Published in Protein Sci on November 01, 2007
The SWISS-MODEL Repository and associated resources. Nucleic Acids Res (2008) 11.61
The JCSG high-throughput structural biology pipeline. Acta Crystallogr Sect F Struct Biol Cryst Commun (2010) 1.87
Understanding the physical properties that control protein crystallization by analysis of large-scale experimental data. Nat Biotechnol (2009) 1.78
On the need for an international effort to capture, share and use crystallization screening data. Acta Crystallogr Sect F Struct Biol Cryst Commun (2012) 1.72
Contributions to the NIH-NIGMS Protein Structure Initiative from the PSI Production Centers. Structure (2008) 1.52
Improving the chances of successful protein structure determination with a random forest classifier. Acta Crystallogr D Biol Crystallogr (2014) 1.50
High-throughput crystallography for structural genomics. Curr Opin Struct Biol (2009) 1.44
Solution NMR structure determination of proteins revisited. J Biomol NMR (2008) 1.39
Lessons from structural genomics. Annu Rev Biophys (2009) 1.33
Improved sequence-based prediction of disordered regions with multilayer fusion of multiple information sources. Bioinformatics (2010) 1.30
Modeling effects of human single nucleotide polymorphisms on protein-protein interactions. Biophys J (2009) 1.18
Predicting protein crystallization propensity from protein sequence. J Struct Funct Genomics (2010) 1.04
PSiFR: an integrated resource for prediction of protein structure and function. Bioinformatics (2010) 1.01
CRYSTALP2: sequence-based protein crystallization propensity prediction. BMC Struct Biol (2009) 0.99
Crystallization screening: the influence of history on current practice. Acta Crystallogr F Struct Biol Commun (2014) 0.98
Genome pool strategy for structural coverage of protein families. Structure (2008) 0.97
Sequence-based prediction of protein crystallization, purification and production propensity. Bioinformatics (2011) 0.95
Bioinformatic analysis of xenobiotic reactive metabolite target proteins and their interacting partners. BMC Chem Biol (2009) 0.94
Structure of Ddn, the deazaflavin-dependent nitroreductase from Mycobacterium tuberculosis involved in bioreductive activation of PA-824. Structure (2012) 0.94
Electrostatics and aggregation: how charge can turn a crystal into a gel. J Chem Phys (2011) 0.87
Benefits of structural genomics for drug discovery research. Infect Disord Drug Targets (2009) 0.87
Synthetic symmetrization in the crystallization and structure determination of CelA from Thermotoga maritima. Protein Sci (2011) 0.84
Functional consequences of somatic mutations in cancer using protein pocket-based prioritization approach. Genome Med (2014) 0.84
Heterologous expression of mycobacterial Esx complexes in Escherichia coli for structural studies is facilitated by the use of maltose binding protein fusions. PLoS One (2013) 0.82
Association of the small GTPase Rheb with the NMDA receptor subunit NR3A. Neurosignals (2010) 0.81
Unexpected features of the dark proteome. Proc Natl Acad Sci U S A (2015) 0.81
Molecular replacement: tricks and treats. Acta Crystallogr D Biol Crystallogr (2013) 0.80
Statistical analysis of crystallization database links protein physico-chemical features with crystallization mechanisms. PLoS One (2014) 0.79
Covering complete proteomes with X-ray structures: a current snapshot. Acta Crystallogr D Biol Crystallogr (2014) 0.78
Functional Diversification after Gene Duplication: Paralog Specific Regions of Structural Disorder and Phosphorylation in p53, p63, and p73. PLoS One (2016) 0.78
Computational approaches to selecting and optimising targets for structural biology. Methods (2011) 0.77
X-ray diffraction experiment--the last experiment in the structure elucidation process. Adv Protein Chem Struct Biol (2009) 0.76
Modeling, molecular dynamics, and docking assessment of transcription factor rho: a potential drug target in Brucella melitensis 16M. Drug Des Devel Ther (2015) 0.76
Papillomavirus binding factor (PBF) is an intrinsically disordered protein with potential participation in osteosarcoma genesis, in silico evidence. Theor Biol Med Model (2014) 0.75
Avoiding regions symptomatic of conformational and functional flexibility to identify antiviral targets in current and future coronaviruses. Genome Biol Evol (2016) 0.75
Evolution of intrinsic disorder in eukaryotic proteins. Cell Mol Life Sci (2017) 0.75
Is unphosphorylated Rex, as multifunctional protein of HTLV-1, a fully intrinsically disordered protein? An in silico study. Biochem Biophys Rep (2016) 0.75
The Protein Data Bank. Nucleic Acids Res (2000) 187.10
A simple method for displaying the hydropathic character of a protein. J Mol Biol (1982) 150.65
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
Predicting coiled coils from protein sequences. Science (1991) 38.18
Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol (1999) 33.07
Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J Mol Biol (2004) 10.13
Sequence complexity of disordered protein. Proteins (2001) 6.97
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
Non-globular domains in protein sequences: automated segmentation using complexity measures. Comput Chem (1994) 4.36
TargetDB: a target registration database for structural genomics projects. Bioinformatics (2004) 4.17
Structural proteomics of an archaeon. Nat Struct Biol (2000) 3.46
Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence. Protein Eng (1990) 2.73
Mining the structural genomics pipeline: identification of protein properties that affect high-throughput experimental analysis. J Mol Biol (2004) 1.57
SPINE: an integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomics. Nucleic Acids Res (2001) 1.52
Addressing the intrinsic disorder bottleneck in structural proteomics. Proteins (2005) 1.44
Protein biophysical properties that correlate with crystallization success in Thermotoga maritima: maximum clustering strategy for structural genomics. J Mol Biol (2004) 1.40
Will my protein crystallize? A sequence-based predictor. Proteins (2006) 1.30
A normalised scale for structural genomics target ranking: the OB-Score. FEBS Lett (2006) 1.15
NMR and X-ray crystallography, complementary tools in structural proteomics of small proteins. J Am Chem Soc (2005) 1.12
Target selection and deselection at the Berkeley Structural Genomics Center. Proteins (2006) 0.98
Making decisions for structural genomics. Brief Bioinform (2003) 0.92
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics (2006) 43.68
The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol (2007) 13.99
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
Protein tyrosine phosphatases in the human genome. Cell (2004) 8.09
3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics (2003) 7.99
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
ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Res (2003) 6.86
The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature (2008) 6.70
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
The importance of alignment accuracy for molecular replacement. Acta Crystallogr D Biol Crystallogr (2004) 6.49
Glycan microarray analysis of the hemagglutinins from modern and pandemic influenza viruses reveals different receptor specificities. J Mol Biol (2005) 6.17
Structural basis of preexisting immunity to the 2009 H1N1 pandemic influenza virus. Science (2010) 6.10
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
A highly conserved neutralizing epitope on group 2 influenza A viruses. Science (2011) 5.66
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
FFAS03: a server for profile--profile sequence alignments. Nucleic Acids Res (2005) 4.99
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
Cryo-EM structure of a fully glycosylated soluble cleaved HIV-1 envelope trimer. Science (2013) 4.61
Bio3d: an R package for the comparative analysis of protein structures. Bioinformatics (2006) 4.44
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
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
New world bats harbor diverse influenza A viruses. PLoS Pathog (2013) 4.10
Protein production and purification. Nat Methods (2008) 3.97
Crystal structure of human toll-like receptor 3 (TLR3) ectodomain. Science (2005) 3.72
Antibody vs. HIV in a clash of evolutionary titans. Proc Natl Acad Sci U S A (2005) 3.57
Rational HIV immunogen design to target specific germline B cell receptors. Science (2013) 3.55
Broadly neutralizing antibodies present new prospects to counter highly antigenically diverse viruses. Science (2012) 3.53
Neutralizing antibodies derived from the B cells of 1918 influenza pandemic survivors. Nature (2008) 3.47
Highly conserved protective epitopes on influenza B viruses. Science (2012) 3.47
Shotgun metaproteomics of the human distal gut microbiota. ISME J (2008) 3.43
Exploration of uncharted regions of the protein universe. PLoS Biol (2009) 3.41
Lifespan extension induced by AMPK and calcineurin is mediated by CRTC-1 and CREB. Nature (2011) 3.32
Structural rationale for the broad neutralization of HIV-1 by human monoclonal antibody 447-52D. Structure (2004) 3.31
Combining the polymerase incomplete primer extension method for cloning and mutagenesis with microscreening to accelerate structural genomics efforts. Proteins (2008) 3.29
A Blueprint for HIV Vaccine Discovery. Cell Host Microbe (2012) 3.27
Vaccination with a synthetic peptide from the influenza virus hemagglutinin provides protection against distinct viral subtypes. Proc Natl Acad Sci U S A (2010) 3.24
A dynamic knockout reveals that conformational fluctuations influence the chemical step of enzyme catalysis. Science (2011) 3.19
Structure and function of a potent agonist for the semi-invariant natural killer T cell receptor. Nat Immunol (2005) 3.12
Supersite of immune vulnerability on the glycosylated face of HIV-1 envelope glycoprotein gp120. Nat Struct Mol Biol (2013) 3.11
Crystal structure of a bacterial cocaine esterase. Nat Struct Biol (2002) 3.06
The amphioxus genome illuminates vertebrate origins and cephalochordate biology. Genome Res (2008) 3.04
Recent avian H5N1 viruses exhibit increased propensity for acquiring human receptor specificity. J Mol Biol (2008) 3.00
Asymmetric recognition of the HIV-1 trimer by broadly neutralizing antibody PG9. Proc Natl Acad Sci U S A (2013) 2.96
Glycan microarray technologies: tools to survey host specificity of influenza viruses. Nat Rev Microbiol (2006) 2.83
Genetic and phenotypic analyses of human immunodeficiency virus type 1 escape from a small-molecule CCR5 inhibitor. J Virol (2004) 2.80
HIV-1 and influenza antibodies: seeing antigens in new ways. Nat Immunol (2009) 2.80
Structure and function of broadly reactive antibody PG16 reveal an H3 subdomain that mediates potent neutralization of HIV-1. Proc Natl Acad Sci U S A (2010) 2.77
Reduced histone deacetylase 7 activity restores function to misfolded CFTR in cystic fibrosis. Nat Chem Biol (2009) 2.70
Broadly neutralizing antibody PGT121 allosterically modulates CD4 binding via recognition of the HIV-1 gp120 V3 base and multiple surrounding glycans. PLoS Pathog (2013) 2.66
Structural characterization of the 1918 influenza virus H1N1 neuraminidase. J Virol (2008) 2.63
CAFASP3: the third critical assessment of fully automated structure prediction methods. Proteins (2003) 2.60
T cell activation by lipopeptide antigens. Science (2004) 2.59
ELM: the status of the 2010 eukaryotic linear motif resource. Nucleic Acids Res (2009) 2.59
Dissection of the carbohydrate specificity of the broadly neutralizing anti-HIV-1 antibody 2G12. Proc Natl Acad Sci U S A (2005) 2.50
FATCAT: a web server for flexible structure comparison and structure similarity searching. Nucleic Acids Res (2004) 2.49
Cross-neutralization of influenza A viruses mediated by a single antibody loop. Nature (2012) 2.44
Mitochondrial fission in apoptosis, neurodegeneration and aging. Curr Opin Cell Biol (2003) 2.44
CutDB: a proteolytic event database. Nucleic Acids Res (2006) 2.41
Trimeric HIV-1 glycoprotein gp140 immunogens and native HIV-1 envelope glycoproteins display the same closed and open quaternary molecular architectures. Proc Natl Acad Sci U S A (2011) 2.38
Three-dimensional structural view of the central metabolic network of Thermotoga maritima. Science (2009) 2.33
The Polymerase Incomplete Primer Extension (PIPE) method applied to high-throughput cloning and site-directed mutagenesis. Methods Mol Biol (2009) 2.32
Outcome of a workshop on archiving structural models of biological macromolecules. Structure (2006) 2.32
Pre-calculated protein structure alignments at the RCSB PDB website. Bioinformatics (2010) 2.28
Tafamidis, a potent and selective transthyretin kinetic stabilizer that inhibits the amyloid cascade. Proc Natl Acad Sci U S A (2012) 2.27
XtalPred: a web server for prediction of protein crystallizability. Bioinformatics (2007) 2.26