Published in BMC Bioinformatics on December 16, 2014
Compartmentalization and Functionality of Nuclear Disorder: Intrinsic Disorder and Protein-Protein Interactions in Intra-Nuclear Compartments. Int J Mol Sci (2015) 0.77
Advances in translational bioinformatics facilitate revealing the landscape of complex disease mechanisms. BMC Bioinformatics (2014) 0.76
Erratum to: Improving protein order-disorder classification using charge-hydropathy plots. BMC Bioinformatics (2015) 0.75
Basic local alignment search tool. J Mol Biol (1990) 659.07
A simple method for displaying the hydropathic character of a protein. J Mol Biol (1982) 150.65
The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol (1977) 90.57
Prediction of protein antigenic determinants from amino acid sequences. Proc Natl Acad Sci U S A (1981) 32.98
Receiver-operating characteristic (ROC) plots: a fundamental evaluation tool in clinical medicine. Clin Chem (1993) 27.24
Intrinsically unstructured proteins and their functions. Nat Rev Mol Cell Biol (2005) 17.63
Analysis of membrane and surface protein sequences with the hydrophobic moment plot. J Mol Biol (1984) 13.69
Diagnostic tests 2: Predictive values. BMJ (1994) 12.97
Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics (2000) 11.75
Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. J Mol Biol (1999) 11.38
Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J Mol Biol (2004) 10.13
IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics (2005) 9.02
Intrinsic disorder and protein function. Biochemistry (2002) 8.54
Intrinsically disordered protein. J Mol Graph Model (2001) 8.54
The solubility of amino acids and two glycine peptides in aqueous ethanol and dioxane solutions. Establishment of a hydrophobicity scale. J Biol Chem (1971) 8.06
Why are "natively unfolded" proteins unstructured under physiologic conditions? Proteins (2000) 7.61
Sequence complexity of disordered protein. Proteins (2001) 6.97
Coupling of folding and binding for unstructured proteins. Curr Opin Struct Biol (2002) 6.53
Protein identification and analysis tools in the ExPASy server. Methods Mol Biol (1999) 6.31
The DISOPRED server for the prediction of protein disorder. Bioinformatics (2004) 5.98
The nature of the accessible and buried surfaces in proteins. J Mol Biol (1976) 5.92
Hydrophobicity of amino acid residues in globular proteins. Science (1985) 5.64
Intrinsic disorder in cell-signaling and cancer-associated proteins. J Mol Biol (2002) 5.64
FoldIndex: a simple tool to predict whether a given protein sequence is intrinsically unfolded. Bioinformatics (2005) 5.44
The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins. J Mol Biol (2005) 5.05
A conformational preference parameter to predict helices in integral membrane proteins. Biochim Biophys Acta (1986) 4.91
DisProt: the Database of Disordered Proteins. Nucleic Acids Res (2006) 4.46
Affinities of amino acid side chains for solvent water. Biochemistry (1981) 4.46
AAindex: amino acid index database, progress report 2008. Nucleic Acids Res (2007) 4.21
Surface and inside volumes in globular proteins. Nature (1979) 3.91
AAindex: amino acid index database. Nucleic Acids Res (2000) 3.83
Correlation of sequence hydrophobicities measures similarity in three-dimensional protein structure. J Mol Biol (1983) 3.78
ExPASy: SIB bioinformatics resource portal. Nucleic Acids Res (2012) 3.70
Length-dependent prediction of protein intrinsic disorder. BMC Bioinformatics (2006) 3.70
PONDR-FIT: a meta-predictor of intrinsically disordered amino acids. Biochim Biophys Acta (2010) 3.62
AAindex: Amino Acid Index Database. Nucleic Acids Res (1999) 3.52
Analysis of molecular recognition features (MoRFs). J Mol Biol (2006) 3.40
Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins. Protein Eng (1996) 3.00
Coupled folding and binding with alpha-helix-forming molecular recognition elements. Biochemistry (2005) 2.94
Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions. J Proteome Res (2007) 2.61
Protein disorder and the evolution of molecular recognition: theory, predictions and observations. Pac Symp Biocomput (1998) 2.37
Cluster analysis of amino acid indices for prediction of protein structure and function. Protein Eng (1988) 2.37
Protein flexibility and intrinsic disorder. Protein Sci (2004) 2.33
Predicting intrinsic disorder in proteins: an overview. Cell Res (2009) 2.24
Characterization of molecular recognition features, MoRFs, and their binding partners. J Proteome Res (2007) 2.23
Identification and functions of usefully disordered proteins. Adv Protein Chem (2002) 2.23
Optimizing long intrinsic disorder predictors with protein evolutionary information. J Bioinform Comput Biol (2005) 2.20
Accuracy of protein flexibility predictions. Proteins (1994) 2.14
Standardizing predictive values in diagnostic imaging research. J Magn Reson Imaging (2011) 2.08
Development of hydrophobicity parameters to analyze proteins which bear post- or cotranslational modifications. Anal Biochem (1991) 2.02
DisProt: a database of protein disorder. Bioinformatics (2004) 1.99
Prediction of sequential antigenic regions in proteins. FEBS Lett (1985) 1.95
Functional anthology of intrinsic disorder. 3. Ligands, post-translational modifications, and diseases associated with intrinsically disordered proteins. J Proteome Res (2007) 1.92
Amino acid side-chain partition energies and distribution of residues in soluble proteins. Biophys J (1985) 1.92
Hydrophilicity of polar amino acid side-chains is markedly reduced by flanking peptide bonds. J Mol Biol (1988) 1.90
Hydrophobic character of amino acid residues in globular proteins. Nature (1978) 1.71
TOP-IDP-scale: a new amino acid scale measuring propensity for intrinsic disorder. Protein Pept Lett (2008) 1.70
The predictive value of microbiologic diagnostic tests if asymptomatic carriers are present. Stat Med (2002) 1.65
Composition Profiler: a tool for discovery and visualization of amino acid composition differences. BMC Bioinformatics (2007) 1.64
Surface tension of amino acid solutions: a hydrophobicity scale of the amino acid residues. Arch Biochem Biophys (1974) 1.63
Functional anthology of intrinsic disorder. 2. Cellular components, domains, technical terms, developmental processes, and coding sequence diversities correlated with long disordered regions. J Proteome Res (2007) 1.48
Evaluation of disorder predictions in CASP9. Proteins (2011) 1.46
Assessment of disorder predictions in CASP8. Proteins (2009) 1.44
SPINE-D: accurate prediction of short and long disordered regions by a single neural-network based method. J Biomol Struct Dyn (2012) 1.32
Exploring the binding diversity of intrinsically disordered proteins involved in one-to-many binding. Protein Sci (2013) 1.23
Extension of the fragment method to calculate amino acid zwitterion and side chain partition coefficients. Proteins (1987) 1.21
A comprehensive overview of computational protein disorder prediction methods. Mol Biosyst (2011) 1.10
To be folded or to be unfolded? Protein Sci (2004) 1.07
Comprehensive comparative assessment of in-silico predictors of disordered regions. Curr Protein Pept Sci (2012) 1.04
CDF it all: consensus prediction of intrinsically disordered proteins based on various cumulative distribution functions. FEBS Lett (2009) 1.03
A functionally required unfoldome from the plant kingdom: intrinsically disordered N-terminal domains of GRAS proteins are involved in molecular recognition during plant development. Plant Mol Biol (2011) 0.99
Subclassifying disordered proteins by the CH-CDF plot method. Pac Symp Biocomput (2012) 0.88
The conformational mobility of proteins and its functional significance. Biochem Soc Trans (1978) 0.81
Optimization of linear disorder predictors yields tight association between crystallographic disorder and hydrophobicity. Protein Sci (2007) 0.77
The Pathway Tools software. Bioinformatics (2002) 14.89
Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science (2011) 14.29
Dasatinib in imatinib-resistant Philadelphia chromosome-positive leukemias. N Engl J Med (2006) 13.54
Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell (2010) 8.74
Gene expression profiling spares early breast cancer patients from adjuvant therapy: derived and validated in two population-based cohorts. Breast Cancer Res (2005) 8.73
TLR3 deficiency in patients with herpes simplex encephalitis. Science (2007) 5.86
Flexible nets. The roles of intrinsic disorder in protein interaction networks. FEBS J (2005) 5.36
Protective variant for hippocampal atrophy identified by whole exome sequencing. Ann Neurol (2015) 5.10
DisProt: the Database of Disordered Proteins. Nucleic Acids Res (2006) 4.46
Function and structure of inherently disordered proteins. Curr Opin Struct Biol (2008) 4.19
Intrinsically disordered proteins in human diseases: introducing the D2 concept. Annu Rev Biophys (2008) 3.98
Type I interferon inhibits interleukin-1 production and inflammasome activation. Immunity (2011) 3.97
Intrinsic disorder and functional proteomics. Biophys J (2006) 3.84
IL-17 markedly up-regulates beta-defensin-2 expression in human airway epithelium via JAK and NF-kappaB signaling pathways. J Immunol (2004) 3.84
Identification of common variants associated with human hippocampal and intracranial volumes. Nat Genet (2012) 3.73
PONDR-FIT: a meta-predictor of intrinsically disordered amino acids. Biochim Biophys Acta (2010) 3.62
Effector function of human tumor-specific CD8 T cells in melanoma lesions: a state of local functional tolerance. Cancer Res (2004) 3.59
Showing your ID: intrinsic disorder as an ID for recognition, regulation and cell signaling. J Mol Recognit (2005) 3.57
An epithelial-mesenchymal transition gene signature predicts resistance to EGFR and PI3K inhibitors and identifies Axl as a therapeutic target for overcoming EGFR inhibitor resistance. Clin Cancer Res (2012) 3.48
Analysis of molecular recognition features (MoRFs). J Mol Biol (2006) 3.40
Baseline MRI predictors of conversion from MCI to probable AD in the ADNI cohort. Curr Alzheimer Res (2009) 3.31
Exhaustion of tumor-specific CD8⁺ T cells in metastases from melanoma patients. J Clin Invest (2011) 3.28
Intrinsic disorder is a common feature of hub proteins from four eukaryotic interactomes. PLoS Comput Biol (2006) 3.23
Results and harmonization guidelines from two large-scale international Elispot proficiency panels conducted by the Cancer Vaccine Consortium (CVC/SVI). Cancer Immunol Immunother (2007) 3.16
Rapid and strong human CD8+ T cell responses to vaccination with peptide, IFA, and CpG oligodeoxynucleotide 7909. J Clin Invest (2005) 3.11
Intrinsic disorder in transcription factors. Biochemistry (2006) 3.06
Characterization of three H5N5 and one H5N8 highly pathogenic avian influenza viruses in China. Vet Microbiol (2013) 3.05
Innate and adaptive immunity in female genital tract: cellular responses and interactions. Immunol Rev (2005) 3.01
A real-time photoacoustic tomography system for small animals. Opt Express (2009) 2.97
Tumour immunity: effector response to tumour and role of the microenvironment. Lancet (2008) 2.94
Coupled folding and binding with alpha-helix-forming molecular recognition elements. Biochemistry (2005) 2.94
"MIATA"-minimal information about T cell assays. Immunity (2009) 2.90
Alzheimer's Disease Neuroimaging Initiative biomarkers as quantitative phenotypes: Genetics core aims, progress, and plans. Alzheimers Dement (2010) 2.79
The unfoldomics decade: an update on intrinsically disordered proteins. BMC Genomics (2008) 2.72
Voxelwise genome-wide association study (vGWAS). Neuroimage (2010) 2.69
Proteomic profiling identifies dysregulated pathways in small cell lung cancer and novel therapeutic targets including PARP1. Cancer Discov (2012) 2.68
Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions. J Proteome Res (2007) 2.61
Alternative splicing in concert with protein intrinsic disorder enables increased functional diversity in multicellular organisms. Proc Natl Acad Sci U S A (2006) 2.57
Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners. BMC Genomics (2008) 2.50
Classification of intrinsically disordered regions and proteins. Chem Rev (2014) 2.48
Evolutionary rate heterogeneity in proteins with long disordered regions. J Mol Evol (2002) 2.46
Comparing and combining predictors of mostly disordered proteins. Biochemistry (2005) 2.45
Association analyses identify six new psoriasis susceptibility loci in the Chinese population. Nat Genet (2010) 2.41
Generation and replication-dependent dilution of 5fC and 5caC during mouse preimplantation development. Cell Res (2011) 2.36
Assessing protein disorder and induced folding. Proteins (2006) 2.33
The Alzheimer's Disease Neuroimaging Initiative: a review of papers published since its inception. Alzheimers Dement (2013) 2.32
Predicting intrinsic disorder in proteins: an overview. Cell Res (2009) 2.24
Characterization of molecular recognition features, MoRFs, and their binding partners. J Proteome Res (2007) 2.23
Increased numbers of circulating polyfunctional Th17 memory cells in patients with seronegative spondylarthritides. Arthritis Rheum (2008) 2.15
A commonly carried allele of the obesity-related FTO gene is associated with reduced brain volume in the healthy elderly. Proc Natl Acad Sci U S A (2010) 2.12
A bimodal distribution of two distinct categories of intrinsically disordered structures with separate functions in FG nucleoporins. Mol Cell Proteomics (2010) 2.09
Diabetes prevalence and determinants in adults in China mainland from 2000 to 2010: a systematic review. Diabetes Res Clin Pract (2012) 2.07
Dietary resistant starch upregulates total GLP-1 and PYY in a sustained day-long manner through fermentation in rodents. Am J Physiol Endocrinol Metab (2008) 2.05
Longitudinal MRI atrophy biomarkers: relationship to conversion in the ADNI cohort. Neurobiol Aging (2010) 2.05
AID/APOBEC deaminases disfavor modified cytosines implicated in DNA demethylation. Nat Chem Biol (2012) 2.04
Up-regulation of CC chemokine ligand 20 expression in human airway epithelium by IL-17 through a JAK-independent but MEK/NF-kappaB-dependent signaling pathway. J Immunol (2005) 2.03
Curved array photoacoustic tomographic system for small animal imaging. J Biomed Opt (2008) 2.01
Tet1 controls meiosis by regulating meiotic gene expression. Nature (2012) 2.01
The herbicide paraquat causes up-regulation and aggregation of alpha-synuclein in mice: paraquat and alpha-synuclein. J Biol Chem (2001) 1.99
Weighted fourier series representation and its application to quantifying the amount of gray matter. IEEE Trans Med Imaging (2007) 1.99
Genome-wide analysis reveals novel genes influencing temporal lobe structure with relevance to neurodegeneration in Alzheimer's disease. Neuroimage (2010) 1.94
Mining alpha-helix-forming molecular recognition features with cross species sequence alignments. Biochemistry (2007) 1.93
Functional anthology of intrinsic disorder. 3. Ligands, post-translational modifications, and diseases associated with intrinsically disordered proteins. J Proteome Res (2007) 1.92
Rifampicin inhibits alpha-synuclein fibrillation and disaggregates fibrils. Chem Biol (2004) 1.91
EDEM3, a soluble EDEM homolog, enhances glycoprotein endoplasmic reticulum-associated degradation and mannose trimming. J Biol Chem (2006) 1.91
The ENIGMA Consortium: large-scale collaborative analyses of neuroimaging and genetic data. Brain Imaging Behav (2014) 1.90
Chronic cocaine-regulated epigenomic changes in mouse nucleus accumbens. Genome Biol (2014) 1.88
Pathway analysis of genomic data: concepts, methods, and prospects for future development. Trends Genet (2012) 1.86
High-efficiency broadband meta-hologram with polarization-controlled dual images. Nano Lett (2013) 1.85
Harmonization of immune biomarker assays for clinical studies. Sci Transl Med (2011) 1.84
Human natural Treg microRNA signature: role of microRNA-31 and microRNA-21 in FOXP3 expression. Eur J Immunol (2009) 1.81
In silico functional profiling of human disease-associated and polymorphic amino acid substitutions. Hum Mutat (2010) 1.81
Cooperation of human tumor-reactive CD4+ and CD8+ T cells after redirection of their specificity by a high-affinity p53A2.1-specific TCR. Immunity (2005) 1.81
Ex vivo characterization of human CD8+ T subsets with distinct replicative history and partial effector functions. Blood (2003) 1.78
Malleable machines take shape in eukaryotic transcriptional regulation. Nat Chem Biol (2008) 1.76
Engaging hospitals to meet tuberculosis control targets in China: using the Internet as a tool to put policy into practice. Bull World Health Organ (2010) 1.76
D²P²: database of disordered protein predictions. Nucleic Acids Res (2012) 1.75
New generation vaccine induces effective melanoma-specific CD8+ T cells in the circulation but not in the tumor site. J Immunol (2006) 1.74
Cytoplasmic serine hydroxymethyltransferase regulates the metabolic partitioning of methylenetetrahydrofolate but is not essential in mice. J Biol Chem (2008) 1.73