Published in Nucleic Acids Res on November 27, 2012
Pfam: the protein families database. Nucleic Acids Res (2013) 22.48
The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res (2013) 10.24
PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Res (2013) 7.63
DrugBank 4.0: shedding new light on drug metabolism. Nucleic Acids Res (2013) 6.73
Scalable web services for the PSIPRED Protein Analysis Workbench. Nucleic Acids Res (2013) 4.24
The RCSB Protein Data Bank: views of structural biology for basic and applied research and education. Nucleic Acids Res (2014) 3.57
MEROPS: the database of proteolytic enzymes, their substrates and inhibitors. Nucleic Acids Res (2013) 3.28
The Protein Model Portal--a comprehensive resource for protein structure and model information. Database (Oxford) (2013) 2.76
The immune epitope database (IEDB) 3.0. Nucleic Acids Res (2014) 2.50
Classification of intrinsically disordered regions and proteins. Chem Rev (2014) 2.48
Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res (2014) 2.37
The transporter classification database. Nucleic Acids Res (2013) 2.12
MMDB and VAST+: tracking structural similarities between macromolecular complexes. Nucleic Acids Res (2013) 1.79
IMGT®, the international ImMunoGeneTics information system® 25 years on. Nucleic Acids Res (2014) 1.64
MobiDB 2.0: an improved database of intrinsically disordered and mobile proteins. Nucleic Acids Res (2014) 1.64
SCOP2 prototype: a new approach to protein structure mining. Nucleic Acids Res (2013) 1.55
The neXtProt knowledgebase on human proteins: current status. Nucleic Acids Res (2015) 1.42
Whole-genome sequencing of six dog breeds from continuous altitudes reveals adaptation to high-altitude hypoxia. Genome Res (2014) 1.42
BioDB extractor: customized data extraction system for commonly used bioinformatics databases. BioData Min (2015) 1.40
New insights on the mechanism of the K(+-) independent activity of crenarchaeota pyruvate kinases. PLoS One (2015) 1.39
DNASU plasmid and PSI:Biology-Materials repositories: resources to accelerate biological research. Nucleic Acids Res (2013) 1.33
iPfam: a database of protein family and domain interactions found in the Protein Data Bank. Nucleic Acids Res (2013) 1.26
The Nucleic Acid Database: new features and capabilities. Nucleic Acids Res (2013) 1.23
Human antimicrobial peptides and proteins. Pharmaceuticals (Basel) (2014) 1.23
APD3: the antimicrobial peptide database as a tool for research and education. Nucleic Acids Res (2015) 1.22
Navigating the changing learning landscape: perspective from bioinformatics.ca. Brief Bioinform (2013) 1.18
50 years of allosteric interactions: the twists and turns of the models. Nat Rev Mol Cell Biol (2013) 1.17
canSAR: updated cancer research and drug discovery knowledgebase. Nucleic Acids Res (2013) 1.15
Evaluation of predictions in the CASP10 model refinement category. Proteins (2014) 1.15
3did: a catalog of domain-based interactions of known three-dimensional structure. Nucleic Acids Res (2013) 1.14
ModBase, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res (2013) 1.12
MoonProt: a database for proteins that are known to moonlight. Nucleic Acids Res (2014) 1.11
Structure of a designed protein cage that self-assembles into a highly porous cube. Nat Chem (2014) 1.05
MultitaskProtDB: a database of multitasking proteins. Nucleic Acids Res (2013) 1.02
TFClass: a classification of human transcription factors and their rodent orthologs. Nucleic Acids Res (2014) 1.01
CancerPPD: a database of anticancer peptides and proteins. Nucleic Acids Res (2014) 0.99
IDEAL in 2014 illustrates interaction networks composed of intrinsically disordered proteins and their binding partners. Nucleic Acids Res (2013) 0.98
RepeatsDB: a database of tandem repeat protein structures. Nucleic Acids Res (2013) 0.97
Structure of a PL17 family alginate lyase demonstrates functional similarities among exotype depolymerases. J Biol Chem (2014) 0.95
Platinum: a database of experimentally measured effects of mutations on structurally defined protein-ligand complexes. Nucleic Acids Res (2014) 0.94
FeatureViewer, a BioJS component for visualization of position-based annotations in protein sequences. F1000Res (2014) 0.93
Genome-scale identification and characterization of moonlighting proteins. Biol Direct (2014) 0.92
Helminth.net: expansions to Nematode.net and an introduction to Trematode.net. Nucleic Acids Res (2014) 0.91
Database-Guided Discovery of Potent Peptides to Combat HIV-1 or Superbugs. Pharmaceuticals (Basel) (2013) 0.90
From sequence to enzyme mechanism using multi-label machine learning. BMC Bioinformatics (2014) 0.90
BioBenchmark Toyama 2012: an evaluation of the performance of triple stores on biological data. J Biomed Semantics (2014) 0.90
Small molecule annotation for the Protein Data Bank. Database (Oxford) (2014) 0.90
The HIV mutation browser: a resource for human immunodeficiency virus mutagenesis and polymorphism data. PLoS Comput Biol (2014) 0.89
Improved methods for classification, prediction, and design of antimicrobial peptides. Methods Mol Biol (2015) 0.89
The RCSB protein data bank: integrative view of protein, gene and 3D structural information. Nucleic Acids Res (2016) 0.89
Evidence for Adaptation to the Tibetan Plateau Inferred from Tibetan Loach Transcriptomes. Genome Biol Evol (2015) 0.88
CapR: revealing structural specificities of RNA-binding protein target recognition using CLIP-seq data. Genome Biol (2014) 0.88
RCSB PDB Mobile: iOS and Android mobile apps to provide data access and visualization to the RCSB Protein Data Bank. Bioinformatics (2014) 0.87
dbSNO 2.0: a resource for exploring structural environment, functional and disease association and regulatory network of protein S-nitrosylation. Nucleic Acids Res (2014) 0.87
Selecting targets from eukaryotic parasites for structural genomics and drug discovery. Methods Mol Biol (2014) 0.87
Identifying the macromolecular targets of de novo-designed chemical entities through self-organizing map consensus. Proc Natl Acad Sci U S A (2014) 0.87
Navigating 3D electron microscopy maps with EM-SURFER. BMC Bioinformatics (2015) 0.86
Improving the accuracy of the structure prediction of the third hypervariable loop of the heavy chains of antibodies. Bioinformatics (2014) 0.86
SysPTM 2.0: an updated systematic resource for post-translational modification. Database (Oxford) (2014) 0.86
Combining machine learning systems and multiple docking simulation packages to improve docking prediction reliability for network pharmacology. PLoS One (2013) 0.86
PEPstrMOD: structure prediction of peptides containing natural, non-natural and modified residues. Biol Direct (2015) 0.85
An estimated 5% of new protein structures solved today represent a new Pfam family. Acta Crystallogr D Biol Crystallogr (2013) 0.85
Systematic detection of internal symmetry in proteins using CE-Symm. J Mol Biol (2014) 0.85
Most partial domains in proteins are alignment and annotation artifacts. Genome Biol (2015) 0.85
Preventing E-cadherin aberrant N-glycosylation at Asn-554 improves its critical function in gastric cancer. Oncogene (2015) 0.85
Computational methods and resources for the interpretation of genomic variants in cancer. BMC Genomics (2015) 0.85
Beyond protein expression, MOPED goes multi-omics. Nucleic Acids Res (2014) 0.85
Recent improvements to Binding MOAD: a resource for protein-ligand binding affinities and structures. Nucleic Acids Res (2014) 0.84
New mini- zincin structures provide a minimal scaffold for members of this metallopeptidase superfamily. BMC Bioinformatics (2014) 0.84
Structure-Based, Rational Design of T Cell Receptors. Front Immunol (2013) 0.84
What's that gene (or protein)? Online resources for exploring functions of genes, transcripts, and proteins. Mol Biol Cell (2014) 0.84
PoSSuM v.2.0: data update and a new function for investigating ligand analogs and target proteins of small-molecule drugs. Nucleic Acids Res (2014) 0.84
EzCatDB: the enzyme reaction database, 2015 update. Nucleic Acids Res (2014) 0.84
Histone proteolysis: a proposal for categorization into 'clipping' and 'degradation'. Bioessays (2014) 0.84
Systems biology of the structural proteome. BMC Syst Biol (2016) 0.84
SeqDepot: streamlined database of biological sequences and precomputed features. Bioinformatics (2013) 0.83
Structural insight into operator dre-sites recognition and effector binding in the GntR/HutC transcription regulator NagR. Nucleic Acids Res (2015) 0.83
GeneProf data: a resource of curated, integrated and reusable high-throughput genomics experiments. Nucleic Acids Res (2013) 0.83
PLIC: protein-ligand interaction clusters. Database (Oxford) (2014) 0.83
Routine phasing of coiled-coil protein crystal structures with AMPLE. IUCrJ (2015) 0.82
A novel p.Leu(381)Phe mutation in presenilin 1 is associated with very early onset and unusually fast progressing dementia as well as lysosomal inclusions typically seen in Kufs disease. J Alzheimers Dis (2014) 0.82
ABS-Scan: In silico alanine scanning mutagenesis for binding site residues in protein-ligand complex. F1000Res (2014) 0.82
MP:PD--a data base of internal packing densities, internal packing defects and internal waters of helical membrane proteins. Nucleic Acids Res (2013) 0.82
The RCSB PDB "Molecule of the Month": Inspiring a Molecular View of Biology. PLoS Biol (2015) 0.81
ProteomeScout: a repository and analysis resource for post-translational modifications and proteins. Nucleic Acids Res (2014) 0.81
Biophysical constraints on the evolution of tissue structure and function. J Physiol (2014) 0.80
Structure based approach for understanding organism specific recognition of protein-RNA complexes. Biol Direct (2015) 0.80
VarMod: modelling the functional effects of non-synonymous variants. Nucleic Acids Res (2014) 0.80
Cyclic diguanylate monophosphate directly binds to human siderocalin and inhibits its antibacterial activity. Nat Commun (2015) 0.80
Molecule Targeting Glucosyltransferase Inhibits Streptococcus mutans Biofilm Formation and Virulence. Antimicrob Agents Chemother (2015) 0.79
ProBLM web server: protein and membrane placement and orientation package. Comput Math Methods Med (2014) 0.79
A WXW motif is required for the anticancer activity of the TAT-RasGAP317-326 peptide. J Biol Chem (2014) 0.79
Integrative visual analysis of protein sequence mutations. BMC Proc (2014) 0.79
FluKB: A Knowledge-Based System for Influenza Vaccine Target Discovery and Analysis of the Immunological Properties of Influenza Viruses. J Immunol Res (2015) 0.79
Structural and biochemical basis for mannan utilization by Caldanaerobius polysaccharolyticus strain ATCC BAA-17. J Biol Chem (2014) 0.79
KBDOCK 2013: a spatial classification of 3D protein domain family interactions. Nucleic Acids Res (2013) 0.79
Curcumin Reduces the Motility of Salmonella enterica Serovar Typhimurium by Binding to the Flagella, Thereby Leading to Flagellar Fragility and Shedding. J Bacteriol (2016) 0.78
Network understanding of herb medicine via rapid identification of ingredient-target interactions. Sci Rep (2014) 0.78
Epitope mapping of M36, a human antibody domain with potent and broad HIV-1 inhibitory activity. PLoS One (2013) 0.78
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31
The Protein Data Bank. Nucleic Acids Res (2000) 187.10
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
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers (1983) 99.69
SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol (1995) 74.88
The Pfam protein families database. Nucleic Acids Res (2011) 33.46
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng (1998) 28.09
BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences. FEMS Microbiol Lett (1999) 25.40
Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res (2011) 18.50
Announcing the worldwide Protein Data Bank. Nat Struct Biol (2003) 17.06
TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res (2005) 14.15
HMMER web server: interactive sequence similarity searching. Nucleic Acids Res (2011) 13.00
BioMagResBank. Nucleic Acids Res (2007) 10.21
Pfam: multiple sequence alignments and HMM-profiles of protein domains. Nucleic Acids Res (1998) 8.87
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2011) 8.62
The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Res (2010) 7.68
The Gene Ontology: enhancements for 2011. Nucleic Acids Res (2011) 5.82
Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics (2003) 5.46
Remediation of the protein data bank archive. Nucleic Acids Res (2007) 4.89
The Transporter Classification Database: recent advances. Nucleic Acids Res (2008) 4.26
Advances and pitfalls of protein structural alignment. Curr Opin Struct Biol (2009) 4.17
EMDataBank.org: unified data resource for CryoEM. Nucleic Acids Res (2010) 3.32
The structure and evolution of the major capsid protein of a large, lipid-containing DNA virus. Proc Natl Acad Sci U S A (2002) 3.07
PDBe: Protein Data Bank in Europe. Nucleic Acids Res (2011) 3.03
Extending CATH: increasing coverage of the protein structure universe and linking structure with function. Nucleic Acids Res (2010) 2.93
The Molecular Biology Toolkit (MBT): a modular platform for developing molecular visualization applications. BMC Bioinformatics (2005) 2.60
Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format. Nucleic Acids Res (2011) 2.57
Pre-calculated protein structure alignments at the RCSB PDB website. Bioinformatics (2010) 2.28
Ligand Depot: a data warehouse for ligands bound to macromolecules. Bioinformatics (2004) 2.21
PDP: protein domain parser. Bioinformatics (2003) 1.94
Generating triangulated macromolecular surfaces by Euclidean Distance Transform. PLoS One (2009) 1.54
Mitogenic conversion of transforming growth factor-beta1 effect by oncogenic Ha-Ras-induced activation of the mitogen-activated protein kinase signaling pathway in human prostate cancer. Cancer Res (2000) 1.33
Drawing the PDB: Protein-Ligand Complexes in Two Dimensions. ACS Med Chem Lett (2010) 1.31
Substrate specificity within a family of outer membrane carboxylate channels. PLoS Biol (2012) 1.23
Will widgets and semantic tagging change computational biology? PLoS Comput Biol (2010) 1.21
Fold recognition methods. Methods Biochem Anal (2003) 1.20
Detection of spatial correlations in protein structures and molecular complexes. Structure (2012) 1.11
Promoting a structural view of biology for varied audiences: an overview of RCSB PDB resources and experiences. J Appl Crystallogr (2010) 1.09
Structural and functional insights into DNA-end processing by the archaeal HerA helicase-NurA nuclease complex. Nucleic Acids Res (2011) 1.02
Interesting structures: education and outreach at the RCSB Protein Data Bank. PLoS Biol (2008) 0.90
Crystal structure of Hsp33 chaperone (TM1394) from Thermotoga maritima at 2.20 A resolution. Proteins (2005) 0.85
AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem (2009) 23.19
The Protein Data Bank. Acta Crystallogr D Biol Crystallogr (2002) 14.44
The Protein Data Bank: unifying the archive. Nucleic Acids Res (2002) 12.37
A semiempirical free energy force field with charge-based desolvation. J Comput Chem (2007) 8.40
The Protein Data Bank and structural genomics. Nucleic Acids Res (2003) 8.34
The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema. Nucleic Acids Res (2005) 7.81
The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Res (2010) 7.68
Ten simple rules for getting published. PLoS Comput Biol (2005) 7.22
The distribution and query systems of the RCSB Protein Data Bank. Nucleic Acids Res (2004) 7.03
The RCSB PDB information portal for structural genomics. Nucleic Acids Res (2006) 6.36
RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution). RNA (2008) 5.94
Remediation of the protein data bank archive. Nucleic Acids Res (2007) 4.89
BioLit: integrating biological literature with databases. Nucleic Acids Res (2008) 4.85
Outcome of the first electron microscopy validation task force meeting. Structure (2012) 4.35
TargetDB: a target registration database for structural genomics projects. Bioinformatics (2004) 4.17
SuperTarget and Matador: resources for exploring drug-target relationships. Nucleic Acids Res (2007) 3.82
PDBML: the representation of archival macromolecular structure data in XML. Bioinformatics (2004) 3.64
The RNA Ontology Consortium: an open invitation to the RNA community. RNA (2006) 3.60
EMDataBank.org: unified data resource for CryoEM. Nucleic Acids Res (2010) 3.32
Ten simple rules for getting grants. PLoS Comput Biol (2006) 3.13
Ten simple rules for a successful collaboration. PLoS Comput Biol (2007) 3.12
Automated and accurate deposition of structures solved by X-ray diffraction to the Protein Data Bank. Acta Crystallogr D Biol Crystallogr (2004) 3.11
BioJava: an open-source framework for bioinformatics in 2012. Bioinformatics (2012) 2.94
Catabolite activator protein: DNA binding and transcription activation. Curr Opin Struct Biol (2004) 2.91
Drug discovery using chemical systems biology: identification of the protein-ligand binding network to explain the side effects of CETP inhibitors. PLoS Comput Biol (2009) 2.84
Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock. Proteins (2002) 2.70
Structural basis of transcription activation: the CAP-alpha CTD-DNA complex. Science (2002) 2.67
The Molecular Biology Toolkit (MBT): a modular platform for developing molecular visualization applications. BMC Bioinformatics (2005) 2.60
Empirical entropic contributions in computational docking: evaluation in APS reductase complexes. J Comput Chem (2008) 2.59
Ten simple rules for making good oral presentations. PLoS Comput Biol (2007) 2.57
Structural evolution of the protein kinase-like superfamily. PLoS Comput Biol (2005) 2.48
Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments. Proc Natl Acad Sci U S A (2008) 2.44
Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins. Nucleic Acids Res (2003) 2.37
Phylogeny determined by protein domain content. Proc Natl Acad Sci U S A (2005) 2.37
Drug discovery using chemical systems biology: repositioning the safe medicine Comtan to treat multi-drug and extensively drug resistant tuberculosis. PLoS Comput Biol (2009) 2.35
The Protein Feature Ontology: a tool for the unification of protein feature annotations. Bioinformatics (2008) 2.33
The cAMP binding domain: an ancient signaling module. Proc Natl Acad Sci U S A (2004) 2.32
Outcome of a workshop on archiving structural models of biological macromolecules. Structure (2006) 2.32
Drug discovery using chemical systems biology: weak inhibition of multiple kinases may contribute to the anti-cancer effect of nelfinavir. PLoS Comput Biol (2011) 2.31
Data deposition and annotation at the worldwide protein data bank. Mol Biotechnol (2008) 2.30
Pre-calculated protein structure alignments at the RCSB PDB website. Bioinformatics (2010) 2.28
ElliPro: a new structure-based tool for the prediction of antibody epitopes. BMC Bioinformatics (2008) 2.26
Ligand Depot: a data warehouse for ligands bound to macromolecules. Bioinformatics (2004) 2.21
MSDsite: a database search and retrieval system for the analysis and viewing of bound ligands and active sites. Proteins (2005) 2.17
Open access: taking full advantage of the content. PLoS Comput Biol (2008) 2.14
Antibody-protein interactions: benchmark datasets and prediction tools evaluation. BMC Struct Biol (2007) 2.14
Immune epitope database analysis resource (IEDB-AR). Nucleic Acids Res (2008) 2.14
Modern proteomes contain putative imprints of ancient shifts in trace metal geochemistry. Proc Natl Acad Sci U S A (2006) 2.10
Immune epitope database analysis resource. Nucleic Acids Res (2012) 2.09
The Mycobacterium tuberculosis drugome and its polypharmacological implications. PLoS Comput Biol (2010) 2.07
Outcome of a workshop on applications of protein models in biomedical research. Structure (2009) 2.05
Functional coverage of the human genome by existing structures, structural genomics targets, and homology models. PLoS Comput Biol (2005) 2.04
The protein structure initiative structural genomics knowledgebase. Nucleic Acids Res (2008) 2.03
The Protein Model Portal. J Struct Funct Genomics (2008) 2.01
An ontology driven architecture for derived representations of macromolecular structure. Bioinformatics (2002) 1.97
Drug off-target effects predicted using structural analysis in the context of a metabolic network model. PLoS Comput Biol (2010) 1.97
Biodiversity data should be published, cited, and peer reviewed. Trends Ecol Evol (2013) 1.97
RNA conformational classes. Nucleic Acids Res (2004) 1.92
BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions. J Biomol NMR (2008) 1.89
Ten simple rules for reviewers. PLoS Comput Biol (2006) 1.84
Ten simple rules for selecting a postdoctoral position. PLoS Comput Biol (2006) 1.77
Novel computational approaches to polypharmacology as a means to define responses to individual drugs. Annu Rev Pharmacol Toxicol (2011) 1.76
Validation of protein structures for protein data bank. Methods Enzymol (2003) 1.73
History of biological metal utilization inferred through phylogenomic analysis of protein structures. Proc Natl Acad Sci U S A (2010) 1.71
A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites. BMC Bioinformatics (2007) 1.70