Published in Nucleic Acids Res on May 15, 2008
Transmembrane topology and signal peptide prediction using dynamic bayesian networks. PLoS Comput Biol (2008) 3.56
Multi-genome identification and characterization of chlamydiae-specific type III secretion substrates: the Inc proteins. BMC Genomics (2011) 1.18
GeNMR: a web server for rapid NMR-based protein structure determination. Nucleic Acids Res (2009) 1.04
TMKink: a method to predict transmembrane helix kinks. Protein Sci (2011) 0.98
Structural characterization of the caveolin scaffolding domain in association with cholesterol-rich membranes. Biochemistry (2011) 0.95
CoBaltDB: Complete bacterial and archaeal orfeomes subcellular localization database and associated resources. BMC Microbiol (2010) 0.90
Time-resolved analysis of the matrix metalloproteinase 10 substrate degradome. Mol Cell Proteomics (2013) 0.81
Understanding structural/functional properties of amidase from Rhodococcus erythropolis by computational approaches. J Mol Model (2008) 0.79
Insight into the dynamic interaction between different flavonoids and bovine serum albumin using molecular dynamics simulations and free energy calculations. J Mol Model (2012) 0.77
A nested leucine rich repeat (LRR) domain: the precursor of LRRs is a ten or eleven residue motif. BMC Microbiol (2010) 0.77
Bioinformatics Analysis Reveals Abundant Short Alpha-Helices as a Common Structural Feature of Oomycete RxLR Effector Proteins. PLoS One (2015) 0.76
A folding pathway-dependent score to recognize membrane proteins. PLoS One (2011) 0.76
Local tertiary structure probing of ribonucleoprotein particles by nuclease fusion proteins. PLoS One (2012) 0.76
Molecular Mechanism of Mot1, a TATA-binding Protein (TBP)-DNA Dissociating Enzyme. J Biol Chem (2016) 0.76
Tandem Duplication Events in the Expansion of the Small Heat Shock Protein Gene Family in Solanum lycopersicum (cv. Heinz 1706). G3 (Bethesda) (2016) 0.75
Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol (2001) 66.87
Improved prediction of signal peptides: SignalP 3.0. J Mol Biol (2004) 48.40
Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol (1999) 33.07
SWISS-MODEL: An automated protein homology-modeling server. Nucleic Acids Res (2003) 25.86
BASys: a web server for automated bacterial genome annotation. Nucleic Acids Res (2005) 13.30
The PredictProtein server. Nucleic Acids Res (2004) 10.89
Escherichia coli K-12: a cooperatively developed annotation snapshot--2005. Nucleic Acids Res (2006) 7.93
Application of multiple sequence alignment profiles to improve protein secondary structure prediction. Proteins (2000) 6.22
Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM. Proteins (2001) 4.85
Cyclic coordinate descent: A robotics algorithm for protein loop closure. Protein Sci (2003) 4.82
Advanced sequencing technologies and their wider impact in microbiology. J Exp Biol (2007) 3.77
MIPS: analysis and annotation of proteins from whole genomes in 2005. Nucleic Acids Res (2006) 3.68
EVA: continuous automatic evaluation of protein structure prediction servers. Bioinformatics (2001) 3.24
WebMol--a Java-based PDB viewer. Trends Biochem Sci (1997) 3.12
Use of chemical shifts in macromolecular structure determination. Methods Enzymol (2001) 2.91
PRED-TMBB: a web server for predicting the topology of beta-barrel outer membrane proteins. Nucleic Acids Res (2004) 2.76
Porter: a new, accurate server for protein secondary structure prediction. Bioinformatics (2004) 2.54
Comparing and combining predictors of mostly disordered proteins. Biochemistry (2005) 2.45
Comparing function and structure between entire proteomes. Protein Sci (2001) 2.18
All are not equal: a benchmark of different homology modeling programs. Protein Sci (2005) 1.99
Accurate prediction of protein secondary structure and solvent accessibility by consensus combiners of sequence and structure information. BMC Bioinformatics (2007) 1.66
Improving the accuracy of protein secondary structure prediction using structural alignment. BMC Bioinformatics (2006) 1.66
BacMap: an interactive picture atlas of annotated bacterial genomes. Nucleic Acids Res (2005) 1.65
Automated bacterial genome analysis and annotation. Curr Opin Microbiol (2006) 1.52
PEP: Predictions for Entire Proteomes. Nucleic Acids Res (2003) 1.39
A comparative study of available software for high-accuracy homology modeling: from sequence alignments to structural models. Protein Sci (2006) 1.13
TMB-Hunt: a web server to screen sequence sets for transmembrane beta-barrel proteins. Nucleic Acids Res (2005) 1.10
Static benchmarking of membrane helix predictions. Nucleic Acids Res (2003) 1.05
PPT-DB: the protein property prediction and testing database. Nucleic Acids Res (2007) 0.98
Beta-sheet secondary structure of an LDL receptor domain from complement factor I by consensus structure predictions and spectroscopy. FEBS Lett (1995) 0.81
PHAST: a fast phage search tool. Nucleic Acids Res (2011) 19.09
DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res (2006) 15.19
DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res (2007) 13.94
DrugBank 3.0: a comprehensive resource for 'omics' research on drugs. Nucleic Acids Res (2010) 13.68
HMDB: the Human Metabolome Database. Nucleic Acids Res (2007) 13.38
BASys: a web server for automated bacterial genome annotation. Nucleic Acids Res (2005) 13.30
HMDB: a knowledgebase for the human metabolome. Nucleic Acids Res (2008) 11.23
HMDB 3.0--The Human Metabolome Database in 2013. Nucleic Acids Res (2012) 9.21
Circular genome visualization and exploration using CGView. Bioinformatics (2004) 7.78
DrugBank 4.0: shedding new light on drug metabolism. Nucleic Acids Res (2013) 6.73
MetaboAnalyst: a web server for metabolomic data analysis and interpretation. Nucleic Acids Res (2009) 5.70
MetaboAnalyst 2.0--a comprehensive server for metabolomic data analysis. Nucleic Acids Res (2012) 5.68
The human serum metabolome. PLoS One (2011) 5.55
Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts. J Biomol NMR (2003) 4.39
The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli. Nucleic Acids Res (2004) 4.29
SuperPose: a simple server for sophisticated structural superposition. Nucleic Acids Res (2004) 4.09
VADAR: a web server for quantitative evaluation of protein structure quality. Nucleic Acids Res (2003) 3.95
RefDB: a database of uniformly referenced protein chemical shifts. J Biomol NMR (2003) 3.68
SMPDB: The Small Molecule Pathway Database. Nucleic Acids Res (2009) 3.18
A simple method to predict protein flexibility using secondary chemical shifts. J Am Chem Soc (2005) 3.15
Web-based inference of biological patterns, functions and pathways from metabolomic data using MetaboAnalyst. Nat Protoc (2011) 3.00
The human urine metabolome. PLoS One (2013) 2.78
PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites. Nucleic Acids Res (2008) 2.63
SHIFTX2: significantly improved protein chemical shift prediction. J Biomol NMR (2011) 2.47
CS23D: a web server for rapid protein structure generation using NMR chemical shifts and sequence data. Nucleic Acids Res (2008) 2.41
MSEA: a web-based tool to identify biologically meaningful patterns in quantitative metabolomic data. Nucleic Acids Res (2010) 2.32
BioSpider: a web server for automating metabolome annotations. Pac Symp Biocomput (2007) 2.32
Applications of machine learning in cancer prediction and prognosis. Cancer Inform (2007) 2.31
MetPA: a web-based metabolomics tool for pathway analysis and visualization. Bioinformatics (2010) 2.26
MetaboMiner--semi-automated identification of metabolites from 2D NMR spectra of complex biofluids. BMC Bioinformatics (2008) 2.25
Translational biomarker discovery in clinical metabolomics: an introductory tutorial. Metabolomics (2012) 2.18
PREDITOR: a web server for predicting protein torsion angle restraints. Nucleic Acids Res (2006) 2.00
Dynamic cellular automata: an alternative approach to cellular simulation. In Silico Biol (2005) 1.85
Intermolecular transmission of superoxide dismutase 1 misfolding in living cells. Proc Natl Acad Sci U S A (2011) 1.82
Multi-platform characterization of the human cerebrospinal fluid metabolome: a comprehensive and quantitative update. Genome Med (2012) 1.74
METAGENassist: a comprehensive web server for comparative metagenomics. Nucleic Acids Res (2012) 1.70
Accurate prediction of protein torsion angles using chemical shifts and sequence homology. Magn Reson Chem (2006) 1.66
Improving the accuracy of protein secondary structure prediction using structural alignment. BMC Bioinformatics (2006) 1.66
BacMap: an interactive picture atlas of annotated bacterial genomes. Nucleic Acids Res (2005) 1.65
Application of the random coil index to studying protein flexibility. J Biomol NMR (2007) 1.60
Recommendations of the wwPDB NMR Validation Task Force. Structure (2013) 1.57
First-trimester metabolomic detection of late-onset preeclampsia. Am J Obstet Gynecol (2012) 1.52
Automated bacterial genome analysis and annotation. Curr Opin Microbiol (2006) 1.52
PlasMapper: a web server for drawing and auto-annotating plasmid maps. Nucleic Acids Res (2004) 1.49
YMDB: the Yeast Metabolome Database. Nucleic Acids Res (2011) 1.48
INMEX--a web-based tool for integrative meta-analysis of expression data. Nucleic Acids Res (2013) 1.48
Proteome Analyst: custom predictions with explanations in a web-based tool for high-throughput proteome annotations. Nucleic Acids Res (2004) 1.46
NMR: prediction of protein flexibility. Nat Protoc (2006) 1.45
ECMDB: the E. coli Metabolome Database. Nucleic Acids Res (2012) 1.38
T3DB: a comprehensively annotated database of common toxins and their targets. Nucleic Acids Res (2009) 1.32
SMPDB 2.0: big improvements to the Small Molecule Pathway Database. Nucleic Acids Res (2013) 1.29
Prediction of skeletal muscle and fat mass in patients with advanced cancer using a metabolomic approach. J Nutr (2011) 1.20
The RCI server: rapid and accurate calculation of protein flexibility using chemical shifts. Nucleic Acids Res (2007) 1.11
Metabolomics and first-trimester prediction of early-onset preeclampsia. J Matern Fetal Neonatal Med (2012) 1.09
Probing the structural determinants of type II' beta-turn formation in peptides and proteins. J Am Chem Soc (2002) 1.08
MetATT: a web-based metabolomics tool for analyzing time-series and two-factor datasets. Bioinformatics (2011) 1.06
Development of Ecom₅₀ and retention index models for nontargeted metabolomics: identification of 1,3-dicyclohexylurea in human serum by HPLC/mass spectrometry. J Chem Inf Model (2012) 1.06
A probabilistic approach for validating protein NMR chemical shift assignments. J Biomol NMR (2010) 1.05
MovieMaker: a web server for rapid rendering of protein motions and interactions. Nucleic Acids Res (2005) 1.04
In silico identification of genes in bacteriophage DNA. Methods Mol Biol (2009) 1.04
GeNMR: a web server for rapid NMR-based protein structure determination. Nucleic Acids Res (2009) 1.04
Detailed biophysical characterization of the acid-induced PrP(c) to PrP(β) conversion process. Biochemistry (2011) 1.03
A simple method to adjust inconsistently referenced 13C and 15N chemical shift assignments of proteins. J Biomol NMR (2005) 1.02
Phenol-Explorer 3.0: a major update of the Phenol-Explorer database to incorporate data on the effects of food processing on polyphenol content. Database (Oxford) (2013) 1.02
Metabolomic data processing, analysis, and interpretation using MetaboAnalyst. Curr Protoc Bioinformatics (2011) 1.02
Synthesis and evaluation of keto-glutamine analogues as potent inhibitors of severe acute respiratory syndrome 3CLpro. J Med Chem (2004) 1.01
The metabolomic profile of umbilical cord blood in neonatal hypoxic ischaemic encephalopathy. PLoS One (2012) 1.01
Towards automatic metabolomic profiling of high-resolution one-dimensional proton NMR spectra. J Biomol NMR (2011) 1.00
Clinical genomicist workstation. AMIA Jt Summits Transl Sci Proc (2013) 0.99
PPT-DB: the protein property prediction and testing database. Nucleic Acids Res (2007) 0.98
Exploring human metabolites using the human metabolome database. Curr Protoc Bioinformatics (2009) 0.98
PROSESS: a protein structure evaluation suite and server. Nucleic Acids Res (2010) 0.97
PA-GOSUB: a searchable database of model organism protein sequences with their predicted Gene Ontology molecular function and subcellular localization. Nucleic Acids Res (2005) 0.97
Spatiotemporal integration of molecular and anatomical data in virtual reality using semantic mapping. Int J Nanomedicine (2009) 0.93
NMR solution structure of the precursor for carnobacteriocin B2, an antimicrobial peptide from Carnobacterium piscicola. Eur J Biochem (2004) 0.92
Development of a novel virtual screening cascade protocol to identify potential trypanothione reductase inhibitors. J Med Chem (2009) 0.91
Computational systems biology in drug discovery and development: methods and applications. Drug Discov Today (2007) 0.91
Identification of novel and known oocyte-specific genes using complementary DNA subtraction and microarray analysis in three different species. Biol Reprod (2005) 0.90
Metabolomic analysis for first-trimester Down syndrome prediction. Am J Obstet Gynecol (2013) 0.89
Genomic sequence and activity of KS10, a transposable phage of the Burkholderia cepacia complex. BMC Genomics (2008) 0.89
Resolution-by-proxy: a simple measure for assessing and comparing the overall quality of NMR protein structures. J Biomol NMR (2012) 0.89
Dynamic relationships among type IIa bacteriocins: temperature effects on antimicrobial activity and on structure of the C-terminal amphipathic alpha helix as a receptor-binding region. Biochemistry (2004) 0.88
Comparative analysis of essential collective dynamics and NMR-derived flexibility profiles in evolutionarily diverse prion proteins. Prion (2011) 0.87