Published in Bioinformatics on April 05, 2010
Efficient large-scale protein sequence comparison and gene matching to identify orthologs and co-orthologs. Nucleic Acids Res (2011) 0.86
Amplitude spectrum distance: measuring the global shape divergence of protein fragments. BMC Bioinformatics (2015) 0.75
The Protein Data Bank. Nucleic Acids Res (2000) 187.10
SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol (1995) 74.88
CATH--a hierarchic classification of protein domain structures. Structure (1997) 29.95
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng (1998) 28.09
DaliLite workbench for protein structure comparison. Bioinformatics (2000) 10.53
The ASTRAL Compendium in 2004. Nucleic Acids Res (2004) 10.03
Structure comparison and structure patterns. J Comput Biol (2000) 5.73
Threading a database of protein cores. Proteins (1995) 5.38
Advances and pitfalls of protein structural alignment. Curr Opin Struct Biol (2009) 4.17
Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures. J Mol Biol (2005) 4.02
Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations. Proc Natl Acad Sci U S A (2003) 3.67
Protein folding by restrained energy minimization and molecular dynamics. J Mol Biol (1983) 2.51
A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3. Nucleic Acids Res (2001) 2.32
Automatic classification of protein structure by using Gauss integrals. Proc Natl Acad Sci U S A (2002) 2.03
Local feature frequency profile: a method to measure structural similarity in proteins. Proc Natl Acad Sci U S A (2004) 2.03
Partitioning protein structures into domains: why is it so difficult? J Mol Biol (2006) 1.51
Recognizing the fold of a protein structure. Bioinformatics (2003) 1.45
The refined crystal structure of an eel pout type III antifreeze protein RD1 at 0.62-A resolution reveals structural microheterogeneity of protein and solvation. Biophys J (2003) 1.36
Multiple structural alignment by secondary structures: algorithm and applications. Protein Sci (2003) 1.32
Building native protein conformation from highly approximate backbone torsion angles. Proc Natl Acad Sci U S A (2005) 1.28
Is protein classification necessary? Toward alternative approaches to function annotation. Curr Opin Struct Biol (2009) 1.23
Protein folding and the organization of the protein topology universe. Trends Biochem Sci (2005) 1.19
Vorolign--fast structural alignment using Voronoi contacts. Bioinformatics (2007) 1.14
Analysis of topological and nontopological structural similarities in the PDB: new examples with old structures. Proteins (1996) 1.14
Comparison of spatial arrangements of secondary structural elements in proteins. Protein Eng (1995) 1.10
SABERTOOTH: protein structural alignment based on a vectorial structure representation. BMC Bioinformatics (2007) 1.07
Efficient recognition of folds in protein 3D structures by the improved PRIDE algorithm. Bioinformatics (2005) 1.02
Rapid detection of similarity in protein structure and function through contact metric distances. Nucleic Acids Res (2006) 1.01
An algorithm for finding maximal common subtopologies in a set of protein structures. J Comput Biol (1996) 1.01
Secondary structure spatial conformation footprint: a novel method for fast protein structure comparison and classification. BMC Struct Biol (2006) 1.00
3-D lookup: fast protein structure database searches at 90% reliability. Proc Int Conf Intell Syst Mol Biol (1995) 1.00
Protein structure mining using a structural alphabet. Proteins (2008) 0.98
What are the baselines for protein fold recognition? Bioinformatics (2001) 0.98
Proteins and their shape strings. An exemplary computer representation of protein structure. IEEE Eng Med Biol Mag (2005) 0.87
Representing and comparing protein structures as paths in three-dimensional space. BMC Bioinformatics (2006) 0.83
Structure-based identification and clustering of protein families and superfamilies. J Comput Aided Mol Des (1994) 0.83
Towards index-based similarity search for protein structure databases. Proc IEEE Comput Soc Bioinform Conf (2003) 0.79
Describing and comparing protein structures using shape strings. Curr Protein Pept Sci (2008) 0.78
WebLogo: a sequence logo generator. Genome Res (2004) 59.58
The Bioperl toolkit: Perl modules for the life sciences. Genome Res (2002) 58.63
SCOP database in 2002: refinements accommodate structural genomics. Nucleic Acids Res (2002) 18.11
SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Res (2004) 15.21
The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol (2007) 13.99
Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res (2007) 13.44
Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (2010) 12.39
The developmental transcriptome of Drosophila melanogaster. Nature (2010) 11.85
Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans. Proc Natl Acad Sci U S A (2002) 10.28
The ASTRAL Compendium in 2004. Nucleic Acids Res (2004) 10.03
Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Res (2010) 9.08
Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements. Nature (2007) 7.12
The impact of structural genomics: expectations and outcomes. Science (2006) 5.30
A large-scale evaluation of computational protein function prediction. Nat Methods (2013) 4.61
ASTRAL compendium enhancements. Nucleic Acids Res (2002) 4.43
The RNA Ontology Consortium: an open invitation to the RNA community. RNA (2006) 3.60
Protein molecular function prediction by Bayesian phylogenomics. PLoS Comput Biol (2005) 3.14
Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations. Protein Sci (2002) 3.01
The evolving roles of alternative splicing. Curr Opin Struct Biol (2004) 2.99
SCOR: a Structural Classification of RNA database. Nucleic Acids Res (2002) 2.79
Conservation of an RNA regulatory map between Drosophila and mammals. Genome Res (2010) 2.43
An unappreciated role for RNA surveillance. Genome Biol (2004) 2.28
Planning the human variome project: the Spain report. Hum Mutat (2009) 2.22
SCOPe: Structural Classification of Proteins--extended, integrating SCOP and ASTRAL data and classification of new structures. Nucleic Acids Res (2013) 2.22
Outcome of a workshop on applications of protein models in biomedical research. Structure (2009) 2.05
Global analysis of positive and negative pre-mRNA splicing regulators in Drosophila. Genes Dev (2005) 2.03
SCOR: Structural Classification of RNA, version 2.0. Nucleic Acids Res (2004) 2.02
Taking geometry to its edge: fast unbound rigid (and hinge-bent) docking. Proteins (2003) 1.95
RNA structural motifs: building blocks of a modular biomolecule. Q Rev Biophys (2006) 1.88
Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences. ISME J (2012) 1.86
Widespread predicted nonsense-mediated mRNA decay of alternatively-spliced transcripts of human normal and disease genes. Bioinformatics (2003) 1.84
Statistical evaluation of pairwise protein sequence comparison with the Bayesian bootstrap. Bioinformatics (2005) 1.77
The coupling of alternative splicing and nonsense-mediated mRNA decay. Adv Exp Med Biol (2007) 1.77
Sulfotransferases and sulfatases in mycobacteria. Chem Biol (2002) 1.74
Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approaches. Proteins (2005) 1.71
MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions. Nucleic Acids Res (2008) 1.52
Genome-wide analysis of alternative pre-mRNA splicing and RNA-binding specificities of the Drosophila hnRNP A/B family members. Mol Cell (2009) 1.52
Genome-wide identification of alternative splice forms down-regulated by nonsense-mediated mRNA decay in Drosophila. PLoS Genet (2009) 1.46
Three-dimensional motifs from the SCOR, structural classification of RNA database: extruded strands, base triples, tetraloops and U-turns. Nucleic Acids Res (2004) 1.43
MeRNA: a database of metal ion binding sites in RNA structures. Nucleic Acids Res (2006) 1.24
The COMBREX project: design, methodology, and initial results. PLoS Biol (2013) 1.24
Spatial chemical conservation of hot spot interactions in protein-protein complexes. BMC Biol (2007) 1.22
Genome-wide analysis reveals an unexpected function for the Drosophila splicing factor U2AF50 in the nuclear export of intronless mRNAs. Mol Cell (2004) 1.21
Automated multi-model reconstruction from single-particle electron microscopy data. J Struct Biol (2010) 1.18
From structure to function: methods and applications. Curr Protein Pept Sci (2005) 1.16
Structural genomics of minimal organisms and protein fold space. J Struct Funct Genomics (2005) 1.16
A method for the alignment of heterogeneous macromolecules from electron microscopy. J Struct Biol (2008) 1.16
EMatch: discovery of high resolution structural homologues of protein domains in intermediate resolution cryo-EM maps. IEEE/ACM Trans Comput Biol Bioinform (2007) 1.12
Genome-scale phylogenetic function annotation of large and diverse protein families. Genome Res (2011) 1.10
An alternative model of amino acid replacement. Bioinformatics (2004) 1.10
A generalized affine gap model significantly improves protein sequence alignment accuracy. Proteins (2005) 1.09
Newborn screening for SCID identifies patients with ataxia telangiectasia. J Clin Immunol (2012) 1.05
Protein secondary structure: entropy, correlations and prediction. Bioinformatics (2004) 1.04
Prediction of interacting single-stranded RNA bases by protein-binding patterns. J Mol Biol (2008) 1.04
Target selection and deselection at the Berkeley Structural Genomics Center. Proteins (2006) 0.98
Structural studies of the Nudix hydrolase DR1025 from Deinococcus radiodurans and its ligand complexes. J Mol Biol (2004) 0.93
Measurements of protein sequence-structure correlations. Proteins (2004) 0.90
Pairwise alignment incorporating dipeptide covariation. Bioinformatics (2005) 0.89
Survey of large protein complexes in D. vulgaris reveals great structural diversity. Proc Natl Acad Sci U S A (2009) 0.86
Association of gut microbiota with post-operative clinical course in Crohn's disease. BMC Gastroenterol (2013) 0.83
Nijmegen breakage syndrome detected by newborn screening for T cell receptor excision circles (TRECs). J Clin Immunol (2015) 0.82
Combined immunodeficiency due to MALT1 mutations, treated by hematopoietic cell transplantation. J Clin Immunol (2015) 0.82
Personalized medicine: from genotypes, molecular phenotypes and the quantified self, towards improved medicine. Pac Symp Biocomput (2015) 0.82
Phylogenetic molecular function annotation. J Phys Conf Ser (2009) 0.81
High-throughput isolation and characterization of untagged membrane protein complexes: outer membrane complexes of Desulfovibrio vulgaris. J Proteome Res (2012) 0.80
Structural genomics and structural biology: compare and contrast. Genome Biol (2004) 0.79
An SF1 affinity model to identify branch point sequences in human introns. Nucleic Acids Res (2010) 0.79
Molecular function prediction for a family exhibiting evolutionary tendencies toward substrate specificity swapping: recurrence of tyrosine aminotransferase activity in the Iα subfamily. Proteins (2013) 0.78
PRECISION MEDICINE: DATA AND DISCOVERY FOR IMPROVED HEALTH AND THERAPY. Pac Symp Biocomput (2016) 0.78
A continuous fluorescence assay for the characterization of Nudix hydrolases. Anal Biochem (2013) 0.77
ANDY: a general, fault-tolerant tool for database searching on computer clusters. Bioinformatics (2006) 0.76
Personalized medicine: from genotypes and molecular phenotypes towards therapy- session introduction. Pac Symp Biocomput (2014) 0.75
A novel plant enzyme with dual activity: an atypical Nudix hydrolase and a dipeptidyl peptidase III. Biol Chem (2017) 0.75
The future of genome-based medicine. Pac Symp Biocomput (2013) 0.75
REGULATORY RNA. Pac Symp Biocomput (2016) 0.75
PRECISION MEDICINE: FROM DIPLOTYPES TO DISPARITIES TOWARDS IMPROVED HEALTH AND THERAPIES. Pac Symp Biocomput (2018) 0.75
PRECISION MEDICINE: DATA AND DISCOVERY FOR IMPROVED HEALTH AND THERAPY. Pac Symp Biocomput (2016) 0.75
PLoS Computational Biology: a new community journal. PLoS Comput Biol (2005) 0.75
Developing computational biology. PLoS Comput Biol (2007) 0.75
Optimal and fast rotational alignment of volumes with missing data in Fourier space. J Struct Biol (2013) 0.75