Published in Nat Protoc on January 01, 2009
I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc (2010) 22.66
A mitochondrial origin for frontotemporal dementia and amyotrophic lateral sclerosis through CHCHD10 involvement. Brain (2014) 9.30
SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res (2014) 8.86
Comparative protein structure modeling using Modeller. Curr Protoc Bioinformatics (2006) 8.72
The Phyre2 web portal for protein modeling, prediction and analysis. Nat Protoc (2015) 8.53
Type VI secretion delivers bacteriolytic effectors to target cells. Nature (2011) 5.56
A transforming KIF5B and RET gene fusion in lung adenocarcinoma revealed from whole-genome and transcriptome sequencing. Genome Res (2011) 4.15
Template-based protein structure modeling using the RaptorX web server. Nat Protoc (2012) 3.68
X-ray structures of LeuT in substrate-free outward-open and apo inward-open states. Nature (2012) 3.24
A novel double-tryptophan peptide pheromone controls competence in Streptococcus spp. via an Rgg regulator. Mol Microbiol (2010) 3.23
I-TASSER: fully automated protein structure prediction in CASP8. Proteins (2009) 3.21
Aicardi-Goutieres syndrome gene and HIV-1 restriction factor SAMHD1 is a dGTP-regulated deoxynucleotide triphosphohydrolase. J Biol Chem (2011) 3.21
Mutations in the formin gene INF2 cause focal segmental glomerulosclerosis. Nat Genet (2009) 3.20
Structural and functional characterization of an archaeal clustered regularly interspaced short palindromic repeat (CRISPR)-associated complex for antiviral defense (CASCADE). J Biol Chem (2011) 2.86
3DLigandSite: predicting ligand-binding sites using similar structures. Nucleic Acids Res (2010) 2.84
Crystal structure of the channelrhodopsin light-gated cation channel. Nature (2012) 2.83
Mutations in INF2 are a major cause of autosomal dominant focal segmental glomerulosclerosis. J Am Soc Nephrol (2011) 2.63
The genetic basis of DOORS syndrome: an exome-sequencing study. Lancet Neurol (2013) 2.40
Unusual biology across a group comprising more than 15% of domain Bacteria. Nature (2015) 2.34
A conserved coatomer-related complex containing Sec13 and Seh1 dynamically associates with the vacuole in Saccharomyces cerevisiae. Mol Cell Proteomics (2011) 2.34
The ISG56/IFIT1 gene family. J Interferon Cytokine Res (2010) 2.32
Expanding the fluorine chemistry of living systems using engineered polyketide synthase pathways. Science (2013) 2.31
Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature (2015) 2.27
Genome-wide association study identifies variants in TMPRSS6 associated with hemoglobin levels. Nat Genet (2009) 2.19
A mitochondrial-focused genetic interaction map reveals a scaffold-like complex required for inner membrane organization in mitochondria. J Cell Biol (2011) 2.15
The systematic functional analysis of Plasmodium protein kinases identifies essential regulators of mosquito transmission. Cell Host Microbe (2010) 2.13
Structures of APC/C(Cdh1) with substrates identify Cdh1 and Apc10 as the D-box co-receptor. Nature (2010) 2.11
Positional cloning and characterization reveal the molecular basis for soybean maturity locus E1 that regulates photoperiodic flowering. Proc Natl Acad Sci U S A (2012) 2.11
Diverse type VI secretion phospholipases are functionally plastic antibacterial effectors. Nature (2013) 2.11
Lysine methylation of the NF-κB subunit RelA by SETD6 couples activity of the histone methyltransferase GLP at chromatin to tonic repression of NF-κB signaling. Nat Immunol (2010) 2.07
Comprehensive molecular structure of the eukaryotic ribosome. Structure (2009) 2.04
Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts. Genome Res (2012) 2.04
Ligand-binding PAS domains in a genomic, cellular, and structural context. Annu Rev Microbiol (2011) 1.99
Atomic resolution insights into curli fiber biogenesis. Structure (2011) 1.93
Uncovering the human methyltransferasome. Mol Cell Proteomics (2010) 1.91
Super-resolution microscopy reveals that mammalian mitochondrial nucleoids have a uniform size and frequently contain a single copy of mtDNA. Proc Natl Acad Sci U S A (2011) 1.90
Two group A streptococcal peptide pheromones act through opposing Rgg regulators to control biofilm development. PLoS Pathog (2011) 1.89
Peptide signaling in the staphylococci. Chem Rev (2010) 1.89
Biosynthesis of the Pseudomonas aeruginosa Extracellular Polysaccharides, Alginate, Pel, and Psl. Front Microbiol (2011) 1.84
Low-homology protein threading. Bioinformatics (2010) 1.83
Amino acid addition to Vibrio cholerae LPS establishes a link between surface remodeling in gram-positive and gram-negative bacteria. Proc Natl Acad Sci U S A (2012) 1.83
A genome-wide metabolic QTL analysis in Europeans implicates two loci shaped by recent positive selection. PLoS Genet (2011) 1.83
Subnanometre-resolution structure of the intact Thermus thermophilus H+-driven ATP synthase. Nature (2011) 1.78
Molecular architecture of the 40S⋅eIF1⋅eIF3 translation initiation complex. Cell (2014) 1.76
OATPs, OATs and OCTs: the organic anion and cation transporters of the SLCO and SLC22A gene superfamilies. Br J Pharmacol (2012) 1.74
Terpene biosynthesis: modularity rules. Angew Chem Int Ed Engl (2011) 1.73
Calcium channel auxiliary α2δ and β subunits: trafficking and one step beyond. Nat Rev Neurosci (2012) 1.73
Adiponutrin functions as a nutritionally regulated lysophosphatidic acid acyltransferase. Cell Metab (2012) 1.71
Small genomes and sparse metabolisms of sediment-associated bacteria from four candidate phyla. MBio (2013) 1.70
Explosive cell lysis as a mechanism for the biogenesis of bacterial membrane vesicles and biofilms. Nat Commun (2016) 1.69
Architecture of the large subunit of the mammalian mitochondrial ribosome. Nature (2013) 1.69
S-nitrosylation of NADPH oxidase regulates cell death in plant immunity. Nature (2011) 1.68
The complete structure of the large subunit of the mammalian mitochondrial ribosome. Nature (2014) 1.67
EbpA vaccine antibodies block binding of Enterococcus faecalis to fibrinogen to prevent catheter-associated bladder infection in mice. Sci Transl Med (2014) 1.67
High-resolution cryo-electron microscopy structure of the Trypanosoma brucei ribosome. Nature (2013) 1.66
Viral protein targeting to the cortical endoplasmic reticulum is required for cell-cell spreading in plants. J Cell Biol (2011) 1.65
Radical S-adenosylmethionine enzymes. Chem Rev (2014) 1.64
Derlin-1 is a rhomboid pseudoprotease required for the dislocation of mutant α-1 antitrypsin from the endoplasmic reticulum. Nat Struct Mol Biol (2011) 1.64
A death effector domain chain DISC model reveals a crucial role for caspase-8 chain assembly in mediating apoptotic cell death. Mol Cell (2012) 1.64
Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains. Nucleic Acids Res (2012) 1.63
Type VI secretion system in Pseudomonas aeruginosa: secretion and multimerization of VgrG proteins. J Biol Chem (2011) 1.63
A role for the universal Kae1/Qri7/YgjD (COG0533) family in tRNA modification. EMBO J (2011) 1.59
An Interbacterial NAD(P)(+) Glycohydrolase Toxin Requires Elongation Factor Tu for Delivery to Target Cells. Cell (2015) 1.59
Hypervariable loci in the human gut virome. Proc Natl Acad Sci U S A (2012) 1.58
Proteomic analysis of skeletal organic matrix from the stony coral Stylophora pistillata. Proc Natl Acad Sci U S A (2013) 1.57
The Tetracycline Destructases: A Novel Family of Tetracycline-Inactivating Enzymes. Chem Biol (2015) 1.57
Antibodies to Interleukin-2 Elicit Selective T Cell Subset Potentiation through Distinct Conformational Mechanisms. Immunity (2015) 1.57
Intrinsic disorder drives N-terminal ubiquitination by Ube2w. Nat Chem Biol (2014) 1.57
Molecular and functional analyses of a maize autoactive NB-LRR protein identify precise structural requirements for activity. PLoS Pathog (2015) 1.56
Molecular basis for specific recognition of bacterial ligands by NAIP/NLRC4 inflammasomes. Mol Cell (2014) 1.55
Position of the general transcription factor TFIIF within the RNA polymerase II transcription preinitiation complex. EMBO J (2009) 1.55
Comparative genome analysis of Trichophyton rubrum and related dermatophytes reveals candidate genes involved in infection. MBio (2012) 1.55
A new quorum-sensing system (TprA/PhrA) for Streptococcus pneumoniae D39 that regulates a lantibiotic biosynthesis gene cluster. Mol Microbiol (2015) 1.53
CasA mediates Cas3-catalyzed target degradation during CRISPR RNA-guided interference. Proc Natl Acad Sci U S A (2014) 1.53
FFAS server: novel features and applications. Nucleic Acids Res (2011) 1.52
FAX1, a novel membrane protein mediating plastid fatty acid export. PLoS Biol (2015) 1.52
Endophytic life strategies decoded by genome and transcriptome analyses of the mutualistic root symbiont Piriformospora indica. PLoS Pathog (2011) 1.52
Computational methods in drug discovery. Pharmacol Rev (2013) 1.51
DNA polymerase δ and ζ switch by sharing accessory subunits of DNA polymerase δ. J Biol Chem (2012) 1.50
Oligomerization but Not Membrane Bending Underlies the Function of Certain F-BAR Proteins in Cell Motility and Cytokinesis. Dev Cell (2015) 1.48
Mutations in Plasmodium falciparum K13 propeller gene from Bangladesh (2009-2013). Malar J (2014) 1.48
CRISPR interference: a structural perspective. Biochem J (2013) 1.48
Diverse sequence determinants control human and mouse receptor interacting protein 3 (RIP3) and mixed lineage kinase domain-like (MLKL) interaction in necroptotic signaling. J Biol Chem (2013) 1.48
Nonspecific recognition is achieved in Pot1pC through the use of multiple binding modes. Structure (2012) 1.47
Vibrio cholerae T3SS effector VopE modulates mitochondrial dynamics and innate immune signaling by targeting Miro GTPases. Cell Host Microbe (2014) 1.47
The Rsb Phosphoregulatory Network Controls Availability of the Primary Sigma Factor in Chlamydia trachomatis and Influences the Kinetics of Growth and Development. PLoS Pathog (2015) 1.47
Electron cryomicroscopy observation of rotational states in a eukaryotic V-ATPase. Nature (2015) 1.47
Systematic Survey of Serine Hydrolase Activity in Mycobacterium tuberculosis Defines Changes Associated with Persistence. Cell Chem Biol (2016) 1.47
Drosophila TIM binds importin α1, and acts as an adapter to transport PER to the nucleus. PLoS Genet (2015) 1.46
A robust pipeline for rapid production of versatile nanobody repertoires. Nat Methods (2014) 1.46
PHF8, a gene associated with cleft lip/palate and mental retardation, encodes for an Nepsilon-dimethyl lysine demethylase. Hum Mol Genet (2009) 1.44
Homology of SMP domains to the TULIP superfamily of lipid-binding proteins provides a structural basis for lipid exchange between ER and mitochondria. Bioinformatics (2010) 1.44
Structure-function mapping of a heptameric module in the nuclear pore complex. J Cell Biol (2012) 1.44
Vibrio cholerae requires the type VI secretion system virulence factor VasX to kill Dictyostelium discoideum. Infect Immun (2011) 1.44
A magnetic protein biocompass. Nat Mater (2015) 1.42
A phosphorylated pseudokinase complex controls cell wall synthesis in mycobacteria. Sci Signal (2012) 1.41
Picomolar Inhibition of Plasmepsin V, an Essential Malaria Protease, Achieved Exploiting the Prime Region. PLoS One (2015) 1.41
Identification of a 3rd Na+ Binding Site of the Glycine Transporter, GlyT2. PLoS One (2016) 1.40
Copy number variation in CEP57L1 predisposes to congenital absence of bilateral ACL and PCL ligaments. Hum Genomics (2015) 1.40
Regulation of ISWI involves inhibitory modules antagonized by nucleosomal epitopes. Nature (2012) 1.40
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31
The Protein Data Bank. Nucleic Acids Res (2000) 187.10
SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol (1995) 74.88
The Pfam protein families database. Nucleic Acids Res (2007) 30.53
Hidden Markov models for detecting remote protein homologies. Bioinformatics (1998) 21.29
The PSIPRED protein structure prediction server. Bioinformatics (2000) 20.58
The Jpred 3 secondary structure prediction server. Nucleic Acids Res (2008) 13.32
Protein structure prediction and structural genomics. Science (2001) 11.76
CDD: a conserved domain database for interactive domain family analysis. Nucleic Acids Res (2006) 11.41
High-resolution structure prediction and the crystallographic phase problem. Nature (2007) 7.67
Protein structure prediction and analysis using the Robetta server. Nucleic Acids Res (2004) 7.39
Template-based modeling and free modeling by I-TASSER in CASP7. Proteins (2007) 6.45
The 20 years of PROSITE. Nucleic Acids Res (2007) 6.06
The DISOPRED server for the prediction of protein disorder. Bioinformatics (2004) 5.98
Exploring the extremes of sequence/structure space with ensemble fold recognition in the program Phyre. Proteins (2008) 5.90
Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles. Proteins (2002) 5.29
Predicting protein function from sequence and structural data. Curr Opin Struct Biol (2005) 4.31
Protein clefts in molecular recognition and function. Protein Sci (1996) 4.20
Analytical shape computation of macromolecules: I. Molecular area and volume through alpha shape. Proteins (1998) 3.44
Identification of protein biochemical functions by similarity search using the molecular surface database eF-site. Protein Sci (2003) 2.98
An accurate, sensitive, and scalable method to identify functional sites in protein structures. J Mol Biol (2003) 2.87
Predicting novel protein folds by using FRAGFOLD. Proteins (2001) 2.65
ConFunc--functional annotation in the twilight zone. Bioinformatics (2008) 2.57
Profile-profile methods provide improved fold-recognition: a study of different profile-profile alignment methods. Proteins (2004) 2.52
Predicting reliable regions in protein alignments from sequence profiles. J Mol Biol (2003) 2.42
Acquisition of triacylglycerol transfer activity by microsomal triglyceride transfer protein during evolution. Biochemistry (2007) 1.94
Discovery of novel alpha-glucosidase inhibitors based on the virtual screening with the homology-modeled protein structure. Bioorg Med Chem (2007) 1.90
Proceedings of the Seventh Meeting on the Critical Assessment of Techniques for Protein Structure Prediction. November 26-30, 2006. Pacific Grove, California, USA. Proteins (2007) 1.87
CAPRI: a Critical Assessment of PRedicted Interactions. Proteins (2003) 6.36
Exploring the extremes of sequence/structure space with ensemble fold recognition in the program Phyre. Proteins (2008) 5.90
A large-scale evaluation of computational protein function prediction. Nat Methods (2013) 4.61
Genetic loci influencing kidney function and chronic kidney disease. Nat Genet (2010) 3.75
Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasma. Nat Genet (2011) 3.18
Prediction of protein-protein interactions by docking methods. Curr Opin Struct Biol (2002) 2.88
3DLigandSite: predicting ligand-binding sites using similar structures. Nucleic Acids Res (2010) 2.84
ConFunc--functional annotation in the twilight zone. Bioinformatics (2008) 2.57
Genetic variation in SCN10A influences cardiac conduction. Nat Genet (2010) 2.30
Genome-wide association study identifies variants in TMPRSS6 associated with hemoglobin levels. Nat Genet (2009) 2.19
Isolation of a small molecule inhibitor of DNA base excision repair. Nucleic Acids Res (2005) 1.98
Automated prediction of protein function and detection of functional sites from structure. Proc Natl Acad Sci U S A (2004) 1.96
Assessing protein co-evolution in the context of the tree of life assists in the prediction of the interactome. J Mol Biol (2005) 1.83
Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains. Nucleic Acids Res (2012) 1.63
Convergent evolution of enzyme active sites is not a rare phenomenon. J Mol Biol (2007) 1.55
Insights into protein flexibility: The relationship between normal modes and conformational change upon protein-protein docking. Proc Natl Acad Sci U S A (2008) 1.51
Polyproline-II helix in proteins: structure and function. J Mol Biol (2013) 1.50
The relationship between the flexibility of proteins and their conformational states on forming protein-protein complexes with an application to protein-protein docking. J Mol Biol (2005) 1.41
Challenges for the prediction of macromolecular interactions. Curr Opin Struct Biol (2011) 1.31
Capturing expert knowledge with argumentation: a case study in bioinformatics. Bioinformatics (2006) 1.27
The effects of non-synonymous single nucleotide polymorphisms (nsSNPs) on protein-protein interactions. J Mol Biol (2013) 1.25
Structural characterization of the human proteome. Genome Res (2002) 1.24
Protein folding requires crowd control in a simulated cell. J Mol Biol (2010) 1.18
Protein-protein interaction sites are hot spots for disease-associated nonsynonymous SNPs. Hum Mutat (2011) 1.17
Evolution of enzymes in metabolism: a network perspective. J Mol Biol (2002) 1.15
ArchDB: automated protein loop classification as a tool for structural genomics. Nucleic Acids Res (2004) 1.12
Prediction of ligand binding sites using homologous structures and conservation at CASP8. Proteins (2009) 1.08
Sequencing delivers diminishing returns for homology detection: implications for mapping the protein universe. Bioinformatics (2010) 1.05
The identification of similarities between biological networks: application to the metabolome and interactome. J Mol Biol (2007) 1.02
Protein flexibility, not disorder, is intrinsic to molecular recognition. F1000 Biol Rep (2013) 1.01
A general approach for developing system-specific functions to score protein-ligand docked complexes using support vector inductive logic programming. Proteins (2007) 1.00
PINALOG: a novel approach to align protein interaction networks--implications for complex detection and function prediction. Bioinformatics (2012) 1.00
Modeling of protein interactions in genomes. Proteins (2002) 0.99
Analysis of phenetic trees based on metabolic capabilites across the three domains of life. J Mol Biol (2004) 0.99
3D-Garden: a system for modelling protein-protein complexes based on conformational refinement of ensembles generated with the marching cubes algorithm. Bioinformatics (2008) 0.97
Functional significance of mutations in the Snf2 domain of ATRX. Hum Mol Genet (2011) 0.96
Prediction of the conformation and geometry of loops in globular proteins: testing ArchDB, a structural classification of loops. Proteins (2005) 0.95
Prediction of viable circular permutants using a graph theoretic approach. Bioinformatics (2006) 0.94
Protein-protein docking using 3D-Dock in rounds 3, 4, and 5 of CAPRI. Proteins (2005) 0.92
Support vector inductive logic programming outperforms the naive Bayes classifier and inductive logic programming for the classification of bioactive chemical compounds. J Comput Aided Mol Des (2007) 0.92
Scaffold hopping in drug discovery using inductive logic programming. J Chem Inf Model (2008) 0.89
3D-GENOMICS: a database to compare structural and functional annotations of proteins between sequenced genomes. Nucleic Acids Res (2004) 0.89
Proteins and domains vary in their tolerance of non-synonymous single nucleotide polymorphisms (nsSNPs). J Mol Biol (2013) 0.87
The proteome: structure, function and evolution. Philos Trans R Soc Lond B Biol Sci (2006) 0.87
CombFunc: predicting protein function using heterogeneous data sources. Nucleic Acids Res (2012) 0.86
Evaluation of the 3D-Dock protein docking suite in rounds 1 and 2 of the CAPRI blind trial. Proteins (2003) 0.86
Integrative top-down system metabolic modeling in experimental disease states via data-driven Bayesian methods. J Proteome Res (2008) 0.86
AMBIENT: Active Modules for Bipartite Networks--using high-throughput transcriptomic data to dissect metabolic response. BMC Syst Biol (2013) 0.85
Clustering of protein domains in the human genome. J Mol Biol (2004) 0.85
Proteomic analysis of the Plasmodium male gamete reveals the key role for glycolysis in flagellar motility. Malar J (2014) 0.82
A novel logic-based approach for quantitative toxicology prediction. J Chem Inf Model (2007) 0.80
The discovery of a highly selective 5,6,7,8-tetrahydrobenzo[4,5]thieno[2,3-d]pyrimidin-4(3H)-one SIRT2 inhibitor that is neuroprotective in an in vitro Parkinson's disease model. ChemMedChem (2014) 0.80
The automatic discovery of structural principles describing protein fold space. J Mol Biol (2003) 0.79
The Discovery of Novel 10,11-Dihydro-5H-dibenz[b,f]azepine SIRT2 Inhibitors. Medchemcomm (2012) 0.79
Assessment of a rule-based virtual screening technology (INDDEx) on a benchmark data set. J Phys Chem B (2012) 0.77
Discovering rules for protein-ligand specificity using support vector inductive logic programming. Protein Eng Des Sel (2009) 0.77
Introduction. Bioinformatics: from molecules to systems. Philos Trans R Soc Lond B Biol Sci (2006) 0.76
Including Functional Annotations and Extending the Collection of Structural Classifications of Protein Loops (ArchDB). Bioinform Biol Insights (2009) 0.75
The fine details of evolution. Biochem Soc Trans (2009) 0.75
A new structural model of the acid-labile subunit: pathogenetic mechanisms of short stature-causing mutations. J Mol Endocrinol (2012) 0.75