Published in Bioinformatics on October 21, 2013
Caspase cleavage sites in the human proteome: CaspDB, a database of predicted substrates. PLoS One (2014) 1.48
Accurate in silico identification of species-specific acetylation sites by integrating protein sequence-derived and functional features. Sci Rep (2014) 0.91
Computational Identification of Protein Pupylation Sites by Using Profile-Based Composition of k-Spaced Amino Acid Pairs. PLoS One (2015) 0.79
Novel extracellular and nuclear caspase-1 and inflammasomes propagate inflammation and regulate gene expression: a comprehensive database mining study. J Hematol Oncol (2016) 0.78
Crysalis: an integrated server for computational analysis and design of protein crystallization. Sci Rep (2016) 0.77
Uterine endoplasmic reticulum stress-unfolded protein response regulation of gestational length is caspase-3 and -7-dependent. Proc Natl Acad Sci U S A (2015) 0.76
Prediction of aptamer-protein interacting pairs using an ensemble classifier in combination with various protein sequence attributes. BMC Bioinformatics (2016) 0.75
Analyses of caspase-1-regulated transcriptomes in various tissues lead to identification of novel IL-1β-, IL-18- and sirtuin-1-independent pathways. J Hematol Oncol (2017) 0.75
Transcriptomic analysis of human norovirus NS1-2 protein highlights a multifunctional role in murine monocytes. BMC Genomics (2017) 0.75
Metacaspases versus caspases in development and cell fate regulation. Cell Death Differ (2017) 0.75
PhosphoPredict: A bioinformatics tool for prediction of human kinase-specific phosphorylation substrates and sites by integrating heterogeneous feature selection. Sci Rep (2017) 0.75
MUSTANG: a multiple structural alignment algorithm. Proteins (2006) 4.69
AB5 subtilase cytotoxin inactivates the endoplasmic reticulum chaperone BiP. Nature (2006) 3.65
A common fold mediates vertebrate defense and bacterial attack. Science (2007) 3.43
A structural basis for the selection of dominant alphabeta T cell receptors in antiviral immunity. Immunity (2003) 3.41
T cell receptor recognition of a 'super-bulged' major histocompatibility complex class I-bound peptide. Nat Immunol (2005) 2.52
The structural basis for membrane binding and pore formation by lymphocyte perforin. Nature (2010) 2.23
The MACPF/CDC family of pore-forming toxins. Cell Microbiol (2008) 2.15
An overview of the serpin superfamily. Genome Biol (2006) 2.14
Protein homology detection using string alignment kernels. Bioinformatics (2004) 2.13
The type III effectors NleE and NleB from enteropathogenic E. coli and OspZ from Shigella block nuclear translocation of NF-kappaB p65. PLoS Pathog (2010) 2.03
The molecular basis for perforin oligomerization and transmembrane pore assembly. Immunity (2009) 1.98
A tale of two specificities: bispecific antibodies for therapeutic and diagnostic applications. Trends Biotechnol (2013) 1.85
Protection from endogenous perforin: glycans and the C terminus regulate exocytic trafficking in cytotoxic lymphocytes. Immunity (2011) 1.73
Functional insights from the distribution and role of homopeptide repeat-containing proteins. Genome Res (2005) 1.70
Genomic diversity and evolution of the head crest in the rock pigeon. Science (2013) 1.68
Structural basis for the inhibition of the essential Plasmodium falciparum M1 neutral aminopeptidase. Proc Natl Acad Sci U S A (2009) 1.63
The 1.5 A crystal structure of a prokaryote serpin: controlling conformational change in a heated environment. Structure (2003) 1.61
IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming. Bioinformatics (2011) 1.59
GABA production by glutamic acid decarboxylase is regulated by a dynamic catalytic loop. Nat Struct Mol Biol (2007) 1.56
Perforin forms transient pores on the target cell plasma membrane to facilitate rapid access of granzymes during killer cell attack. Blood (2013) 1.53
The draft genome of a socially polymorphic halictid bee, Lasioglossum albipes. Genome Biol (2013) 1.52
Computational analysis of evolution and conservation in a protein superfamily. Methods (2004) 1.49
The major human and mouse granzymes are structurally and functionally divergent. J Cell Biol (2006) 1.48
Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information. Bioinformatics (2011) 1.45
APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility. BMC Bioinformatics (2010) 1.44
KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains. Nucleic Acids Res (2004) 1.43
A novel representation of protein sequences for prediction of subcellular location using support vector machines. Protein Sci (2005) 1.38
Molecular basis of α1-antitrypsin deficiency revealed by the structure of a domain-swapped trimer. EMBO Rep (2011) 1.37
Graph kernels for molecular structure-activity relationship analysis with support vector machines. J Chem Inf Model (2005) 1.35
Cascleave: towards more accurate prediction of caspase substrate cleavage sites. Bioinformatics (2010) 1.34
Federated repositories of X-ray diffraction images. Acta Crystallogr D Biol Crystallogr (2008) 1.33
Serpins flex their muscle: I. Putting the clamps on proteolysis in diverse biological systems. J Biol Chem (2010) 1.32
Perforin: structure, function, and role in human immunopathology. Immunol Rev (2010) 1.30
PROSPER: an integrated feature-based tool for predicting protease substrate cleavage sites. PLoS One (2012) 1.28
Automatic generation of protein structure cartoons with Pro-origami. Bioinformatics (2011) 1.28
The type Ialpha inositol polyphosphate 4-phosphatase generates and terminates phosphoinositide 3-kinase signals on endosomes and the plasma membrane. Mol Biol Cell (2005) 1.26
PoPS: a computational tool for modeling and predicting protease specificity. J Bioinform Comput Biol (2005) 1.23
Perforin and granzymes: function, dysfunction and human pathology. Nat Rev Immunol (2015) 1.23
The 1.6 A crystal structure of the catalytic domain of PlyB, a bacteriophage lysin active against Bacillus anthracis. J Mol Biol (2006) 1.23
The X-ray crystal structure of full-length human plasminogen. Cell Rep (2012) 1.22
Serpins in prokaryotes. Mol Biol Evol (2002) 1.22
Plasmodium falciparum neutral aminopeptidases: new targets for anti-malarials. Trends Biochem Sci (2009) 1.21
The high resolution crystal structure of the human tumor suppressor maspin reveals a novel conformational switch in the G-helix. J Biol Chem (2005) 1.21
The murine orthologue of human antichymotrypsin: a structural paradigm for clade A3 serpins. J Biol Chem (2005) 1.20
Enumerating treelike chemical graphs with given path frequency. J Chem Inf Model (2008) 1.18
Role of the M-loop and reactive center loop domains in the folding and bridging of nucleosome arrays by MENT. J Biol Chem (2003) 1.18
Inhibitory activity of a heterochromatin-associated serpin (MENT) against papain-like cysteine proteinases affects chromatin structure and blocks cell proliferation. J Biol Chem (2002) 1.17
Predicting protein-protein interactions from protein sequences using meta predictor. Amino Acids (2010) 1.16
Structural and functional analysis of the Josephin domain of the polyglutamine protein ataxin-3. Biochem Biophys Res Commun (2004) 1.14
Temperature sensitivity of human perforin mutants unmasks subtotal loss of cytotoxicity, delayed FHL, and a predisposition to cancer. Proc Natl Acad Sci U S A (2009) 1.14
Predicting disulfide connectivity from protein sequence using multiple sequence feature vectors and secondary structure. Bioinformatics (2007) 1.14
COOH-terminal clustering of autoantibody and T-cell determinants on the structure of GAD65 provide insights into the molecular basis of autoreactivity. Diabetes (2008) 1.11
The crystal structure of DehI reveals a new alpha-haloacid dehalogenase fold and active-site mechanism. J Mol Biol (2008) 1.11
X-ray crystal structure of the streptococcal specific phage lysin PlyC. Proc Natl Acad Sci U S A (2012) 1.11
A systems biology approach to identify effective cocktail drugs. BMC Syst Biol (2010) 1.11
The subtilisin-like protease AprV2 is required for virulence and uses a novel disulphide-tethered exosite to bind substrates. PLoS Pathog (2010) 1.10
Enumerating tree-like chemical graphs with given upper and lower bounds on path frequencies. BMC Bioinformatics (2011) 1.10
Protecting a serial killer: pathways for perforin trafficking and self-defence ensure sequential target cell death. Trends Immunol (2012) 1.09
Identifying dysregulated pathways in cancers from pathway interaction networks. BMC Bioinformatics (2012) 1.09
Structure of the Plasmodium falciparum M17 aminopeptidase and significance for the design of drugs targeting the neutral exopeptidases. Proc Natl Acad Sci U S A (2010) 1.09
The conjugation protein TcpC from Clostridium perfringens is structurally related to the type IV secretion system protein VirB8 from Gram-negative bacteria. Mol Microbiol (2011) 1.07
Drug discovery in the age of systems biology: the rise of computational approaches for data integration. Curr Opin Biotechnol (2011) 1.07
Bestatin-based chemical biology strategy reveals distinct roles for malaria M1- and M17-family aminopeptidases. Proc Natl Acad Sci U S A (2011) 1.07
The FxRxHrS motif: a conserved region essential for DNA binding of the VirR response regulator from Clostridium perfringens. J Mol Biol (2002) 1.07
Identifying disease genes and module biomarkers by differential interactions. J Am Med Inform Assoc (2011) 1.07
Resolvins E1 and D1 inhibit interstitial fibrosis in the obstructed kidney via inhibition of local fibroblast proliferation. J Pathol (2012) 1.06
An approximation method for solving the steady-state probability distribution of probabilistic Boolean networks. Bioinformatics (2007) 1.05
Cationic sites on granzyme B contribute to cytotoxicity by promoting its uptake into target cells. Mol Cell Biol (2005) 1.04
RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming. Bioinformatics (2010) 1.04
Structural controllability of unidirectional bipartite networks. Sci Rep (2013) 1.04
Leucine-rich repeats 2-4 (Leu60-Glu128) of platelet glycoprotein Ibalpha regulate shear-dependent cell adhesion to von Willebrand factor. J Biol Chem (2006) 1.03
Antithrombin: in control of coagulation. Int J Biochem Cell Biol (2004) 1.03
Global gene profiling of laser-captured pollen mother cells indicates molecular pathways and gene subfamilies involved in rice meiosis. Plant Physiol (2010) 1.02
The matrix refolded. Nat Methods (2005) 1.01
MUSTANG-MR structural sieving server: applications in protein structural analysis and crystallography. PLoS One (2010) 1.01
NARROMI: a noise and redundancy reduction technique improves accuracy of gene regulatory network inference. Bioinformatics (2012) 1.01
RCPdb: An evolutionary classification and codon usage database for repeat-containing proteins. Genome Res (2007) 1.01
Fingerprinting the substrate specificity of M1 and M17 aminopeptidases of human malaria, Plasmodium falciparum. PLoS One (2012) 1.00
Algorithms for finding small attractors in Boolean networks. EURASIP J Bioinform Syst Biol (2007) 1.00
RAB-like 2 has an essential role in male fertility, sperm intra-flagellar transport, and tail assembly. PLoS Genet (2012) 1.00
Subcellular location prediction of proteins using support vector machines with alignment of block sequences utilizing amino acid composition. BMC Bioinformatics (2007) 1.00
Correlation between structure and temperature in prokaryotic metabolic networks. BMC Bioinformatics (2007) 1.00
Breadth-first search approach to enumeration of tree-like chemical compounds. J Bioinform Comput Biol (2013) 0.99
The evolution of enzyme specificity in Fasciola spp. J Mol Evol (2003) 0.99
Maspin (SERPINB5) is an obligate intracellular serpin. J Biol Chem (2010) 0.99
REFOLD: an analytical database of protein refolding methods. Protein Expr Purif (2005) 0.99
Hurpin is a selective inhibitor of lysosomal cathepsin L and protects keratinocytes from ultraviolet-induced apoptosis. Biochemistry (2003) 0.98
hCKSAAP_UbSite: improved prediction of human ubiquitination sites by exploiting amino acid pattern and properties. Biochim Biophys Acta (2013) 0.98
Cloning and expression of the major secreted cathepsin B-like protein from juvenile Fasciola hepatica and analysis of immunogenicity following liver fluke infection. Infect Immun (2003) 0.97
The N terminus of the serpin, tengpin, functions to trap the metastable native state. EMBO Rep (2007) 0.97
Efficient tree-matching methods for accurate carbohydrate database queries. Genome Inform (2003) 0.97
The serpin SQN-5 is a dual mechanistic-class inhibitor of serine and cysteine proteinases. Biochemistry (2002) 0.97
Human monogenic disease genes have frequently functionally redundant paralogs. PLoS Comput Biol (2013) 0.97
Functional analysis of the Listeria monocytogenes secretion chaperone PrsA2 and its multiple contributions to bacterial virulence. Mol Microbiol (2011) 0.96