Published in J Mol Biol on November 10, 2009
Bacterial toxin-antitoxin systems: Translation inhibitors everywhere. Mob Genet Elements (2011) 1.11
Calmodulin and PI(3,4,5)P₃ cooperatively bind to the Itk pleckstrin homology domain to promote efficient calcium signaling and IL-17A production. Sci Signal (2014) 0.81
The inner membrane complex sub-compartment proteins critical for replication of the apicomplexan parasite Toxoplasma gondii adopt a pleckstrin homology fold. J Biol Chem (2014) 0.79
Advances in protein NMR provided by the NIGMS Protein Structure Initiative: impact on drug discovery. Curr Opin Drug Discov Devel (2010) 0.79
Using HHsearch to tackle proteins of unknown function: A pilot study with PH domains. Traffic (2016) 0.79
Structural and Biophysical Characterization of the Interactions between Calmodulin and the Pleckstrin Homology Domain of Akt. J Biol Chem (2015) 0.77
Pleckstrin homology-like domain, family A, member 1 (PHLDA1) and cancer. Biomed Rep (2016) 0.76
The SHOCT domain: a widespread domain under-represented in model organisms. PLoS One (2013) 0.75
The Interplay Between Calmodulin and Membrane Interactions with the Pleckstrin Homology Domain of Akt. J Biol Chem (2016) 0.75
Computational Analysis of the Binding Specificities of PH Domains. Biomed Res Int (2015) 0.75
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31
Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr (2004) 227.01
The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr (1994) 187.88
Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr (1997) 137.43
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 (2004) 56.46
Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci U S A (2001) 42.14
Automated MAD and MIR structure solution. Acta Crystallogr D Biol Crystallogr (1999) 41.65
Substructure solution with SHELXD. Acta Crystallogr D Biol Crystallogr (2002) 27.16
TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res (2005) 14.15
Dali: a network tool for protein structure comparison. Trends Biochem Sci (1995) 14.13
MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes. Nucleic Acids Res (2004) 9.86
SMART 6: recent updates and new developments. Nucleic Acids Res (2008) 9.80
Generation, representation and flow of phase information in structure determination: recent developments in and around SHARP 2.0. Acta Crystallogr D Biol Crystallogr (2003) 7.82
Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline. Proc Natl Acad Sci U S A (2002) 6.00
Towards complete validated models in the next generation of ARP/wARP. Acta Crystallogr D Biol Crystallogr (2004) 5.90
Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server. Nucleic Acids Res (2007) 5.29
Remarks about protein structure precision. Acta Crystallogr D Biol Crystallogr (1999) 5.22
FFAS03: a server for profile--profile sequence alignments. Nucleic Acids Res (2005) 4.99
An automated system to mount cryo-cooled protein crystals on a synchrotron beam line, using compact sample cassettes and a small-scale robot. J Appl Crystallogr (2002) 4.85
The extracytoplasmic function (ECF) sigma factors. Adv Microb Physiol (2002) 4.65
SCOOP: a simple method for identification of novel protein superfamily relationships. Bioinformatics (2007) 4.19
Global analysis of the general stress response of Bacillus subtilis. J Bacteriol (2001) 3.45
Combining the polymerase incomplete primer extension method for cloning and mutagenesis with microscreening to accelerate structural genomics efforts. Proteins (2008) 3.29
Eukaryotic signalling domain homologues in archaea and bacteria. Ancient ancestry and horizontal gene transfer. J Mol Biol (1999) 3.28
Lysine methylation as a routine rescue strategy for protein crystallization. Structure (2006) 3.14
Structure and ligand recognition of the phosphotyrosine binding domain of Shc. Nature (1995) 2.59
TEXshade: shading and labeling of multiple sequence alignments using LATEX2 epsilon. Bioinformatics (2000) 2.54
Defining the Bacillus subtilis sigma(W) regulon: a comparative analysis of promoter consensus search, run-off transcription/macroarray analysis (ROMA), and transcriptional profiling approaches. J Mol Biol (2002) 2.44
Crystal structure at 2.2 A resolution of the pleckstrin homology domain from human dynamin. Cell (1994) 2.41
Matt: local flexibility aids protein multiple structure alignment. PLoS Comput Biol (2008) 2.41
ESCRT-I core and ESCRT-II GLUE domain structures reveal role for GLUE in linking to ESCRT-I and membranes. Cell (2006) 2.38
Antibiotics that inhibit cell wall biosynthesis induce expression of the Bacillus subtilis sigma(W) and sigma(M) regulons. Mol Microbiol (2002) 2.32
Assembly reflects evolution of protein complexes. Nature (2008) 2.27
The crystal structure of the GroES co-chaperonin at 2.8 A resolution. Nature (1996) 2.25
Structural and evolutionary division of phosphotyrosine binding (PTB) domains. J Mol Biol (2005) 2.19
Pleckstrin homology domains: a common fold with diverse functions. Annu Rev Biophys Biomol Struct (1998) 2.06
Alkaline shock induces the Bacillus subtilis sigma(W) regulon. Mol Microbiol (2001) 1.88
Structure of the pleckstrin homology domain from beta-spectrin. Nature (1994) 1.75
Exo84 and Sec5 are competitive regulatory Sec6/8 effectors to the RalA GTPase. EMBO J (2005) 1.75
Pleckstrin homology (PH) domains and phosphoinositides. Biochem Soc Symp (2007) 1.74
Structural basis of adhesion-molecule recognition by ERM proteins revealed by the crystal structure of the radixin-ICAM-2 complex. EMBO J (2003) 1.70
Solution structure of a pleckstrin-homology domain. Nature (1994) 1.68
The PH superfold: a structural scaffold for multiple functions. Trends Biochem Sci (1999) 1.67
Structural basis of dcp2 recognition and activation by dcp1. Mol Cell (2008) 1.65
Complete genomic sequence of bacteriophage ul36: demonstration of phage heterogeneity within the P335 quasi-species of lactococcal phages. Virology (2002) 1.65
Structural basis for ubiquitin recognition by the human ESCRT-II EAP45 GLUE domain. Nat Struct Mol Biol (2006) 1.41
Crystal structure of the pleckstrin homology domain from dynamin. Nat Struct Biol (1994) 1.37
Molecular basis for substrate recognition by MTMR2, a myotubularin family phosphoinositide phosphatase. Proc Natl Acad Sci U S A (2006) 1.30
Structural basis for CD44 recognition by ERM proteins. J Biol Chem (2008) 1.26
Structural insight into the TFIIE-TFIIH interaction: TFIIE and p53 share the binding region on TFIIH. EMBO J (2008) 1.17
Changes in the extracellular proteome caused by the absence of the bldA gene product, a developmentally significant tRNA, reveal a new target for the pleiotropic regulator AdpA in Streptomyces coelicolor. J Bacteriol (2005) 1.10
Proteomic analysis of acrylamide gel separated proteins immobilized on polyvinylidene difluoride membranes following proteolytic digestion in the presence of 80% acetonitrile. Proteomics (2003) 1.10
Gel-free and gel-based proteomics in Bacillus subtilis: a comparative study. Mol Cell Proteomics (2006) 0.95
Distant homology recognition using structural classification of proteins. Proteins (1997) 0.95
Cell envelope stress response in Bacillus licheniformis: integrating comparative genomics, transcriptional profiling, and regulon mining to decipher a complex regulatory network. J Bacteriol (2006) 0.95
Clustering of protein domains in the human genome. J Mol Biol (2004) 0.85
Isolation, characterization and complete nucleotide sequence of a novel temperate bacteriophage Min1, isolated from the nematode pathogen Microbacterium nematophilum. Res Microbiol (2007) 0.83
Multidimensional analysis of the insoluble sub-proteome of Oceanobacillus iheyensis HTE831, an alkaliphilic and halotolerant deep-sea bacterium isolated from the Iheya ridge. Proteomics (2007) 0.82
Oligomerization of mouse alpha 1-syntrophin and self-association of its pleckstrin homology domain 1 containing sequences. Biochemistry (2000) 0.77
The Pfam protein families database. Nucleic Acids Res (2004) 56.46
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics (2006) 43.68
miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res (2006) 39.25
The Pfam protein families database. Nucleic Acids Res (2009) 37.98
Pfam: clans, web tools and services. Nucleic Acids Res (2006) 34.83
The Pfam protein families database. Nucleic Acids Res (2011) 33.46
The Pfam protein families database. Nucleic Acids Res (2007) 30.53
Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res (2005) 25.49
InterPro: the integrative protein signature database. Nucleic Acids Res (2008) 25.07
The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res (2003) 24.72
Rfam: an RNA family database. Nucleic Acids Res (2003) 22.93
Pfam: the protein families database. Nucleic Acids Res (2013) 22.48
InterPro, progress and status in 2005. Nucleic Acids Res (2005) 17.53
The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol (2007) 13.99
InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res (2011) 13.45
New developments in the InterPro database. Nucleic Acids Res (2007) 12.49
Comparative effectiveness of axitinib versus sorafenib in advanced renal cell carcinoma (AXIS): a randomised phase 3 trial. Lancet (2011) 12.13
Rfam: updates to the RNA families database. Nucleic Acids Res (2008) 11.61
The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet (2013) 11.29
Antibody recognition of a highly conserved influenza virus epitope. Science (2009) 11.26
Broad neutralization coverage of HIV by multiple highly potent antibodies. Nature (2011) 11.07
Structure and receptor specificity of the hemagglutinin from an H5N1 influenza virus. Science (2006) 10.04
HIV vaccine design and the neutralizing antibody problem. Nat Immunol (2004) 9.48
Blu-Ice and the Distributed Control System: software for data acquisition and instrument control at macromolecular crystallography beamlines. J Synchrotron Radiat (2002) 9.48
QuickTree: building huge Neighbour-Joining trees of protein sequences. Bioinformatics (2002) 9.36
Protein tyrosine phosphatases in the human genome. Cell (2004) 8.09
Postoperative pain experience: results from a national survey suggest postoperative pain continues to be undermanaged. Anesth Analg (2003) 7.95
The broadly neutralizing anti-human immunodeficiency virus type 1 antibody 2G12 recognizes a cluster of alpha1-->2 mannose residues on the outer face of gp120. J Virol (2002) 7.82
Structure of a V3-containing HIV-1 gp120 core. Science (2005) 7.69
How TCRs bind MHCs, peptides, and coreceptors. Annu Rev Immunol (2006) 7.57
Printed covalent glycan array for ligand profiling of diverse glycan binding proteins. Proc Natl Acad Sci U S A (2004) 7.55
Structure of HIV-1 gp120 V1/V2 domain with broadly neutralizing antibody PG9. Nature (2011) 7.20
iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions. Bioinformatics (2004) 7.02
Structure of the uncleaved human H1 hemagglutinin from the extinct 1918 influenza virus. Science (2004) 6.70
Antibody domain exchange is an immunological solution to carbohydrate cluster recognition. Science (2003) 6.68
Rfam: Wikipedia, clans and the "decimal" release. Nucleic Acids Res (2010) 6.58
Integrating biological data--the Distributed Annotation System. BMC Bioinformatics (2008) 6.56
The importance of alignment accuracy for molecular replacement. Acta Crystallogr D Biol Crystallogr (2004) 6.49
Structure of an agonist-bound human A2A adenosine receptor. Science (2011) 6.21
Glycan microarray analysis of the hemagglutinins from modern and pandemic influenza viruses reveals different receptor specificities. J Mol Biol (2005) 6.17
Rfam 11.0: 10 years of RNA families. Nucleic Acids Res (2012) 6.14
Structural basis of preexisting immunity to the 2009 H1N1 pandemic influenza virus. Science (2010) 6.10
Enhanced protein domain discovery by using language modeling techniques from speech recognition. Proc Natl Acad Sci U S A (2003) 6.01
Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline. Proc Natl Acad Sci U S A (2002) 6.00
Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites. Proc Natl Acad Sci U S A (2009) 5.86
Structure of the human dopamine D3 receptor in complex with a D2/D3 selective antagonist. Science (2010) 5.86
A highly conserved neutralizing epitope on group 2 influenza A viruses. Science (2011) 5.66
Representative proteomes: a stable, scalable and unbiased proteome set for sequence analysis and functional annotation. PLoS One (2011) 5.64
Fine mapping of the interaction of neutralizing and nonneutralizing monoclonal antibodies with the CD4 binding site of human immunodeficiency virus type 1 gp120. J Virol (2003) 5.59
Crystal structure of a soluble cleaved HIV-1 envelope trimer. Science (2013) 5.53
Natural killer T cells recognize diacylglycerol antigens from pathogenic bacteria. Nat Immunol (2006) 5.51
Tolerating some redundancy significantly speeds up clustering of large protein databases. Bioinformatics (2002) 5.46
Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics (2003) 5.46
A potent and broad neutralizing antibody recognizes and penetrates the HIV glycan shield. Science (2011) 5.44
MEROPS: the peptidase database. Nucleic Acids Res (2009) 5.33
Structure of the human κ-opioid receptor in complex with JDTic. Nature (2012) 5.18
Integrating sequence and structural biology with DAS. BMC Bioinformatics (2007) 5.12
FFAS03: a server for profile--profile sequence alignments. Nucleic Acids Res (2005) 4.99
MEROPS: the database of proteolytic enzymes, their substrates and inhibitors. Nucleic Acids Res (2011) 4.90
The RNA WikiProject: community annotation of RNA families. RNA (2008) 4.83
The NLR gene family: a standard nomenclature. Immunity (2008) 4.77
A single amino acid substitution in 1918 influenza virus hemagglutinin changes receptor binding specificity. J Virol (2005) 4.71
Single mimivirus particles intercepted and imaged with an X-ray laser. Nature (2011) 4.63
Cryo-EM structure of a fully glycosylated soluble cleaved HIV-1 envelope trimer. Science (2013) 4.61
Computational design of proteins targeting the conserved stem region of influenza hemagglutinin. Science (2011) 4.42
A primer on metagenomics. PLoS Comput Biol (2010) 4.40
Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource. Nucleic Acids Res (2010) 4.39
Structures of the CCR5 N terminus and of a tyrosine-sulfated antibody with HIV-1 gp120 and CD4. Science (2007) 4.35
Broadly neutralizing anti-HIV antibody 4E10 recognizes a helical conformation of a highly conserved fusion-associated motif in gp41. Immunity (2005) 4.26
S-nitrosylation of Drp1 mediates beta-amyloid-related mitochondrial fission and neuronal injury. Science (2009) 4.25
A next-generation cleaved, soluble HIV-1 Env trimer, BG505 SOSIP.664 gp140, expresses multiple epitopes for broadly neutralizing but not non-neutralizing antibodies. PLoS Pathog (2013) 4.23
SCOOP: a simple method for identification of novel protein superfamily relationships. Bioinformatics (2007) 4.19
New world bats harbor diverse influenza A viruses. PLoS Pathog (2013) 4.10
The Genomic Standards Consortium. PLoS Biol (2011) 3.99
Protein production and purification. Nat Methods (2008) 3.97
Predicting active site residue annotations in the Pfam database. BMC Bioinformatics (2007) 3.95
Axitinib versus sorafenib as second-line treatment for advanced renal cell carcinoma: overall survival analysis and updated results from a randomised phase 3 trial. Lancet Oncol (2013) 3.79
Crystal structure of a lipid G protein-coupled receptor. Science (2012) 3.78
Crystal structure of human toll-like receptor 3 (TLR3) ectodomain. Science (2005) 3.72