Published in Nucleic Acids Res on October 01, 1996
MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics (2004) 50.89
The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res (2005) 21.68
Quantifying similarity between motifs. Genome Biol (2007) 9.27
Increased coverage of protein families with the blocks database servers. Nucleic Acids Res (2000) 9.18
JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update. Nucleic Acids Res (2007) 8.79
Comparative protein structure modeling using Modeller. Curr Protoc Bioinformatics (2006) 8.72
FFAS03: a server for profile--profile sequence alignments. Nucleic Acids Res (2005) 4.99
STAMP: a web tool for exploring DNA-binding motif similarities. Nucleic Acids Res (2007) 4.92
Reliable prediction of regulator targets using 12 Drosophila genomes. Genome Res (2007) 4.89
Histone acetyltransferase activity of yeast Gcn5p is required for the activation of target genes in vivo. Genes Dev (1998) 4.23
Recent enhancements to the Blocks Database servers. Nucleic Acids Res (1997) 3.01
Alignment of protein sequences by their profiles. Protein Sci (2004) 2.80
DNA familial binding profiles made easy: comparison of various motif alignment and clustering strategies. PLoS Comput Biol (2007) 2.37
A Z-DNA binding domain present in the human editing enzyme, double-stranded RNA adenosine deaminase. Proc Natl Acad Sci U S A (1997) 2.35
Identification of the yeast gene encoding the tRNA m1G methyltransferase responsible for modification at position 9. RNA (2003) 2.23
Integrated analysis of yeast regulatory sequences for biologically linked clusters of genes. Funct Integr Genomics (2003) 1.98
Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments. Nucleic Acids Res (2013) 1.96
Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection. Nucleic Acids Res (2006) 1.96
Adaptive evolution of centromere proteins in plants and animals. J Biol (2004) 1.90
Finding weak similarities between proteins by sequence profile comparison. Nucleic Acids Res (2003) 1.88
Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay. Genome Res (2013) 1.78
Superior performance in protein homology detection with the Blocks Database servers. Nucleic Acids Res (1998) 1.77
Scoring profile-to-profile sequence alignments. Protein Sci (2004) 1.71
Evidence for PDZ domains in bacteria, yeast, and plants. Protein Sci (1997) 1.69
Sequence walkers: a graphical method to display how binding proteins interact with DNA or RNA sequences. Nucleic Acids Res (1997) 1.69
Three monophyletic superfamilies account for the majority of the known glycosyltransferases. Protein Sci (2003) 1.68
Evolutionary relationship between K(+) channels and symporters. Biophys J (1999) 1.63
Proteins of the endoplasmic-reticulum-associated degradation pathway: domain detection and function prediction. Biochem J (2000) 1.58
The limits of protein sequence comparison? Curr Opin Struct Biol (2005) 1.57
The construction and use of log-odds substitution scores for multiple sequence alignment. PLoS Comput Biol (2010) 1.54
Recurrent evolution of DNA-binding motifs in the Drosophila centromeric histone. Proc Natl Acad Sci U S A (2002) 1.48
ProPhylER: a curated online resource for protein function and structure based on evolutionary constraint analyses. Genome Res (2009) 1.35
Congenital dyserythropoietic anemia type I is caused by mutations in codanin-1. Am J Hum Genet (2002) 1.32
Accurate statistical model of comparison between multiple sequence alignments. Nucleic Acids Res (2008) 1.28
Profile-profile comparisons by COMPASS predict intricate homologies between protein families. Protein Sci (2003) 1.26
Refining homology models by combining replica-exchange molecular dynamics and statistical potentials. Proteins (2008) 1.25
Shaping up the protein folding funnel by local interaction: lesson from a structure prediction study. Proc Natl Acad Sci U S A (2006) 1.22
Activity, specificity and structure of I-Bth0305I: a representative of a new homing endonuclease family. Nucleic Acids Res (2011) 1.21
A novel Bayesian DNA motif comparison method for clustering and retrieval. PLoS Comput Biol (2008) 1.20
PROCAIN: protein profile comparison with assisting information. Nucleic Acids Res (2009) 1.17
Does the KdpA subunit from the high affinity K(+)-translocating P-type KDP-ATPase have a structure similar to that of K(+) channels? Biophys J (2000) 1.16
COMPASS server for remote homology inference. Nucleic Acids Res (2007) 1.16
Measuring similarities between transcription factor binding sites. BMC Bioinformatics (2005) 1.13
Yeast homologues of three BLOC-1 subunits highlight KxDL proteins as conserved interactors of BLOC-1. Traffic (2011) 1.05
Drosophila genomic sequence annotation using the BLOCKS+ database. Genome Res (2000) 1.04
Origins and evolution of the formin multigene family that is involved in the formation of actin filaments. Mol Biol Evol (2008) 1.03
A family of putative Kir potassium channels in prokaryotes. BMC Evol Biol (2001) 1.03
Iterative orthology prediction uncovers new mitochondrial proteins and identifies C12orf62 as the human ortholog of COX14, a protein involved in the assembly of cytochrome c oxidase. Genome Biol (2012) 1.03
Protein subcellular localization prediction of eukaryotes using a knowledge-based approach. BMC Bioinformatics (2009) 1.02
Detection of distant evolutionary relationships between protein families using theory of sequence profile-profile comparison. BMC Bioinformatics (2010) 0.96
Interaction of heterochromatin protein 2 with HP1 defines a novel HP1-binding domain. Biochemistry (2005) 0.96
Comparative Protein Structure Modeling Using MODELLER. Curr Protoc Bioinformatics (2016) 0.95
Global versus local regulatory roles for Lrp-related proteins: Haemophilus influenzae as a case study. J Bacteriol (2001) 0.92
Clustering the annotation space of proteins. BMC Bioinformatics (2005) 0.91
PHOG-BLAST--a new generation tool for fast similarity search of protein families. BMC Evol Biol (2006) 0.91
COMPASS server for homology detection: improved statistical accuracy, speed and functionality. Nucleic Acids Res (2009) 0.90
MRFalign: protein homology detection through alignment of Markov random fields. PLoS Comput Biol (2014) 0.89
Regulatory element identification in subsets of transcripts: comparison and integration of current computational methods. RNA (2009) 0.89
Differential gene expression between squamous cell carcinoma of esophageus and its normal epithelium; altered pattern of mal, akr1c2, and rab11a expression. World J Gastroenterol (2004) 0.88
Homology modeling a fast tool for drug discovery: current perspectives. Indian J Pharm Sci (2012) 0.87
MATLIGN: a motif clustering, comparison and matching tool. BMC Bioinformatics (2007) 0.86
An assessment of substitution scores for protein profile-profile comparison. Bioinformatics (2011) 0.85
Consensus sequences improve PSI-BLAST through mimicking profile-profile alignments. Nucleic Acids Res (2007) 0.84
One-Block CYRCA: an automated procedure for identifying multiple-block alignments from single block queries. Nucleic Acids Res (2005) 0.83
Binding site graphs: a new graph theoretical framework for prediction of transcription factor binding sites. PLoS Comput Biol (2007) 0.82
Tools and resources for identifying protein families, domains and motifs. Genome Biol (2001) 0.82
FISim: a new similarity measure between transcription factor binding sites based on the fuzzy integral. BMC Bioinformatics (2009) 0.81
SPIC: a novel similarity metric for comparing transcription factor binding site motifs based on information contents. BMC Syst Biol (2013) 0.79
BioShell Threader: protein homology detection based on sequence profiles and secondary structure profiles. Nucleic Acids Res (2012) 0.79
New modularity of DAP-kinases: alternative splicing of the DRP-1 gene produces a ZIPk-like isoform. PLoS One (2011) 0.79
CORAL: aligning conserved core regions across domain families. Bioinformatics (2009) 0.79
Positional clustering improves computational binding site detection and identifies novel cis-regulatory sites in mammalian GABAA receptor subunit genes. Nucleic Acids Res (2007) 0.78
Estimates of statistical significance for comparison of individual positions in multiple sequence alignments. BMC Bioinformatics (2004) 0.78
Using multiple alignments to improve seeded local alignment algorithms. Nucleic Acids Res (2005) 0.78
Jaccard index based similarity measure to compare transcription factor binding site models. Algorithms Mol Biol (2013) 0.78
Linear array of conserved sequence motifs to discriminate protein subfamilies: study on pyridine nucleotide-disulfide reductases. BMC Bioinformatics (2007) 0.77
Heterogeneity of transcription factor binding specificity models within and across cell lines. Genome Res (2016) 0.76
Accurate identification of polyadenylation sites from 3' end deep sequencing using a naive Bayes classifier. Bioinformatics (2013) 0.76
Considering scores between unrelated proteins in the search database improves profile comparison. BMC Bioinformatics (2009) 0.75
MISCORE: a new scoring function for characterizing DNA regulatory motifs in promoter sequences. BMC Syst Biol (2012) 0.75
CLIMP: Clustering Motifs via Maximal Cliques with Parallel Computing Design. PLoS One (2016) 0.75
Promoter shape varies across populations and affects promoter evolution and expression noise. Nat Genet (2017) 0.75
Geometric aspects of biological sequence comparison. J Comput Biol (2009) 0.75
Genetic dissection of the divergent activities of the multifunctional membrane sensor BglF. J Bacteriol (2007) 0.75
Basic local alignment search tool. J Mol Biol (1990) 659.07
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res (1994) 392.47
Identification of common molecular subsequences. J Mol Biol (1981) 130.53
Distantly related sequences in the alpha- and beta-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J (1982) 38.14
Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science (1993) 36.84
Sequence logos: a new way to display consensus sequences. Nucleic Acids Res (1990) 36.74
Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins (1991) 32.50
Improved sensitivity of profile searches through the use of sequence weights and gap excision. Comput Appl Biosci (1994) 31.96
Profile analysis: detection of distantly related proteins. Proc Natl Acad Sci U S A (1987) 29.26
Position-based sequence weights. J Mol Biol (1994) 24.41
Amino acid substitution matrices from an information theoretic perspective. J Mol Biol (1991) 23.38
Protein-DNA recognition. Annu Rev Biochem (1984) 22.02
Detection of conserved segments in proteins: iterative scanning of sequence databases with alignment blocks. Proc Natl Acad Sci U S A (1994) 18.46
Automatic generation of primary sequence patterns from sets of related protein sequences. Proc Natl Acad Sci U S A (1990) 12.96
Systematic method for the detection of potential lambda Cro-like DNA-binding regions in proteins. J Mol Biol (1987) 11.67
A flexible method to align large numbers of biological sequences. J Mol Evol (1989) 11.34
Using substitution probabilities to improve position-specific scoring matrices. Comput Appl Biosci (1996) 11.32
Automated assembly of protein blocks for database searching. Nucleic Acids Res (1991) 10.84
Rad51 protein involved in repair and recombination in S. cerevisiae is a RecA-like protein. Cell (1992) 10.78
DMC1: a meiosis-specific yeast homolog of E. coli recA required for recombination, synaptonemal complex formation, and cell cycle progression. Cell (1992) 10.48
The SWISS-PROT protein sequence data bank. Nucleic Acids Res (1991) 9.45
Modular arrangement of proteins as inferred from analysis of homology. Protein Sci (1994) 9.38
Crystal structure of the lactose operon repressor and its complexes with DNA and inducer. Science (1996) 9.34
PROSITE: a dictionary of sites and patterns in proteins. Nucleic Acids Res (1991) 9.18
Transcription factors: structural families and principles of DNA recognition. Annu Rev Biochem (1992) 9.16
Prediction of the occurrence of the ADP-binding beta alpha beta-fold in proteins, using an amino acid sequence fingerprint. J Mol Biol (1986) 9.13
Improved detection of helix-turn-helix DNA-binding motifs in protein sequences. Nucleic Acids Res (1990) 6.99
Duplex opening by dnaA protein at novel sequences in initiation of replication at the origin of the E. coli chromosome. Cell (1988) 6.42
Gibbs motif sampling: detection of bacterial outer membrane protein repeats. Protein Sci (1995) 5.96
Protein database searches for multiple alignments. Proc Natl Acad Sci U S A (1990) 5.52
Structure of the recA protein-ADP complex. Nature (1992) 5.33
Protein family classification based on searching a database of blocks. Genomics (1994) 5.24
Similarity of the yeast RAD51 filament to the bacterial RecA filament. Science (1993) 4.96
Homologous genetic recombination: the pieces begin to fall into place. Crit Rev Microbiol (1994) 4.48
The RecA protein: structure and function. Crit Rev Biochem Mol Biol (1990) 4.33
Comparison of methods for searching protein sequence databases. Protein Sci (1995) 4.29
A common set of conserved motifs in a vast variety of putative nucleic acid-dependent ATPases including MCM proteins involved in the initiation of eukaryotic DNA replication. Nucleic Acids Res (1993) 3.54
Ancient conserved regions in new gene sequences and the protein databases. Science (1993) 3.00
PRINTS--a database of protein motif fingerprints. Nucleic Acids Res (1994) 2.86
Yeast chromosome III: new gene functions. EMBO J (1994) 2.85
RNA recognition and translational regulation by a homeodomain protein. Nature (1996) 2.49
The initiator protein DnaA: evolution, properties and function. Biochim Biophys Acta (1994) 2.29
Detecting patterns in protein sequences. J Mol Biol (1994) 2.16
Refined crystal structure of dogfish M4 apo-lactate dehydrogenase. J Mol Biol (1987) 1.98
Homologous DNA pairing promoted by a 20-amino acid peptide derived from RecA. Science (1996) 1.90
Determining residue-base interactions between AraC protein and araI DNA. J Mol Biol (1989) 1.84
Structural relationship of bacterial RecA proteins to recombination proteins from bacteriophage T4 and yeast. Science (1993) 1.83
Sequence similarity analysis of Escherichia coli proteins: functional and evolutionary implications. Proc Natl Acad Sci U S A (1995) 1.82
Detection of Caenorhabditis transposon homologs in diverse organisms. New Biol (1992) 1.78
recA-like genes from three archaean species with putative protein products similar to Rad51 and Dmc1 proteins of the yeast Saccharomyces cerevisiae. Nucleic Acids Res (1996) 1.76
Dynamic programming algorithms for biological sequence comparison. Methods Enzymol (1992) 1.65
Evolutionary conservation of RecA genes in relation to protein structure and function. J Bacteriol (1996) 1.49
Blocks database and its applications. Methods Enzymol (1996) 1.47
Structure of the active ternary complex of pig heart lactate dehydrogenase with S-lac-NAD at 2.7 A resolution. J Mol Biol (1981) 1.38
Activation of glycosylasparaginase. Formation of active N-terminal threonine by intramolecular autoproteolysis. J Biol Chem (1996) 1.38
gamma-Glutamyl transpeptidase. What does the organization and expression of a multipromoter gene tell us about its functions? Am J Pathol (1995) 1.25
FAD-binding site of glutathione reductase. J Mol Biol (1982) 1.18
Glycosaparaginase from human leukocytes. Inactivation and covalent modification with diazo-oxonorvaline. J Biol Chem (1991) 1.10
Identification of active site residues of Escherichia coli fumarate reductase by site-directed mutagenesis. J Biol Chem (1991) 1.06
Aspartylglycosaminuria: protein chemistry and molecular biology of the most common lysosomal storage disorder of glycoprotein degradation. FASEB J (1993) 1.06
Latent proteinase activity of gamma-glutamyl transpeptidase light subunit. J Biol Chem (1979) 1.04
Cloning and sequencing of IS1086, an Alcaligenes eutrophus insertion element related to IS30 and IS4351. J Bacteriol (1992) 1.01
Molecular basis of allosteric activation of bacterial L-lactate dehydrogenase. J Mol Biol (1993) 1.01
Molecular cloning and sequence analysis of Flavobacterium meningosepticum glycosylasparaginase: a single gene encodes the alpha and beta subunits. Arch Biochem Biophys (1995) 1.00
The N-terminal domain of the insertion sequence 30 transposase interacts specifically with the terminal inverted repeats of the element. J Biol Chem (1990) 0.97
The sequence of the flavoprotein subunit of bovine heart succinate dehydrogenase. J Biol Chem (1992) 0.95
Effect of site-directed mutations on processing and activity of gamma-glutamyltranspeptidase of Escherichia coli K-12. J Biochem (1995) 0.93
Studies on Phe-228 and Leu-307 recombinant mutants of porcine kidney D-amino acid oxidase: expression, purification, and characterization. J Biochem (1991) 0.87
Characterization of a processing protease that converts the precursor form of gamma-glutamyltranspeptidase to its subunits. Biochem Int (1984) 0.84
Cloning and sequence analysis of a cDNA for human glycosylasparaginase. A single gene encodes the subunits of this lysosomal amidase. FEBS Lett (1990) 0.83
The Blocks database--a system for protein classification. Nucleic Acids Res (1996) 1.38