Published in BMC Bioinformatics on August 28, 2007
Accurate statistical model of comparison between multiple sequence alignments. Nucleic Acids Res (2008) 1.28
Discrete-continuous duality of protein structure space. Curr Opin Struct Biol (2009) 1.24
PROCAIN: protein profile comparison with assisting information. Nucleic Acids Res (2009) 1.17
A comparative assessment and analysis of 20 representative sequence alignment methods for protein structure prediction. Sci Rep (2013) 0.97
Cholera- and anthrax-like toxins are among several new ADP-ribosyltransferases. PLoS Comput Biol (2010) 0.96
Detection of distant evolutionary relationships between protein families using theory of sequence profile-profile comparison. BMC Bioinformatics (2010) 0.96
COMPASS server for homology detection: improved statistical accuracy, speed and functionality. Nucleic Acids Res (2009) 0.90
Using homology relations within a database markedly boosts protein sequence similarity search. Proc Natl Acad Sci U S A (2015) 0.79
Proteases in malaria parasites - a phylogenomic perspective. Curr Genomics (2011) 0.79
How a spatial arrangement of secondary structure elements is dispersed in the universe of protein folds. PLoS One (2014) 0.78
PROCAIN server for remote protein sequence similarity search. Bioinformatics (2009) 0.78
Linear predictive coding representation of correlated mutation for protein sequence alignment. BMC Bioinformatics (2010) 0.76
Considering scores between unrelated proteins in the search database improves profile comparison. BMC Bioinformatics (2009) 0.75
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers (1983) 99.69
SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol (1995) 74.88
Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol (1999) 33.07
CATH--a hierarchic classification of protein domain structures. Structure (1997) 29.95
Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res (2001) 22.33
Protein homology detection by HMM-HMM comparison. Bioinformatics (2004) 21.92
Dali: a network tool for protein structure comparison. Trends Biochem Sci (1995) 14.13
Mapping the protein universe. Science (1996) 13.72
The ASTRAL compendium for protein structure and sequence analysis. Nucleic Acids Res (2000) 11.38
Scoring function for automated assessment of protein structure template quality. Proteins (2004) 10.99
The ASTRAL Compendium in 2004. Nucleic Acids Res (2004) 10.03
LGA: A method for finding 3D similarities in protein structures. Nucleic Acids Res (2003) 9.44
COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance. J Mol Biol (2003) 8.35
Large-scale comparison of protein sequence alignment algorithms with structure alignments. Proteins (2000) 8.17
Protein structure prediction servers at University College London. Nucleic Acids Res (2005) 6.70
Within the twilight zone: a sensitive profile-profile comparison tool based on information theory. J Mol Biol (2002) 4.99
Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures. J Mol Biol (2005) 4.02
MaxSub: an automated measure for the assessment of protein structure prediction quality. Bioinformatics (2000) 3.86
Dictionary of recurrent domains in protein structures. Proteins (1998) 3.40
Mismatch string kernels for discriminative protein classification. Bioinformatics (2004) 3.27
PROMALS: towards accurate multiple sequence alignments of distantly related proteins. Bioinformatics (2007) 3.26
EVA: continuous automatic evaluation of protein structure prediction servers. Bioinformatics (2001) 3.24
Processing and evaluation of predictions in CASP4. Proteins (2001) 2.91
CAFASP3: the third critical assessment of fully automated structure prediction methods. Proteins (2003) 2.60
Critical assessment of methods of protein structure prediction (CASP)--round 6. Proteins (2005) 2.58
Profile-profile methods provide improved fold-recognition: a study of different profile-profile alignment methods. Proteins (2004) 2.52
A modified definition of Sov, a segment-based measure for protein secondary structure prediction assessment. Proteins (1999) 2.35
FAST: a novel protein structure alignment algorithm. Proteins (2005) 2.27
Progress of structural genomics initiatives: an analysis of solved target structures. J Mol Biol (2005) 2.22
An overview of structural genomics. Nat Struct Biol (2000) 2.09
Functional coverage of the human genome by existing structures, structural genomics targets, and homology models. PLoS Comput Biol (2005) 2.04
All are not equal: a benchmark of different homology modeling programs. Protein Sci (2005) 1.99
MUMMALS: multiple sequence alignment improved by using hidden Markov models with local structural information. Nucleic Acids Res (2006) 1.85
Spectral clustering of protein sequences. Nucleic Acids Res (2006) 1.74
Scoring profile-to-profile sequence alignments. Protein Sci (2004) 1.71
The limits of protein sequence comparison? Curr Opin Struct Biol (2005) 1.57
LiveBench-8: the large-scale, continuous assessment of automated protein structure prediction. Protein Sci (2005) 1.38
New methods for accurate prediction of protein secondary structure. Proteins (1999) 1.32
Practical lessons from protein structure prediction. Nucleic Acids Res (2005) 1.25
A comparison of sequence and structure protein domain families as a basis for structural genomics. Bioinformatics (1999) 1.25
4SCOPmap: automated assignment of protein structures to evolutionary superfamilies. BMC Bioinformatics (2004) 1.25
A study on protein sequence alignment quality. Proteins (2002) 1.11
Protein family comparison using statistical models and predicted structural information. BMC Bioinformatics (2004) 0.98
Exploring dynamics of protein structure determination and homology-based prediction to estimate the number of superfamilies and folds. BMC Struct Biol (2006) 0.94
Genome sequencing in microfabricated high-density picolitre reactors. Nature (2005) 150.21
Substrate and functional diversity of lysine acetylation revealed by a proteomics survey. Mol Cell (2006) 11.38
A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Biol Direct (2006) 11.31
Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature (2010) 7.51
PROMALS3D: a tool for multiple protein sequence and structure alignments. Nucleic Acids Res (2008) 7.16
Cell-free formation of RNA granules: low complexity sequence domains form dynamic fibers within hydrogels. Cell (2012) 6.83
Cell type-specific delivery of siRNAs with aptamer-siRNA chimeras. Nat Biotechnol (2006) 6.30
Frequent mutations of chromatin remodeling genes in transitional cell carcinoma of the bladder. Nat Genet (2011) 5.73
Identification of the acyltransferase that octanoylates ghrelin, an appetite-stimulating peptide hormone. Cell (2008) 5.10
Isoprenoid pathway optimization for Taxol precursor overproduction in Escherichia coli. Science (2010) 4.96
An Aboriginal Australian genome reveals separate human dispersals into Asia. Science (2011) 4.84
Yersinia YopJ acetylates and inhibits kinase activation by blocking phosphorylation. Science (2006) 4.71
An index of substitution saturation and its application. Mol Phylogenet Evol (2003) 4.71
A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis. Nucleic Acids Res (2002) 4.39
Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli. Mol Cell Proteomics (2008) 4.36
Structural classification of zinc fingers: survey and summary. Nucleic Acids Res (2003) 3.94
Genome trees and the tree of life. Trends Genet (2002) 3.79
Identification of a candidate therapeutic autophagy-inducing peptide. Nature (2013) 3.76
Frequent mutations of genes encoding ubiquitin-mediated proteolysis pathway components in clear cell renal cell carcinoma. Nat Genet (2011) 3.66
Structure prediction for CASP8 with all-atom refinement using Rosetta. Proteins (2009) 3.64
Biochemical identification of Argonaute 2 as the sole protein required for RNA-induced silencing complex activity. Proc Natl Acad Sci U S A (2004) 3.63
FoxM1 promotes β-catenin nuclear localization and controls Wnt target-gene expression and glioma tumorigenesis. Cancer Cell (2011) 3.58
AMPylation of Rho GTPases by Vibrio VopS disrupts effector binding and downstream signaling. Science (2008) 3.44
A sequence variation (I148M) in PNPLA3 associated with nonalcoholic fatty liver disease disrupts triglyceride hydrolysis. J Biol Chem (2009) 3.41
PROMALS: towards accurate multiple sequence alignments of distantly related proteins. Bioinformatics (2007) 3.26
PCMA: fast and accurate multiple sequence alignment based on profile consistency. Bioinformatics (2003) 3.23
The lipodystrophy protein seipin is found at endoplasmic reticulum lipid droplet junctions and is important for droplet morphology. Proc Natl Acad Sci U S A (2007) 3.11
Adhesive phase separation at the dentin interface under wet bonding conditions. J Biomed Mater Res (2002) 3.08
Ubiquitin-induced oligomerization of the RNA sensors RIG-I and MDA5 activates antiviral innate immune response. Immunity (2012) 3.07
Xist RNA is a potent suppressor of hematologic cancer in mice. Cell (2013) 2.93
Manipulating surface states in topological insulator nanoribbons. Nat Nanotechnol (2011) 2.70
Large electrocaloric effect in ferroelectric polymers near room temperature. Science (2008) 2.66
EGFR-mediated Beclin 1 phosphorylation in autophagy suppression, tumor progression, and tumor chemoresistance. Cell (2013) 2.63
Atypical angiopoietin-like protein that regulates ANGPTL3. Proc Natl Acad Sci U S A (2012) 2.62
Noninvasive characterization of epicardial activation in humans with diverse atrial fibrillation patterns. Circulation (2010) 2.57
Structural basis for converting a general transcription factor into an operon-specific virulence regulator. Mol Cell (2007) 2.56
Secreted kinase phosphorylates extracellular proteins that regulate biomineralization. Science (2012) 2.55
Genetic defects in surfactant protein A2 are associated with pulmonary fibrosis and lung cancer. Am J Hum Genet (2008) 2.53
An E3 ligase possessing an iron-responsive hemerythrin domain is a regulator of iron homeostasis. Science (2009) 2.49
Autophagic proteins regulate cigarette smoke-induced apoptosis: protective role of heme oxygenase-1. Autophagy (2008) 2.38
Evolution of protein structures and functions. Curr Opin Struct Biol (2002) 2.38
Purified NPC1 protein: II. Localization of sterol binding to a 240-amino acid soluble luminal loop. J Biol Chem (2007) 2.34
Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. Nucleic Acids Res (2012) 2.32
Relationship of solvent to the photopolymerization process, properties, and structure in model dentin adhesives. J Biomed Mater Res A (2007) 2.26
High operative risk of cool-tip radiofrequency ablation for unresectable pancreatic head cancer. J Surg Oncol (2006) 2.19
Role of hyperphosphatemia and 1,25-dihydroxyvitamin D in vascular calcification and mortality in fibroblastic growth factor 23 null mice. J Am Soc Nephrol (2007) 2.16
Serologic survey of pandemic (H1N1) 2009 virus, Guangxi Province, China. Emerg Infect Dis (2009) 2.13
Overexpression of cyclin D1 promotes tumor cell growth and confers resistance to cisplatin-mediated apoptosis in an elastase-myc transgene-expressing pancreatic tumor cell line. Clin Cancer Res (2005) 2.13
The Arabidopsis NPR1 protein is a receptor for the plant defense hormone salicylic acid. Cell Rep (2012) 2.13
MicroRNA expression signatures of bladder cancer revealed by deep sequencing. PLoS One (2011) 2.10
Newcastle disease virus-based live attenuated vaccine completely protects chickens and mice from lethal challenge of homologous and heterologous H5N1 avian influenza viruses. J Virol (2006) 2.08
C3PO, an endoribonuclease that promotes RNAi by facilitating RISC activation. Science (2009) 2.04
Bone marrow graft-versus-host disease: early destruction of hematopoietic niche after MHC-mismatched hematopoietic stem cell transplantation. Blood (2010) 2.04
DNMT1 stability is regulated by proteins coordinating deubiquitination and acetylation-driven ubiquitination. Sci Signal (2010) 2.04
Microfluidic device for multimodal characterization of pancreatic islets. Lab Chip (2008) 1.99
Adhesive/Dentin interface: the weak link in the composite restoration. Ann Biomed Eng (2010) 1.96
The conserved plant sterility gene HAP2 functions after attachment of fusogenic membranes in Chlamydomonas and Plasmodium gametes. Genes Dev (2008) 1.95
P450 enzymes: their structure, reactivity, and selectivity-modeled by QM/MM calculations. Chem Rev (2010) 1.95
Fido, a novel AMPylation domain common to fic, doc, and AvrB. PLoS One (2009) 1.92
CASP9 assessment of free modeling target predictions. Proteins (2011) 1.90
Ionizing radiation and busulfan induce premature senescence in murine bone marrow hematopoietic cells. Cancer Res (2003) 1.86
Milnacipran for the treatment of fibromyalgia in adults: a 15-week, multicenter, randomized, double-blind, placebo-controlled, multiple-dose clinical trial. Clin Ther (2008) 1.86
Detecting distant homology with Meta-BASIC. Nucleic Acids Res (2004) 1.86
MUMMALS: multiple sequence alignment improved by using hidden Markov models with local structural information. Nucleic Acids Res (2006) 1.85
Side-chain modeling with an optimized scoring function. Protein Sci (2002) 1.84
Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea. ISME J (2010) 1.84
Sequence and structure classification of kinases. J Mol Biol (2002) 1.84
Integrated profiling of microRNAs and mRNAs: microRNAs located on Xq27.3 associate with clear cell renal cell carcinoma. PLoS One (2010) 1.82
Human monoclonal antibodies to a novel cluster of conformational epitopes on HCV E2 with resistance to neutralization escape in a genotype 2a isolate. PLoS Pathog (2012) 1.79
CASP9 target classification. Proteins (2011) 1.75
A novel glucokinase activator modulates pancreatic islet and hepatocyte function. Endocrinology (2005) 1.75
Mitigation of hematologic radiation toxicity in mice through pharmacological quiescence induced by CDK4/6 inhibition. J Clin Invest (2010) 1.74
Characterization of photopolymerization of dentin adhesives as a function of light source and irradiance. J Biomed Mater Res B Appl Biomater (2007) 1.73
CASP5 assessment of fold recognition target predictions. Proteins (2003) 1.73
Plasma microRNAs as novel biomarkers for early detection of lung cancer. Int J Clin Exp Pathol (2011) 1.73
Crystal structure of human riboflavin kinase reveals a beta barrel fold and a novel active site arch. Structure (2003) 1.69
Bariatric surgery reduces visceral adipose inflammation and improves endothelial function in type 2 diabetic mice. Arterioscler Thromb Vasc Biol (2011) 1.69
A minimal domain responsible for Munc13 activity. Nat Struct Mol Biol (2005) 1.68
N'-[4-(Dimethyl-amino)benzyl-idene]benzohydrazide. Acta Crystallogr Sect E Struct Rep Online (2009) 1.68
Complete biosynthesis of erythromycin A and designed analogs using E. coli as a heterologous host. Chem Biol (2010) 1.68
Halogen bonding--a novel interaction for rational drug design? J Med Chem (2009) 1.68
Transitional cell carcinoma in renal transplant recipients: a single center experience. Int J Urol (2008) 1.67
Genetic variation in ANGPTL4 provides insights into protein processing and function. J Biol Chem (2009) 1.64
Antiemetic placebo: reduce adverse drug interactions between chemotherapeutic agents and antiemetic drugs in cancer patients. Med Hypotheses (2007) 1.62
Comprehensive molecular etiology analysis of nonsyndromic hearing impairment from typical areas in China. J Transl Med (2009) 1.62
Alignment of molecular networks by integer quadratic programming. Bioinformatics (2007) 1.61
The HicAB cassette, a putative novel, RNA-targeting toxin-antitoxin system in archaea and bacteria. Bioinformatics (2006) 1.60
NOA: a novel Network Ontology Analysis method. Nucleic Acids Res (2011) 1.60
PROMALS3D: multiple protein sequence alignment enhanced with evolutionary and three-dimensional structural information. Methods Mol Biol (2014) 1.59
PROMALS3D web server for accurate multiple protein sequence and structure alignments. Nucleic Acids Res (2008) 1.58
NESdb: a database of NES-containing CRM1 cargoes. Mol Biol Cell (2012) 1.57
Phenotypic and genotypic analyses of genetic skin disease through the Online Mendelian Inheritance in Man (OMIM) database. J Invest Dermatol (2009) 1.57
Nanophase separation of polymers exposed to simulated bonding conditions. J Biomed Mater Res B Appl Biomater (2009) 1.56
Helix-stabilized cyclic peptides as selective inhibitors of steroid receptor-coactivator interactions. Proc Natl Acad Sci U S A (2003) 1.54
Efficacy, safety and tolerability of bosentan in Chinese patients with pulmonary arterial hypertension. J Heart Lung Transplant (2010) 1.54
Carbon monoxide protects against hyperoxia-induced endothelial cell apoptosis by inhibiting reactive oxygen species formation. J Biol Chem (2006) 1.53