Published in Nucleic Acids Res on August 26, 2006
PROMALS3D: a tool for multiple protein sequence and structure alignments. Nucleic Acids Res (2008) 7.16
Fast statistical alignment. PLoS Comput Biol (2009) 5.92
Recent evolutions of multiple sequence alignment algorithms. PLoS Comput Biol (2007) 4.88
Structure prediction for CASP8 with all-atom refinement using Rosetta. Proteins (2009) 3.64
Upcoming challenges for multiple sequence alignment methods in the high-throughput era. Bioinformatics (2009) 2.64
Phylogenetic assessment of alignments reveals neglected tree signal in gaps. Genome Biol (2010) 2.27
Issues in bioinformatics benchmarking: the case study of multiple sequence alignment. Nucleic Acids Res (2010) 2.05
Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases. BMC Bioinformatics (2007) 1.74
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
Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses. Nucleic Acids Res (2008) 1.49
Accounting for alignment uncertainty in phylogenomics. PLoS One (2012) 1.35
PROMALS web server for accurate multiple protein sequence alignments. Nucleic Acids Res (2007) 1.20
PicXAA: greedy probabilistic construction of maximum expected accuracy alignment of multiple sequences. Nucleic Acids Res (2010) 1.16
A cytogenetic abnormality and rare coding variants identify ABCA13 as a candidate gene in schizophrenia, bipolar disorder, and depression. Am J Hum Genet (2009) 1.08
A comprehensive system for evaluation of remote sequence similarity detection. BMC Bioinformatics (2007) 1.05
A new protein linear motif benchmark for multiple sequence alignment software. BMC Bioinformatics (2008) 0.99
Optimizing substitution matrix choice and gap parameters for sequence alignment. BMC Bioinformatics (2009) 0.96
Structural basis for the methylation of A1408 in 16S rRNA by a panaminoglycoside resistance methyltransferase NpmA from a clinical isolate and analysis of the NpmA interactions with the 30S ribosomal subunit. Nucleic Acids Res (2010) 0.95
Protein sequence alignment with family-specific amino acid similarity matrices. BMC Res Notes (2011) 0.89
Improving accuracy of multiple sequence alignment algorithms based on alignment of neighboring residues. Nucleic Acids Res (2008) 0.89
Revisiting gap locations in amino acid sequence alignments and a proposal for a method to improve them by introducing solvent accessibility. Proteins (2011) 0.89
MSACompro: protein multiple sequence alignment using predicted secondary structure, solvent accessibility, and residue-residue contacts. BMC Bioinformatics (2011) 0.87
RBT-GA: a novel metaheuristic for solving the Multiple Sequence Alignment problem. BMC Genomics (2009) 0.86
Identification of two conserved aspartic acid residues required for DNA digestion by a novel thermophilic Exonuclease VII in Thermotoga maritima. Nucleic Acids Res (2008) 0.84
PicXAA-Web: a web-based platform for non-progressive maximum expected accuracy alignment of multiple biological sequences. Nucleic Acids Res (2011) 0.82
Prediction of prognostic biomarkers for interferon-based therapy to hepatitis C virus patients: a meta-analysis of the NS5A protein in subtypes 1a, 1b, and 3a. Virol J (2010) 0.82
Characterization of multiple sequence alignment errors using complete-likelihood score and position-shift map. BMC Bioinformatics (2016) 0.80
Improving the alignment quality of consistency based aligners with an evaluation function using synonymous protein words. PLoS One (2011) 0.76
PR2ALIGN: a stand-alone software program and a web-server for protein sequence alignment using weighted biochemical properties of amino acids. BMC Res Notes (2015) 0.75
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31
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
MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res (2004) 168.89
A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol (1970) 155.96
Identification of common molecular subsequences. J Mol Biol (1981) 130.53
SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol (1995) 74.88
Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A (1992) 61.33
T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol (2000) 57.88
Profile hidden Markov models. Bioinformatics (1998) 56.04
Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol (1999) 33.07
MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res (2005) 31.64
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng (1998) 28.09
CDD: a Conserved Domain Database for protein classification. Nucleic Acids Res (2005) 18.85
Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments. J Mol Biol (1996) 15.98
Mapping the protein universe. Science (1996) 13.72
A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Res (1999) 12.56
ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Res (2005) 11.90
Hidden Markov models. Curr Opin Struct Biol (1996) 11.56
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
An evolutionary trace method defines binding surfaces common to protein families. J Mol Biol (1996) 9.31
COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance. J Mol Biol (2003) 8.35
3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics (2003) 7.99
BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations. Nucleic Acids Res (2001) 6.67
BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark. Proteins (2005) 6.57
3DCoffee: combining protein sequences and structures within multiple sequence alignments. J Mol Biol (2004) 6.01
Optimal protein structure alignments by multiple linkage clustering: application to distantly related proteins. Protein Eng (1995) 5.55
Processing and analysis of CASP3 protein structure predictions. Proteins (1999) 4.95
APDB: a novel measure for benchmarking sequence alignment methods without reference alignments. Bioinformatics (2003) 4.88
M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res (2006) 4.53
Review: protein secondary structure prediction continues to rise. J Struct Biol (2001) 3.91
Dictionary of recurrent domains in protein structures. Proteins (1998) 3.40
PCMA: fast and accurate multiple sequence alignment based on profile consistency. Bioinformatics (2003) 3.23
SABmark--a benchmark for sequence alignment that covers the entire known fold space. Bioinformatics (2004) 3.11
Molecular recognition. Conformational analysis of limited proteolytic sites and serine proteinase protein inhibitors. J Mol Biol (1991) 3.04
Multiple sequence alignment. Curr Opin Struct Biol (2006) 2.93
Multiple sequence alignments. Curr Opin Struct Biol (2005) 2.05
HOMSTRAD: adding sequence information to structure-based alignments of homologous protein families. Bioinformatics (2001) 1.97
Prediction of CASP6 structures using automated Robetta protocols. Proteins (2005) 1.94
LiveBench-6: large-scale automated evaluation of protein structure prediction servers. Proteins (2003) 1.90
A reliable sequence alignment method based on probabilities of residue correspondences. Protein Eng (1995) 1.86
Searching for functional sites in protein structures. Curr Opin Chem Biol (2004) 1.84
CASP5 assessment of fold recognition target predictions. Proteins (2003) 1.73
Pcons5: combining consensus, structural evaluation and fold recognition scores. Bioinformatics (2005) 1.71
SPEM: improving multiple sequence alignment with sequence profiles and predicted secondary structures. Bioinformatics (2005) 1.52
Structure-derived substitution matrices for alignment of distantly related sequences. Protein Eng (2000) 1.39
Predicting reliable regions in protein sequence alignments. Bioinformatics (2002) 1.34
Pairwise sequence alignment below the twilight zone. J Mol Biol (2001) 1.32
Integrating protein secondary structure prediction and multiple sequence alignment. Curr Protein Pept Sci (2004) 1.23
Comparative modeling in CASP6 using consensus approach to template selection, sequence-structure alignment, and structure assessment. Proteins (2005) 1.20
Improved pairwise alignments of proteins in the Twilight Zone using local structure predictions. Bioinformatics (2005) 0.99
Combining evolutionary and structural information for local protein structure prediction. Proteins (2004) 0.90
Identical pentapeptides with different backbones. Nature (1985) 0.84
NdPASA: a novel pairwise protein sequence alignment algorithm that incorporates neighbor-dependent amino acid propensities. Proteins (2005) 0.83
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
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
Identification of the acyltransferase that octanoylates ghrelin, an appetite-stimulating peptide hormone. Cell (2008) 5.10
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
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
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
Ubiquitin-induced oligomerization of the RNA sensors RIG-I and MDA5 activates antiviral innate immune response. Immunity (2012) 3.07
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
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
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
C3PO, an endoribonuclease that promotes RNAi by facilitating RISC activation. Science (2009) 2.04
The conserved plant sterility gene HAP2 functions after attachment of fusogenic membranes in Chlamydomonas and Plasmodium gametes. Genes Dev (2008) 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
Detecting distant homology with Meta-BASIC. Nucleic Acids Res (2004) 1.86
Side-chain modeling with an optimized scoring function. Protein Sci (2002) 1.84
Sequence and structure classification of kinases. J Mol Biol (2002) 1.84
CASP9 target classification. Proteins (2011) 1.75
CASP5 assessment of fold recognition target predictions. Proteins (2003) 1.73
Crystal structure of human riboflavin kinase reveals a beta barrel fold and a novel active site arch. Structure (2003) 1.69
A minimal domain responsible for Munc13 activity. Nat Struct Mol Biol (2005) 1.68
Genetic variation in ANGPTL4 provides insights into protein processing and function. J Biol Chem (2009) 1.64
The HicAB cassette, a putative novel, RNA-targeting toxin-antitoxin system in archaea and bacteria. Bioinformatics (2006) 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
Kinetic and structural insights into the mechanism of AMPylation by VopS Fic domain. J Biol Chem (2010) 1.51
Reconstruction of ancestral protein sequences and its applications. BMC Evol Biol (2004) 1.48
Structural drift: a possible path to protein fold change. Bioinformatics (2004) 1.46
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
Prediction of functional specificity determinants from protein sequences using log-likelihood ratios. Bioinformatics (2005) 1.41
A comprehensive update of the sequence and structure classification of kinases. BMC Struct Biol (2005) 1.40
Analysis of CASP8 targets, predictions and assessment methods. Database (Oxford) (2009) 1.38
Structure of human nicotinamide/nicotinic acid mononucleotide adenylyltransferase. Basis for the dual substrate specificity and activation of the oncolytic agent tiazofurin. J Biol Chem (2002) 1.38
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
SelT, SelW, SelH, and Rdx12: genomics and molecular insights into the functions of selenoproteins of a novel thioredoxin-like family. Biochemistry (2007) 1.31
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
Site-2 protease regulated intramembrane proteolysis: sequence homologs suggest an ancient signaling cascade. Protein Sci (2005) 1.25
Practical lessons from protein structure prediction. Nucleic Acids Res (2005) 1.25
4SCOPmap: automated assignment of protein structures to evolutionary superfamilies. BMC Bioinformatics (2004) 1.25
Unusually rapid evolution of Neuroligin-4 in mice. Proc Natl Acad Sci U S A (2008) 1.25
Remote homology between Munc13 MUN domain and vesicle tethering complexes. J Mol Biol (2009) 1.24
Discrete-continuous duality of protein structure space. Curr Opin Struct Biol (2009) 1.24
Structural characterization of a human cytosolic NMN/NaMN adenylyltransferase and implication in human NAD biosynthesis. J Biol Chem (2003) 1.24
Protein domain of unknown function DUF1023 is an alpha/beta hydrolase. Proteins (2005) 1.23
PROMALS web server for accurate multiple protein sequence alignments. Nucleic Acids Res (2007) 1.20
Evolution of the regulators of G-protein signaling multigene family in mouse and human. Genomics (2002) 1.18
PROCAIN: protein profile comparison with assisting information. Nucleic Acids Res (2009) 1.17
COMPASS server for remote homology inference. Nucleic Acids Res (2007) 1.16
Crystal structures of E. coli nicotinate mononucleotide adenylyltransferase and its complex with deamido-NAD. Structure (2002) 1.15
Longin-like folds identified in CHiPS and DUF254 proteins: vesicle trafficking complexes conserved in eukaryotic evolution. Protein Sci (2006) 1.15
Sequence and structural analyses of nuclear export signals in the NESdb database. Mol Biol Cell (2012) 1.15
Beclin 2 functions in autophagy, degradation of G protein-coupled receptors, and metabolism. Cell (2013) 1.14
Searching for three-dimensional secondary structural patterns in proteins with ProSMoS. Bioinformatics (2007) 1.14
Concerted regulation of myofiber-specific gene expression and muscle performance by the transcriptional repressor Sox6. Proc Natl Acad Sci U S A (2011) 1.13
CREST--a large and diverse superfamily of putative transmembrane hydrolases. Biol Direct (2011) 1.12
PALSSE: a program to delineate linear secondary structural elements from protein structures. BMC Bioinformatics (2005) 1.12
Structurally analogous proteins do exist! Structure (2004) 1.12
Succination of Keap1 and activation of Nrf2-dependent antioxidant pathways in FH-deficient papillary renal cell carcinoma type 2. Cancer Cell (2011) 1.12
Double-stranded DNA bacteriophage prohead protease is homologous to herpesvirus protease. Protein Sci (2004) 1.10
Paramecium bursaria chlorella virus-1 encodes an unusual arginine decarboxylase that is a close homolog of eukaryotic ornithine decarboxylases. J Biol Chem (2004) 1.10
Discrimination between distant homologs and structural analogs: lessons from manually constructed, reliable data sets. J Mol Biol (2008) 1.08
Crystal structure of Haemophilus influenzae NadR protein. A bifunctional enzyme endowed with NMN adenyltransferase and ribosylnicotinimide kinase activities. J Biol Chem (2002) 1.07
MESSA: MEta-Server for protein Sequence Analysis. BMC Biol (2012) 1.06
A comprehensive system for evaluation of remote sequence similarity detection. BMC Bioinformatics (2007) 1.05
Structural classification of thioredoxin-like fold proteins. Proteins (2005) 1.05
Comparative genomics in Chlamydomonas and Plasmodium identifies an ancient nuclear envelope protein family essential for sexual reproduction in protists, fungi, plants, and vertebrates. Genes Dev (2013) 1.04
Structural analysis and functional implications of the negative mTORC1 regulator REDD1. Biochemistry (2010) 1.04
Structural classification of small, disulfide-rich protein domains. J Mol Biol (2006) 1.03
Bifunctional NMN adenylyltransferase/ADP-ribose pyrophosphatase: structure and function in bacterial NAD metabolism. Structure (2008) 1.03
The human Ago2 MC region does not contain an eIF4E-like mRNA cap binding motif. Biol Direct (2009) 1.02
Effective scoring function for protein sequence design. Proteins (2004) 1.01
CASP5 target classification. Proteins (2003) 1.01
Gaps in structurally similar proteins: towards improvement of multiple sequence alignment. Proteins (2004) 1.00
Eukaryotic domain of unknown function DUF738 belongs to Gcn5-related N-acetyltransferase superfamily. Cell Cycle (2006) 0.99
Peptidase family U34 belongs to the superfamily of N-terminal nucleophile hydrolases. Protein Sci (2003) 0.99
Quality of alignment comparison by COMPASS improves with inclusion of diverse confident homologs. Bioinformatics (2004) 0.99
Using protein design for homology detection and active site searches. Proc Natl Acad Sci U S A (2003) 0.99
Expansion of type II CAAX proteases reveals evolutionary origin of γ-secretase subunit APH-1. J Mol Biol (2011) 0.97
Three-dimensional structure of the rSly1 N-terminal domain reveals a conformational change induced by binding to syntaxin 5. J Mol Biol (2004) 0.96
MALISAM: a database of structurally analogous motifs in proteins. Nucleic Acids Res (2007) 0.96