Published in Genome Biol on February 02, 2009
Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions. Nucleic Acids Res (2013) 1.83
Plant-mPLoc: a top-down strategy to augment the power for predicting plant protein subcellular localization. PLoS One (2010) 1.67
iLoc-Euk: a multi-label classifier for predicting the subcellular localization of singleplex and multiplex eukaryotic proteins. PLoS One (2011) 1.59
A new method for predicting the subcellular localization of eukaryotic proteins with both single and multiple sites: Euk-mPLoc 2.0. PLoS One (2010) 1.44
Divergent evolution in enolase superfamily: strategies for assigning functions. J Biol Chem (2011) 1.40
Sma3s: a three-step modular annotator for large sequence datasets. DNA Res (2014) 1.23
Combining heterogeneous data sources for accurate functional annotation of proteins. BMC Bioinformatics (2013) 1.15
SwissTargetPrediction: a web server for target prediction of bioactive small molecules. Nucleic Acids Res (2014) 1.14
ProtoNet 6.0: organizing 10 million protein sequences in a compact hierarchical family tree. Nucleic Acids Res (2011) 1.07
A multi-label classifier for predicting the subcellular localization of gram-negative bacterial proteins with both single and multiple sites. PLoS One (2011) 1.03
A multi-label predictor for identifying the subcellular locations of singleplex and multiplex eukaryotic proteins. PLoS One (2012) 1.01
FINDSITE-metal: integrating evolutionary information and machine learning for structure-based metal-binding site prediction at the proteome level. Proteins (2010) 1.00
Annotations for all by all - the BioSapiens network. Genome Biol (2009) 1.00
Quantitative comparison of catalytic mechanisms and overall reactions in convergently evolved enzymes: implications for classification of enzyme function. PLoS Comput Biol (2010) 1.00
Systematic structural characterization of metabolites in Arabidopsis via candidate substrate-product pair networks. Plant Cell (2014) 1.00
Exploring Biomolecular Literature with EVEX: Connecting Genes through Events, Homology, and Indirect Associations. Adv Bioinformatics (2012) 0.98
Maps of protein structure space reveal a fundamental relationship between protein structure and function. Proc Natl Acad Sci U S A (2011) 0.97
Structural annotation of Mycobacterium tuberculosis proteome. PLoS One (2011) 0.97
Phyletic profiling with cliques of orthologs is enhanced by signatures of paralogy relationships. PLoS Comput Biol (2013) 0.95
Compressive genomics for protein databases. Bioinformatics (2013) 0.94
Ligand-binding site prediction of proteins based on known fragment-fragment interactions. Bioinformatics (2010) 0.91
PANDORA: analysis of protein and peptide sets through the hierarchical integration of annotations. Nucleic Acids Res (2010) 0.89
Functional annotation of conserved hypothetical proteins from Haemophilus influenzae Rd KW20. PLoS One (2013) 0.88
Benefits of structural genomics for drug discovery research. Infect Disord Drug Targets (2009) 0.87
Prediction and experimental validation of enzyme substrate specificity in protein structures. Proc Natl Acad Sci U S A (2013) 0.87
A structural systems biology approach for quantifying the systemic consequences of missense mutations in proteins. PLoS Comput Biol (2012) 0.87
MemPype: a pipeline for the annotation of eukaryotic membrane proteins. Nucleic Acids Res (2011) 0.87
eFindSite: improved prediction of ligand binding sites in protein models using meta-threading, machine learning and auxiliary ligands. J Comput Aided Mol Des (2013) 0.86
Computational tools for comparative phenomics: the role and promise of ontologies. Mamm Genome (2012) 0.85
Integration of molecular network data reconstructs Gene Ontology. Bioinformatics (2014) 0.85
Hierarchical ensemble methods for protein function prediction. ISRN Bioinform (2014) 0.84
Computational prediction of protein interfaces: A review of data driven methods. FEBS Lett (2015) 0.83
Charged residues at protein interaction interfaces: unexpected conservation and orchestrated divergence. Protein Sci (2011) 0.83
Composite structural motifs of binding sites for delineating biological functions of proteins. PLoS One (2012) 0.81
Combining modularity, conservation, and interactions of proteins significantly increases precision and coverage of protein function prediction. BMC Genomics (2010) 0.81
Biochemical functional predictions for protein structures of unknown or uncertain function. Comput Struct Biotechnol J (2015) 0.81
Determining microbial products and identifying molecular targets in the human microbiome. Cell Metab (2014) 0.80
How to inherit statistically validated annotation within BAR+ protein clusters. BMC Bioinformatics (2013) 0.80
Predictive sequence analysis of the Candidatus Liberibacter asiaticus proteome. PLoS One (2012) 0.80
Protein function annotation with Structurally Aligned Local Sites of Activity (SALSAs). BMC Bioinformatics (2013) 0.79
Short toxin-like proteins attack the defense line of innate immunity. Toxins (Basel) (2013) 0.79
INGA: protein function prediction combining interaction networks, domain assignments and sequence similarity. Nucleic Acids Res (2015) 0.79
Accuracy of functional surfaces on comparatively modeled protein structures. J Struct Funct Genomics (2011) 0.78
Metric learning for enzyme active-site search. Bioinformatics (2010) 0.78
High speed BLASTN: an accelerated MegaBLAST search tool. Nucleic Acids Res (2015) 0.78
The utility of geometrical and chemical restraint information extracted from predicted ligand-binding sites in protein structure refinement. J Struct Biol (2010) 0.78
Ballast: a ball-based algorithm for structural motifs. J Comput Biol (2013) 0.77
SUS-BAR: a database of pig proteins with statistically validated structural and functional annotation. Database (Oxford) (2013) 0.77
A property-based analysis of human transcription factors. BMC Res Notes (2015) 0.77
Protein surface characterization using an invariant descriptor. Int J Biomed Imaging (2011) 0.76
Towards New Drug Targets? Function Prediction of Putative Proteins of Neisseria meningitidis MC58 and Their Virulence Characterization. OMICS (2015) 0.76
Discriminative structural approaches for enzyme active-site prediction. BMC Bioinformatics (2011) 0.76
ProtoBug: functional families from the complete proteomes of insects. Database (Oxford) (2015) 0.76
Entropy-driven partitioning of the hierarchical protein space. Bioinformatics (2014) 0.76
Conformational diversity analysis reveals three functional mechanisms in proteins. PLoS Comput Biol (2017) 0.76
Computational approaches for classification and prediction of P-type ATPase substrate specificity in Arabidopsis. Physiol Mol Biol Plants (2016) 0.75
Structure-based functional annotation of hypothetical proteins from Candida dubliniensis: a quest for potential drug targets. 3 Biotech (2014) 0.75
Exploring the "dark matter" of a mammalian proteome by protein structure and function modeling. Proteome Sci (2013) 0.75
High-Resolution Identification of Specificity Determining Positions in the LacI Protein Family Using Ensembles of Sub-Sampled Alignments. PLoS One (2016) 0.75
Improvement in Protein Domain Identification Is Reached by Breaking Consensus, with the Agreement of Many Profiles and Domain Co-occurrence. PLoS Comput Biol (2016) 0.75
PROSNET: INTEGRATING HOMOLOGY WITH MOLECULAR NETWORKS FOR PROTEIN FUNCTION PREDICTION. Pac Symp Biocomput (2016) 0.75
Trends in genome dynamics among major orders of insects revealed through variations in protein families. BMC Genomics (2015) 0.75
A novel index of protein-protein interface propensity improves interface residue recognition. BMC Syst Biol (2016) 0.75
Interspecies gene function prediction using semantic similarity. BMC Syst Biol (2016) 0.75
Developing eThread pipeline using SAGA-pilot abstraction for large-scale structural bioinformatics. Biomed Res Int (2014) 0.75
Ergot alkaloids: From witchcraft till in silico analysis. Multi-receptor analysis of ergotamine metabolites. Toxicol Rep (2015) 0.75
To be disordered or not to be disordered: is that still a question for proteins in the cell? Cell Mol Life Sci (2017) 0.75
Functional Association Prediction by Community Profiling. Methods (2017) 0.75
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31
Basic local alignment search tool. J Mol Biol (1990) 659.07
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet (2000) 336.52
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
The COG database: an updated version includes eukaryotes. BMC Bioinformatics (2003) 60.98
Protein structure comparison by alignment of distance matrices. J Mol Biol (1993) 34.74
Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr D Biol Crystallogr (2004) 31.52
The Pfam protein families database. Nucleic Acids Res (2007) 30.53
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
Comparative assessment of large-scale data sets of protein-protein interactions. Nature (2002) 24.25
The Database of Interacting Proteins: 2004 update. Nucleic Acids Res (2004) 23.67
PIRSF: family classification system at the Protein Information Resource. Nucleic Acids Res (2004) 19.62
SMART 5: domains in the context of genomes and networks. Nucleic Acids Res (2006) 17.13
The relation between the divergence of sequence and structure in proteins. EMBO J (1986) 16.66
The universal protein resource (UniProt). Nucleic Acids Res (2007) 16.33
New developments in the InterPro database. Nucleic Acids Res (2007) 12.49
CDD: a conserved domain database for interactive domain family analysis. Nucleic Acids Res (2006) 11.41
ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res (2005) 10.60
An evolutionary trace method defines binding surfaces common to protein families. J Mol Biol (1996) 9.31
CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. Nucleic Acids Res (2006) 9.19
The ProDom database of protein domain families: more emphasis on 3D. Nucleic Acids Res (2005) 7.66
The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data. Nucleic Acids Res (2004) 7.21
iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions. Bioinformatics (2004) 7.02
Protein structure alignment. J Mol Biol (1989) 6.90
SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. J Mol Graph (1995) 6.64
The 20 years of PROSITE. Nucleic Acids Res (2007) 6.06
ProFunc: a server for predicting protein function from 3D structure. Nucleic Acids Res (2005) 5.79
Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics (2003) 5.46
Threading a database of protein cores. Proteins (1995) 5.38
Integrating sequence and structural biology with DAS. BMC Bioinformatics (2007) 5.12
Domain combinations in archaeal, eubacterial and eukaryotic proteomes. J Mol Biol (2001) 4.69
The MIPS mammalian protein-protein interaction database. Bioinformatics (2004) 4.66
The SUPERFAMILY database in 2007: families and functions. Nucleic Acids Res (2006) 4.27
Protein clefts in molecular recognition and function. Protein Sci (1996) 4.20
Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures. J Mol Biol (2005) 4.02
A large-scale experiment to assess protein structure prediction methods. Proteins (1995) 3.51
How complete are current yeast and human protein-interaction networks? Genome Biol (2006) 3.50
Recognition of spatial motifs in protein structures. J Mol Biol (1999) 2.94
Inference of protein function from protein structure. Structure (2005) 2.90
The predictive power of the CluSTr database. Bioinformatics (2005) 2.85
Gene3D: comprehensive structural and functional annotation of genomes. Nucleic Acids Res (2007) 2.75
Ten thousand interactions for the molecular biologist. Nat Biotechnol (2004) 2.30
3did: interacting protein domains of known three-dimensional structure. Nucleic Acids Res (2005) 2.18
Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures. Nucleic Acids Res (2003) 2.14
Integrating biological data through the genome. Hum Mol Genet (2006) 2.12
Progress from CASP6 to CASP7. Proteins (2007) 2.04
Inferring protein domain interactions from databases of interacting proteins. Genome Biol (2005) 1.97
ProtoNet 4.0: a hierarchical classification of one million protein sequences. Nucleic Acids Res (2005) 1.74
The ConSurf-HSSP database: the mapping of evolutionary conservation among homologs onto PDB structures. Proteins (2005) 1.72
Co-evolutionary analysis of domains in interacting proteins reveals insights into domain-domain interactions mediating protein-protein interactions. J Mol Biol (2006) 1.60
Automated discovery of 3D motifs for protein function annotation. Bioinformatics (2006) 1.60
DOMINE: a database of protein domain interactions. Nucleic Acids Res (2007) 1.54
Characterizing the microenvironment surrounding protein sites. Protein Sci (1995) 1.54
JAFA: a protein function annotation meta-server. Nucleic Acids Res (2006) 1.52
CATHEDRAL: a fast and effective algorithm to predict folds and domain boundaries from multidomain protein structures. PLoS Comput Biol (2007) 1.51
PDBSiteScan: a program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins. Nucleic Acids Res (2004) 1.41
Prediction of enzyme function based on 3D templates of evolutionarily important amino acids. BMC Bioinformatics (2008) 1.41
PDBSite: a database of the 3D structure of protein functional sites. Nucleic Acids Res (2005) 1.41
Assessment of predictions submitted for the CASP7 domain prediction category. Proteins (2007) 1.39
Functional sites in protein families uncovered via an objective and automated graph theoretic approach. J Mol Biol (2003) 1.37
A domain interaction map based on phylogenetic profiling. J Mol Biol (2004) 1.35
Effective function annotation through catalytic residue conservation. Proc Natl Acad Sci U S A (2005) 1.28
Large scale hierarchical clustering of protein sequences. BMC Bioinformatics (2005) 1.28
Towards fully automated structure-based function prediction in structural genomics: a case study. J Mol Biol (2007) 1.26
De-orphaning the structural proteome through reciprocal comparison of evolutionarily important structural features. PLoS One (2008) 1.20
pvSOAR: detecting similar surface patterns of pocket and void surfaces of amino acid residues on proteins. Nucleic Acids Res (2004) 1.20
SiteEngines: recognition and comparison of binding sites and protein-protein interfaces. Nucleic Acids Res (2005) 1.20
Structural genomics: keeping up with expanding knowledge of the protein universe. Curr Opin Struct Biol (2007) 1.17
The prediction of protein function at CASP6. Proteins (2005) 1.08
Methods of remote homology detection can be combined to increase coverage by 10% in the midnight zone. Bioinformatics (2007) 1.06
Prediction of deleterious functional effects of amino acid mutations using a library of structure-based function descriptors. Proteins (2003) 0.91
SURF'S UP! - protein classification by surface comparisons. J Biosci (2007) 0.90
The role of molecular modelling in biomedical research. FEBS Lett (2006) 0.89
Revisiting the prediction of protein function at CASP6. FEBS J (2006) 0.88
DIMA 2.0--predicted and known domain interactions. Nucleic Acids Res (2007) 0.87
EVEREST: a collection of evolutionary conserved protein domains. Nucleic Acids Res (2006) 0.84
InterPro: the integrative protein signature database. Nucleic Acids Res (2008) 25.07
InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res (2011) 13.45
New developments in the InterPro database. Nucleic Acids Res (2007) 12.49
Prepublication data sharing. Nature (2009) 12.24
The genome sequence of the filamentous fungus Neurospora crassa. Nature (2003) 11.39
A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell (2011) 9.24
The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis. Nucleic Acids Res (2005) 5.59
The European Bioinformatics Institute's data resources: towards systems biology. Nucleic Acids Res (2005) 4.90
Proteome-wide analysis of chaperonin-dependent protein folding in Escherichia coli. Cell (2005) 4.78
The MIPS mammalian protein-protein interaction database. Bioinformatics (2004) 4.66
A large-scale evaluation of computational protein function prediction. Nat Methods (2013) 4.61
Deciphering the evolution and metabolism of an anammox bacterium from a community genome. Nature (2006) 4.06
Bioinformatics training: a review of challenges, actions and support requirements. Brief Bioinform (2010) 4.02
The implications of alternative splicing in the ENCODE protein complement. Proc Natl Acad Sci U S A (2007) 3.93
The European dimension for the mouse genome mutagenesis program. Nat Genet (2004) 3.84
Protein abundance profiling of the Escherichia coli cytosol. BMC Genomics (2008) 3.78
Critical assessment of methods of protein structure prediction (CASP)--round x. Proteins (2013) 3.78
STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins. Nucleic Acids Res (2004) 3.71
Illuminating the evolutionary history of chlamydiae. Science (2004) 3.39
Predicting protein function from sequence and structure. Nat Rev Mol Cell Biol (2007) 3.37
Critical assessment of methods of protein structure prediction-Round VII. Proteins (2007) 3.23
Extending CATH: increasing coverage of the protein structure universe and linking structure with function. Nucleic Acids Res (2010) 2.93
The CATH classification revisited--architectures reviewed and new ways to characterize structural divergence in superfamilies. Nucleic Acids Res (2008) 2.92
Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers. Brief Bioinform (2011) 2.79
Gene3D: comprehensive structural and functional annotation of genomes. Nucleic Acids Res (2007) 2.75
Construction, visualisation, and clustering of transcription networks from microarray expression data. PLoS Comput Biol (2007) 2.73
Evaluation of annotation strategies using an entire genome sequence. Bioinformatics (2003) 2.66
Quantifying the similarities within fold space. J Mol Biol (2002) 2.65
Critical assessment of methods of protein structure prediction (CASP)--round 6. Proteins (2005) 2.58
The European Bioinformatics Institute's data resources. Nucleic Acids Res (2009) 2.55
Gene3D: merging structure and function for a Thousand genomes. Nucleic Acids Res (2009) 2.34
Outcome of a workshop on archiving structural models of biological macromolecules. Structure (2006) 2.32
Critical assessment of methods of protein structure prediction - Round VIII. Proteins (2009) 2.25
Assessment of predictions in the model quality assessment category. Proteins (2007) 2.25
Ocean currents help explain population genetic structure. Proc Biol Sci (2010) 2.16
Structural diversity of domain superfamilies in the CATH database. J Mol Biol (2006) 2.10
Critical assessment of methods of protein structure prediction (CASP)--round IX. Proteins (2011) 2.08
Transient protein-protein interactions: structural, functional, and network properties. Structure (2010) 2.07
Remarkably similar antigen receptors among a subset of patients with chronic lymphocytic leukemia. J Clin Invest (2004) 1.94
The PMDB Protein Model Database. Nucleic Acids Res (2006) 1.94
Identification of 42 possible cytochrome C genes in the Shewanella oneidensis genome and characterization of six soluble cytochromes. OMICS (2004) 1.92
PSI-2: structural genomics to cover protein domain family space. Structure (2009) 1.92
Visualizing cold spots: TRPM8-expressing sensory neurons and their projections. J Neurosci (2008) 1.92
Structural and chemical profiling of the human cytosolic sulfotransferases. PLoS Biol (2007) 1.90
Binding of the hepatitis C virus E2 glycoprotein to CD81 is strain specific and is modulated by a complex interplay between hypervariable regions 1 and 2. J Virol (2003) 1.89
The PEDANT genome database in 2005. Nucleic Acids Res (2005) 1.88
ProtoNet: hierarchical classification of the protein space. Nucleic Acids Res (2003) 1.88
Ten simple rules for developing a short bioinformatics training course. PLoS Comput Biol (2011) 1.84
PEDANT covers all complete RefSeq genomes. Nucleic Acids Res (2008) 1.78
ProtoNet 4.0: a hierarchical classification of one million protein sequences. Nucleic Acids Res (2005) 1.74
Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space. Bioinformatics (2008) 1.72
Asthma in General Practice. J Coll Gen Pract Res Newsl (1958) 1.66
Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis. Nucleic Acids Res (2011) 1.65
Novel unsupervised feature filtering of biological data. Bioinformatics (2006) 1.64
Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains. Nucleic Acids Res (2012) 1.63
The CATH hierarchy revisited-structural divergence in domain superfamilies and the continuity of fold space. Structure (2009) 1.62
Mining sequence annotation databanks for association patterns. Bioinformatics (2005) 1.62
Assessment of the assessment: evaluation of the model quality estimates in CASP10. Proteins (2013) 1.60
PIGS: automatic prediction of antibody structures. Bioinformatics (2008) 1.59
Evaluating the usefulness of protein structure models for molecular replacement. Bioinformatics (2005) 1.58
The CCPN project: an interim report on a data model for the NMR community. Nat Struct Biol (2002) 1.58
Conformational changes observed in enzyme crystal structures upon substrate binding. J Mol Biol (2004) 1.56
Conservation of protein-protein interactions - lessons from ascomycota. Trends Genet (2004) 1.55
Identification and distribution of protein families in 120 completed genomes using Gene3D. Proteins (2005) 1.54
Structural genomics is the largest contributor of novel structural leverage. J Struct Funct Genomics (2009) 1.52
GeMMA: functional subfamily classification within superfamilies of predicted protein structural domains. Nucleic Acids Res (2009) 1.50
Toward more transparent and reproducible omics studies through a common metadata checklist and data publications. OMICS (2014) 1.49
Viral adaptation to host: a proteome-based analysis of codon usage and amino acid preferences. Mol Syst Biol (2009) 1.48
Consensus clustering and functional interpretation of gene-expression data. Genome Biol (2004) 1.48
Evolution of bacterial and archaeal multicomponent monooxygenases. J Mol Evol (2003) 1.46
Evaluation of disorder predictions in CASP9. Proteins (2011) 1.46
Recognizing the fold of a protein structure. Bioinformatics (2003) 1.45
Minimum information about a bioactive entity (MIABE). Nat Rev Drug Discov (2011) 1.44
Evaluation of CASP8 model quality predictions. Proteins (2009) 1.44
TargetSpy: a supervised machine learning approach for microRNA target prediction. BMC Bioinformatics (2010) 1.43
Ictal vomiting in association with left temporal lobe seizures in a left hemisphere language-dominant patient. Epilepsia (2002) 1.43
Evaluation of model quality predictions in CASP9. Proteins (2011) 1.43
Diapause-associated metabolic traits reiterated in long-lived daf-2 mutants in the nematode Caenorhabditis elegans. Mech Ageing Dev (2006) 1.41
Progress towards mapping the universe of protein folds. Genome Biol (2004) 1.41
The double helix 50 years later: implications for psychiatry. Am J Psychiatry (2003) 1.39
Bring climate change back from the future. Nature (2016) 1.38
Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites. Bioinformatics (2008) 1.36
A domain interaction map based on phylogenetic profiling. J Mol Biol (2004) 1.35
Pitfalls of supervised feature selection. Bioinformatics (2009) 1.33
The Negatome database: a reference set of non-interacting protein pairs. Nucleic Acids Res (2009) 1.32
Unsupervised feature selection under perturbations: meeting the challenges of biological data. Bioinformatics (2007) 1.32
Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae. Nucleic Acids Res (2004) 1.31
PROMPT: a protein mapping and comparison tool. BMC Bioinformatics (2006) 1.31
PANDORA: keyword-based analysis of protein sets by integration of annotation sources. Nucleic Acids Res (2003) 1.31
Will my protein crystallize? A sequence-based predictor. Proteins (2006) 1.30