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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

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Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics (2003) 5.46

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The NLR gene family: a standard nomenclature. Immunity (2008) 4.77

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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

A Blueprint for HIV Vaccine Discovery. Cell Host Microbe (2012) 3.27

The amphioxus genome illuminates vertebrate origins and cephalochordate biology. Genome Res (2008) 3.04

CAFASP3: the third critical assessment of fully automated structure prediction methods. Proteins (2003) 2.60

ELM: the status of the 2010 eukaryotic linear motif resource. Nucleic Acids Res (2009) 2.59

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Mitochondrial fission in apoptosis, neurodegeneration and aging. Curr Opin Cell Biol (2003) 2.44

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Three-dimensional structural view of the central metabolic network of Thermotoga maritima. Science (2009) 2.33

Outcome of a workshop on archiving structural models of biological macromolecules. Structure (2006) 2.32

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TOPS++FATCAT: fast flexible structural alignment using constraints derived from TOPS+ Strings Model. BMC Bioinformatics (2008) 2.26

The PAAD/PYRIN-only protein POP1/ASC2 is a modulator of ASC-mediated nuclear-factor-kappa B and pro-caspase-1 regulation. Biochem J (2003) 2.25

The domains of apoptosis: a genomics perspective. Sci STKE (2004) 2.15

Probing metagenomics by rapid cluster analysis of very large datasets. PLoS One (2008) 2.11

Automatic detection of subsystem/pathway variants in genome analysis. Bioinformatics (2005) 2.10

Comprehensive classification of nucleotidyltransferase fold proteins: identification of novel families and their representatives in human. Nucleic Acids Res (2009) 2.09

Outcome of a workshop on applications of protein models in biomedical research. Structure (2009) 2.05

The retinitis pigmentosa GTPase regulator (RPGR)- interacting protein: subserving RPGR function and participating in disk morphogenesis. Proc Natl Acad Sci U S A (2003) 1.96

Comparative analysis of protein domain organization. Genome Res (2004) 1.94

PSI-2: structural genomics to cover protein domain family space. Structure (2009) 1.92

Identification and characterization of a novel bacterial virulence factor that shares homology with mammalian Toll/interleukin-1 receptor family proteins. Infect Immun (2006) 1.91

Between order and disorder in protein structures: analysis of "dual personality" fragments in proteins. Structure (2007) 1.88

Protein structure prediction of CASP5 comparative modeling and fold recognition targets using consensus alignment approach and 3D assessment. Proteins (2003) 1.87

The JCSG high-throughput structural biology pipeline. Acta Crystallogr Sect F Struct Biol Cryst Commun (2010) 1.87

Detecting distant homology with Meta-BASIC. Nucleic Acids Res (2004) 1.86

The challenge of protein structure determination--lessons from structural genomics. Protein Sci (2007) 1.82

Cysteine regulation of protein function--as exemplified by NMDA-receptor modulation. Trends Neurosci (2002) 1.76

The JCSG MR pipeline: optimized alignments, multiple models and parallel searches. Acta Crystallogr D Biol Crystallogr (2007) 1.75

ORFeus: Detection of distant homology using sequence profiles and predicted secondary structure. Nucleic Acids Res (2003) 1.71

Evolutionarily conserved cytoprotection provided by Bax Inhibitor-1 homologs from animals, plants, and yeast. Gene (2003) 1.65

Multiple flexible structure alignment using partial order graphs. Bioinformatics (2005) 1.64

Surprising complexity of the ancestral apoptosis network. Genome Biol (2007) 1.63

Structural basis of neutralization by a human anti-severe acute respiratory syndrome spike protein antibody, 80R. J Biol Chem (2006) 1.53

FFAS server: novel features and applications. Nucleic Acids Res (2011) 1.52

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Structural genomics is the largest contributor of novel structural leverage. J Struct Funct Genomics (2009) 1.52

Crystal structure of TM1367 from Thermotoga maritima at 1.90 A resolution reveals an atypical member of the cyclophilin (peptidylprolyl isomerase) fold. Proteins (2006) 1.51

Cleavage targets and the D-arginine-based inhibitors of the West Nile virus NS3 processing proteinase. Biochem J (2006) 1.49

Crystal structure of thy1, a thymidylate synthase complementing protein from Thermotoga maritima at 2.25 A resolution. Proteins (2002) 1.45

Identification of novel restriction endonuclease-like fold families among hypothetical proteins. Nucleic Acids Res (2005) 1.44

Protein structure prediction for the male-specific region of the human Y chromosome. Proc Natl Acad Sci U S A (2004) 1.43

mRNA cap-1 methyltransferase in the SARS genome. Cell (2003) 1.42

Ligand-Info, searching for similar small compounds using index profiles. Bioinformatics (2003) 1.41

Modeling and analyzing three-dimensional structures of human disease proteins. Pac Symp Biocomput (2006) 1.39

Predicting protein structures accurately. Science (2004) 1.39

Deciphering the genetic determinants for aerobic nicotinic acid degradation: the nic cluster from Pseudomonas putida KT2440. Proc Natl Acad Sci U S A (2008) 1.39

A novel PAAD-containing protein that modulates NF-kappa B induction by cytokines tumor necrosis factor-alpha and interleukin-1beta. J Biol Chem (2002) 1.38

Connecting the protein structure universe by using sparse recurring fragments. Structure (2005) 1.38

Salmonella secreted factor L deubiquitinase of Salmonella typhimurium inhibits NF-kappaB, suppresses IkappaBalpha ubiquitination and modulates innate immune responses. J Immunol (2008) 1.36

Detection of reliable and unexpected protein fold predictions using 3D-Jury. Nucleic Acids Res (2003) 1.35

TOPSAN: use of a collaborative environment for annotating, analyzing and disseminating data on JCSG and PSI structures. Acta Crystallogr Sect F Struct Biol Cryst Commun (2010) 1.35

Database searching by flexible protein structure alignment. Protein Sci (2004) 1.34

CARD8 and NLRP1 undergo autoproteolytic processing through a ZU5-like domain. PLoS One (2011) 1.34

Identification and functional characterization of the BAG protein family in Arabidopsis thaliana. J Biol Chem (2006) 1.34

The Extent of Cooperativity of Protein Motions Observed with Elastic Network Models Is Similar for Atomic and Coarser-Grained Models. J Chem Theory Comput (2006) 1.33

A unique substrate binding mode discriminates membrane type-1 matrix metalloproteinase from other matrix metalloproteinases. J Biol Chem (2002) 1.33

Realm of PD-(D/E)XK nuclease superfamily revisited: detection of novel families with modified transitive meta profile searches. BMC Struct Biol (2007) 1.33

Novel genes dramatically alter regulatory network topology in amphioxus. Genome Biol (2008) 1.32

In search for more accurate alignments in the twilight zone. Protein Sci (2002) 1.31

GOR V server for protein secondary structure prediction. Bioinformatics (2005) 1.30

Contribution of electrostatic interactions, compactness and quaternary structure to protein thermostability: lessons from structural genomics of Thermotoga maritima. J Mol Biol (2005) 1.29

In silico identification, structure prediction and phylogenetic analysis of the 2'-O-ribose (cap 1) methyltransferase domain in the large structural protein of ssRNA negative-strand viruses. Protein Eng (2002) 1.29

Structure of the γ-D-glutamyl-L-diamino acid endopeptidase YkfC from Bacillus cereus in complex with L-Ala-γ-D-Glu: insights into substrate recognition by NlpC/P60 cysteine peptidases. Acta Crystallogr Sect F Struct Biol Cryst Commun (2010) 1.28

Caspases. Regulating death since the origin of life. Plant Physiol (2005) 1.28

Comparative analysis of apoptosis and inflammation genes of mice and humans. Genome Res (2003) 1.26

Heterogeneous nuclear ribonucleoprotein K protein associates with multiple mitochondrial transcripts within the organelle. J Biol Chem (2001) 1.26

Practical lessons from protein structure prediction. Nucleic Acids Res (2005) 1.25