Published in Nucleic Acids Res on January 01, 2005
HMMER web server: interactive sequence similarity searching. Nucleic Acids Res (2011) 13.00
Ongoing and future developments at the Universal Protein Resource. Nucleic Acids Res (2010) 11.32
Remediation of the protein data bank archive. Nucleic Acids Res (2007) 4.89
Predicting active site residue annotations in the Pfam database. BMC Bioinformatics (2007) 3.95
SOAP-based services provided by the European Bioinformatics Institute. Nucleic Acids Res (2005) 3.93
PDBe: Protein Data Bank in Europe. Nucleic Acids Res (2009) 3.48
PDBe: Protein Data Bank in Europe. Nucleic Acids Res (2011) 3.03
The SWISS-MODEL Repository: new features and functionalities. Nucleic Acids Res (2006) 3.00
BioJava: an open-source framework for bioinformatics in 2012. Bioinformatics (2012) 2.94
Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking. J Med Chem (2012) 2.86
The Protein Model Portal--a comprehensive resource for protein structure and model information. Database (Oxford) (2013) 2.76
COFACTOR: an accurate comparative algorithm for structure-based protein function annotation. Nucleic Acids Res (2012) 2.75
SIFTS: Structure Integration with Function, Taxonomy and Sequences resource. Nucleic Acids Res (2012) 2.61
BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions. Nucleic Acids Res (2012) 2.56
E-MSD: improving data deposition and structure quality. Nucleic Acids Res (2006) 2.41
PDTD: a web-accessible protein database for drug target identification. BMC Bioinformatics (2008) 2.35
Gene3D: merging structure and function for a Thousand genomes. Nucleic Acids Res (2009) 2.34
PDBe: Protein Data Bank in Europe. Nucleic Acids Res (2013) 2.16
PSI-2: structural genomics to cover protein domain family space. Structure (2009) 1.92
Interactome3D: adding structural details to protein networks. Nat Methods (2012) 1.89
TargetMine, an integrated data warehouse for candidate gene prioritisation and target discovery. PLoS One (2011) 1.89
PDBe: Protein Data Bank in Europe. Nucleic Acids Res (2010) 1.88
Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB. Bioinformatics (2012) 1.82
The many faces of protein-protein interactions: A compendium of interface geometry. PLoS Comput Biol (2006) 1.71
FireDB--a database of functionally important residues from proteins of known structure. Nucleic Acids Res (2006) 1.45
Improving disease gene prioritization using the semantic similarity of Gene Ontology terms. Bioinformatics (2010) 1.37
The AnnoLite and AnnoLyze programs for comparative annotation of protein structures. BMC Bioinformatics (2007) 1.33
The Protein Data Bank in Europe (PDBe): bringing structure to biology. Acta Crystallogr D Biol Crystallogr (2011) 1.21
DBAli tools: mining the protein structure space. Nucleic Acids Res (2007) 1.19
PROCOGNATE: a cognate ligand domain mapping for enzymes. Nucleic Acids Res (2007) 1.18
SSMap: a new UniProt-PDB mapping resource for the curation of structural-related information in the UniProt/Swiss-Prot Knowledgebase. BMC Bioinformatics (2008) 1.18
pdbFun: mass selection and fast comparison of annotated PDB residues. Nucleic Acids Res (2005) 1.17
SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein-Protein Interactions. Nucleic Acids Res (2007) 1.15
The role of structural bioinformatics resources in the era of integrative structural biology. Acta Crystallogr D Biol Crystallogr (2013) 1.15
ProBiS-2012: web server and web services for detection of structurally similar binding sites in proteins. Nucleic Acids Res (2012) 1.11
The role of balanced training and testing data sets for binary classifiers in bioinformatics. PLoS One (2013) 1.09
Amino acid changes in disease-associated variants differ radically from variants observed in the 1000 genomes project dataset. PLoS Comput Biol (2013) 1.07
MoKCa database--mutations of kinases in cancer. Nucleic Acids Res (2008) 1.06
Mapping small molecule binding data to structural domains. BMC Bioinformatics (2012) 1.05
Structural similarity-based predictions of protein interactions between HIV-1 and Homo sapiens. Virol J (2010) 1.00
Structural motifs recurring in different folds recognize the same ligand fragments. BMC Bioinformatics (2009) 0.94
Prediction of phenotypes of missense mutations in human proteins from biological assemblies. Proteins (2012) 0.92
3DSwap: curated knowledgebase of proteins involved in 3D domain swapping. Database (Oxford) (2011) 0.90
The Gene3D Web Services: a platform for identifying, annotating and comparing structural domains in protein sequences. Nucleic Acids Res (2011) 0.90
Large-scale analysis of conserved rare codon clusters suggests an involvement in co-translational molecular recognition events. Bioinformatics (2012) 0.88
Exploiting protein structure data to explore the evolution of protein function and biological complexity. Philos Trans R Soc Lond B Biol Sci (2006) 0.85
Vivaldi: visualization and validation of biomacromolecular NMR structures from the PDB. Proteins (2013) 0.85
Novel search method for the discovery of functional relationships. Bioinformatics (2011) 0.84
A new approach to assess and predict the functional roles of proteins across all known structures. J Struct Funct Genomics (2011) 0.83
KB-Rank: efficient protein structure and functional annotation identification via text query. J Struct Funct Genomics (2012) 0.77
FragKB: structural and literature annotation resource of conserved peptide fragments and residues. PLoS One (2010) 0.77
The human "magnesome": detecting magnesium binding sites on human proteins. BMC Bioinformatics (2012) 0.77
Alternative splicing tends to avoid partial removals of protein-protein interaction sites. BMC Genomics (2013) 0.76
A method for supporting retrieval of articles on protein structure analysis considering users' intention. BMC Bioinformatics (2011) 0.75
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The Pfam protein families database. Nucleic Acids Res (2004) 56.46
The KEGG resource for deciphering the genome. Nucleic Acids Res (2004) 53.05
UniProt: the Universal Protein knowledgebase. Nucleic Acids Res (2004) 29.05
The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res (2003) 24.72
The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology. Nucleic Acids Res (2004) 18.75
Announcing the worldwide Protein Data Bank. Nat Struct Biol (2003) 17.06
SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Res (2004) 15.21
IntAct: an open source molecular interaction database. Nucleic Acids Res (2004) 15.02
Database resources of the National Center for Biotechnology Information: update. Nucleic Acids Res (2004) 9.85
MEROPS: the peptidase database. Nucleic Acids Res (2004) 7.27
The EMBL Nucleotide Sequence Database. Nucleic Acids Res (2004) 6.72
IntEnz, the integrated relational enzyme database. Nucleic Acids Res (2004) 4.65
Assigning genomic sequences to CATH. Nucleic Acids Res (2000) 4.22
ASD: the Alternative Splicing Database. Nucleic Acids Res (2004) 3.26
A unifold, mesofold, and superfold model of protein fold use. Proteins (2002) 1.59
PDBSprotEC: a Web-accessible database linking PDB chains to EC numbers via SwissProt. Bioinformatics (2004) 1.41
The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res (2000) 67.44
The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res (2004) 54.37
The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999. Nucleic Acids Res (1999) 39.32
The transcriptional landscape of the mammalian genome. Science (2005) 37.63
A novel method for automatic functional annotation of proteins. Bioinformatics (1999) 33.88
Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr D Biol Crystallogr (2004) 31.52
InterProScan--an integration platform for the signature-recognition methods in InterPro. Bioinformatics (2001) 28.35
Comparative genomics of the eukaryotes. Science (2000) 26.62
InterProScan: protein domains identifier. Nucleic Acids Res (2005) 18.82
IntAct--open source resource for molecular interaction data. Nucleic Acids Res (2006) 13.82
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The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1998. Nucleic Acids Res (1998) 10.20
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The SWISS-PROT protein sequence data bank and its new supplement TREMBL. Nucleic Acids Res (1996) 6.14
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Filtering erroneous protein annotation. Bioinformatics (2004) 6.02
VARSPLIC: alternatively-spliced protein sequences derived from SWISS-PROT and TrEMBL. Bioinformatics (2000) 5.03
CluSTr: a database of clusters of SWISS-PROT+TrEMBL proteins. Nucleic Acids Res (2001) 4.59
Automatic rule generation for protein annotation with the C4.5 data mining algorithm applied on SWISS-PROT. Bioinformatics (2001) 4.35
Accessing and distributing EMBL data using CORBA (common object request broker architecture). Genome Biol (2000) 4.26
SOAP-based services provided by the European Bioinformatics Institute. Nucleic Acids Res (2005) 3.93
PDBe: Protein Data Bank in Europe. Nucleic Acids Res (2009) 3.48
E-MSD: an integrated data resource for bioinformatics. Nucleic Acids Res (2004) 3.43
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The human proteomics initiative (HPI). Trends Biotechnol (2001) 2.65
Removing redundancy in SWISS-PROT and TrEMBL. Bioinformatics (1999) 2.59
E-MSD: improving data deposition and structure quality. Nucleic Acids Res (2006) 2.41
Synergy between medical informatics and bioinformatics: facilitating genomic medicine for future health care. J Biomed Inform (2004) 2.25
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Improvements to CluSTr: the database of SWISS-PROT+TrEMBL protein clusters. Nucleic Acids Res (2003) 1.30
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Clustering and analysis of protein families. Curr Opin Struct Biol (2001) 1.14
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Swissknife - 'lazy parsing' of SWISS-PROT entries. Bioinformatics (1999) 1.02
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Molecular modeling and mutagenesis studies of the N-terminal domains of galectin-3: evidence for participation with the C-terminal carbohydrate recognition domain in oligosaccharide binding. Glycobiology (2000) 0.85
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Gliclazide treatment of streptozotocin diabetic rats restores GLUT4 protein content and basal glucose uptake in skeletal muscle. Metabolism (1997) 0.79
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