairs. PLoS One (2011) 1.18
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Using indirect protein interactions for the prediction of Gene Ontology functions. BMC Bioinformatics (2007) 1.13
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Using amino acid physicochemical distance transformation for fast protein remote homology detection. PLoS One (2012) 1.10
Phylogenetic tree information aids supervised learning for predicting protein-protein interaction based on distance matrices. BMC Bioinformatics (2007) 1.08
MiRTif: a support vector machine-based microRNA target interaction filter. BMC Bioinformatics (2008) 1.07
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FoldMiner: structural motif discovery using an improved superposition algorithm. Protein Sci (2004) 1.06
HIV-1 coreceptor usage prediction without multiple alignments: an application of string kernels. Retrovirology (2008) 1.05
A two-step site and mRNA-level model for predicting microRNA targets. BMC Bioinformatics (2010) 1.04
Prediction of protein phosphorylation sites by using the composition of k-spaced amino acid pairs. PLoS One (2012) 1.02
A Protein Classification Benchmark collection for machine learning. Nucleic Acids Res (2006) 1.01
Prediction of protein binding sites in protein structures using hidden Markov support vector machine. BMC Bioinformatics (2009) 0.98
Combining classifiers to predict gene function in Arabidopsis thaliana using large-scale gene expression measurements. BMC Bioinformatics (2007) 0.97
A graph-based motif detection algorithm models complex nucleotide dependencies in transcription factor binding sites. Nucleic Acids Res (2006) 0.97
Protein ranking by semi-supervised network propagation. BMC Bioinformatics (2006) 0.95
Descriptor-based protein remote homology identification. Protein Sci (2005) 0.94
PostMod: sequence based prediction of kinase-specific phosphorylation sites with indirect relationship. BMC Bioinformatics (2010) 0.94
Motif kernel generated by genetic programming improves remote homology and fold detection. BMC Bioinformatics (2007) 0.93
Sorting the nuclear proteome. Bioinformatics (2011) 0.92
Revisiting amino acid substitution matrices for identifying distantly related proteins. Bioinformatics (2013) 0.91
A clique-based method for the edit distance between unordered trees and its application to analysis of glycan structures. BMC Bioinformatics (2011) 0.90
DescFold: a web server for protein fold recognition. BMC Bioinformatics (2009) 0.90
The effectiveness of position- and composition-specific gap costs for protein similarity searches. Bioinformatics (2008) 0.90
Structural alphabets for protein structure classification: a comparison study. J Mol Biol (2008) 0.90
SUMOhydro: a novel method for the prediction of sumoylation sites based on hydrophobic properties. PLoS One (2012) 0.89
Efficient use of unlabeled data for protein sequence classification: a comparative study. BMC Bioinformatics (2009) 0.88
A comprehensive and universal method for assessing the performance of differential gene expression analyses. PLoS One (2010) 0.88
Searching for evolutionary distant RNA homologs within genomic sequences using partition function posterior probabilities. BMC Bioinformatics (2008) 0.87
Structure- and sequence-based function prediction for non-homologous proteins. J Struct Funct Genomics (2012) 0.87
Intra-relation reconstruction from inter-relation: miRNA to gene expression. BMC Syst Biol (2013) 0.86
Drug repositioning by kernel-based integration of molecular structure, molecular activity, and phenotype data. PLoS One (2013) 0.85
Application of nonnegative matrix factorization to improve profile-profile alignment features for fold recognition and remote homolog detection. BMC Bioinformatics (2008) 0.85
Testing statistical significance scores of sequence comparison methods with structure similarity. BMC Bioinformatics (2006) 0.85
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Novel search method for the discovery of functional relationships. Bioinformatics (2011) 0.84
Structural footprinting in protein structure comparison: the impact of structural fragments. BMC Struct Biol (2007) 0.84
A novel method for protein-protein interaction site prediction using phylogenetic substitution models. Proteins (2011) 0.83
TIM-Finder: a new method for identifying TIM-barrel proteins. BMC Struct Biol (2009) 0.82
Automatic annotation of spatial expression patterns via sparse Bayesian factor models. PLoS Comput Biol (2011) 0.82
Predicting protein function by machine learning on amino acid sequences--a critical evaluation. BMC Genomics (2007) 0.81
Incorporating inter-relationships between different levels of genomic data into cancer clinical outcome prediction. Methods (2014) 0.81
svmPRAT: SVM-based protein residue annotation toolkit. BMC Bioinformatics (2009) 0.81
CarSPred: a computational tool for predicting carbonylation sites of human proteins. PLoS One (2014) 0.81
A novel approach to structural alignment using realistic structural and environmental information. Protein Sci (2005) 0.81
Predicting permanent and transient protein-protein interfaces. Proteins (2013) 0.80
Computational Identification of Protein Pupylation Sites by Using Profile-Based Composition of k-Spaced Amino Acid Pairs. PLoS One (2015) 0.79
Exploring representations of protein structure for automated remote homology detection and mapping of protein structure space. BMC Bioinformatics (2014) 0.78
Surface-histogram: a new shape descriptor for protein-protein docking. Proteins (2011) 0.78
Log-odds sequence logos. Bioinformatics (2014) 0.78
Tools for Predicting the Functional Impact of Nonsynonymous Genetic Variation. Genetics (2016) 0.77
3D representations of amino acids-applications to protein sequence comparison and classification. Comput Struct Biotechnol J (2014) 0.77
Optimization of linear disorder predictors yields tight association between crystallographic disorder and hydrophobicity. Protein Sci (2007) 0.77
Evaluating the efficacy of a structure-derived amino acid substitution matrix in detecting protein homologs by BLAST and PSI-BLAST. Adv Appl Bioinform Chem (2009) 0.77
Searching for repeats, as an example of using the generalised Ruzzo-Tompa algorithm to find optimal subsequences with gaps. Int J Bioinform Res Appl (2014) 0.76
An Ensemble Method to Distinguish Bacteriophage Virion from Non-Virion Proteins Based on Protein Sequence Characteristics. Int J Mol Sci (2015) 0.76
Inferences of drug responses in cancer cells from cancer genomic features and compound chemical and therapeutic properties. Sci Rep (2016) 0.76
Discriminative structural approaches for enzyme active-site prediction. BMC Bioinformatics (2011) 0.76
An efficient weighted graph strategy to identify differentiation associated genes in embryonic stem cells. PLoS One (2013) 0.75
String kernels for protein sequence comparisons: improved fold recognition. BMC Bioinformatics (2017) 0.75
Automatic generation and evaluation of sparse protein signatures for families of protein structural domains. Protein Sci (2005) 0.75
Benchmarking the next generation of homology inference tools. Bioinformatics (2016) 0.75
Discovering patterns in drug-protein interactions based on their fingerprints. BMC Bioinformatics (2012) 0.75
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