Published in Nucleic Acids Res on January 01, 2000
PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr (2010) 108.52
MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr (2009) 53.36
MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics (2004) 50.89
Human non-synonymous SNPs: server and survey. Nucleic Acids Res (2002) 50.45
MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res (2007) 37.31
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2000) 34.79
Protein structure prediction on the Web: a case study using the Phyre server. Nat Protoc (2009) 32.64
The Pfam protein families database. Nucleic Acids Res (2007) 30.53
I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc (2010) 22.66
Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res (2001) 22.33
Database resources of the National Center for Biotechnology Information: 2002 update. Nucleic Acids Res (2002) 19.40
GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res (2012) 19.19
I-TASSER server for protein 3D structure prediction. BMC Bioinformatics (2008) 18.28
Database resources of the National Center for Biotechnology. Nucleic Acids Res (2003) 18.26
The UCSC Genome Browser database: update 2010. Nucleic Acids Res (2009) 16.58
TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res (2005) 14.15
Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res (2007) 13.44
The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res (2006) 13.44
The Jpred 3 secondary structure prediction server. Nucleic Acids Res (2008) 13.32
BASys: a web server for automated bacterial genome annotation. Nucleic Acids Res (2005) 13.30
The Protein Data Bank: unifying the archive. Nucleic Acids Res (2002) 12.37
PDBsum: summaries and analyses of PDB structures. Nucleic Acids Res (2001) 12.21
The Protein Information Resource: an integrated public resource of functional annotation of proteins. Nucleic Acids Res (2002) 12.20
Rfam: updates to the RNA families database. Nucleic Acids Res (2008) 11.61
The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation. Nucleic Acids Res (2006) 11.15
The PredictProtein server. Nucleic Acids Res (2004) 10.89
MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res (2004) 10.71
ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res (2005) 10.60
BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities. Nucleic Acids Res (2006) 10.36
Automated main-chain model building by template matching and iterative fragment extension. Acta Crystallogr D Biol Crystallogr (2002) 10.34
BioMagResBank. Nucleic Acids Res (2007) 10.21
The ASTRAL Compendium in 2004. Nucleic Acids Res (2004) 10.03
MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes. Nucleic Acids Res (2004) 9.86
A crystallographic perspective on sharing data and knowledge. J Comput Aided Mol Des (2014) 9.85
ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Res (2010) 9.68
The IUPHAR/BPS Guide to PHARMACOLOGY: an expert-driven knowledgebase of drug targets and their ligands. Nucleic Acids Res (2013) 9.61
Matthews coefficient probabilities: Improved estimates for unit cell contents of proteins, DNA, and protein-nucleic acid complex crystals. Protein Sci (2003) 9.53
An integrated software suite for surface-based analyses of cerebral cortex. J Am Med Inform Assoc (2001) 9.41
BALBES: a molecular-replacement pipeline. Acta Crystallogr D Biol Crystallogr (2007) 9.29
A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci (2003) 9.25
CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. Nucleic Acids Res (2006) 9.19
ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res (2007) 9.16
ANODE: anomalous and heavy-atom density calculation. J Appl Crystallogr (2011) 8.79
Comparative protein structure modeling using Modeller. Curr Protoc Bioinformatics (2006) 8.72
ESPript/ENDscript: Extracting and rendering sequence and 3D information from atomic structures of proteins. Nucleic Acids Res (2003) 8.66
The Reactome pathway knowledgebase. Nucleic Acids Res (2013) 8.56
SNAP: predict effect of non-synonymous polymorphisms on function. Nucleic Acids Res (2007) 8.46
The Protein Data Bank and structural genomics. Nucleic Acids Res (2003) 8.34
BRENDA, the enzyme database: updates and major new developments. Nucleic Acids Res (2004) 8.21
Escherichia coli K-12: a cooperatively developed annotation snapshot--2005. Nucleic Acids Res (2006) 7.93
The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema. Nucleic Acids Res (2005) 7.81
E-MSD: the European Bioinformatics Institute Macromolecular Structure Database. Nucleic Acids Res (2003) 7.79
The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Res (2010) 7.68
The ProDom database of protein domain families: more emphasis on 3D. Nucleic Acids Res (2005) 7.66
Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level. Nucleic Acids Res (2001) 7.27
The mouse Gene Expression Database (GXD): updates and enhancements. Nucleic Acids Res (2004) 7.26
Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol (2004) 7.17
Global rigid body modeling of macromolecular complexes against small-angle scattering data. Biophys J (2005) 7.10
PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res (2007) 7.07
The distribution and query systems of the RCSB Protein Data Bank. Nucleic Acids Res (2004) 7.03
MMDB: 3D structure data in Entrez. Nucleic Acids Res (2000) 6.93
Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS). Nat Methods (2009) 6.77
The SUPERFAMILY database in 2004: additions and improvements. Nucleic Acids Res (2004) 6.72
Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard. Acta Crystallogr D Biol Crystallogr (2009) 6.47
The RCSB PDB information portal for structural genomics. Nucleic Acids Res (2006) 6.36
Fitness cost of escape mutations in p24 Gag in association with control of human immunodeficiency virus type 1. J Virol (2006) 6.30
BioJava: an open-source framework for bioinformatics. Bioinformatics (2008) 6.17
Finding nuclear localization signals. EMBO Rep (2000) 6.15
ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins. Nucleic Acids Res (2006) 6.13
JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Res (2013) 6.12
Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline. Proc Natl Acad Sci U S A (2002) 6.00
RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution). RNA (2008) 5.94
ProFunc: a server for predicting protein function from 3D structure. Nucleic Acids Res (2005) 5.79
MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res (2006) 5.79
iRefIndex: a consolidated protein interaction database with provenance. BMC Bioinformatics (2008) 5.77
The FAIR Guiding Principles for scientific data management and stewardship. Sci Data (2016) 5.76
The RCSB Protein Data Bank: new resources for research and education. Nucleic Acids Res (2012) 5.73
SCRATCH: a protein structure and structural feature prediction server. Nucleic Acids Res (2005) 5.59
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
Benchmarking sets for molecular docking. J Med Chem (2006) 5.57
Automated structure prediction of weakly homologous proteins on a genomic scale. Proc Natl Acad Sci U S A (2004) 5.44
RNAML: a standard syntax for exchanging RNA information. RNA (2002) 5.34
The HADDOCK web server for data-driven biomolecular docking. Nat Protoc (2010) 5.22
ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement. Nucleic Acids Res (2004) 5.19
Protein kinase CK2: structure, regulation and role in cellular decisions of life and death. Biochem J (2003) 5.11
Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics (2010) 5.08
Ab initio modeling of small proteins by iterative TASSER simulations. BMC Biol (2007) 5.07
Automated ligand fitting by core-fragment fitting and extension into density. Acta Crystallogr D Biol Crystallogr (2006) 5.03
FFAS03: a server for profile--profile sequence alignments. Nucleic Acids Res (2005) 4.99
TTD: Therapeutic Target Database. Nucleic Acids Res (2002) 4.91
Remediation of the protein data bank archive. Nucleic Acids Res (2007) 4.89
STITCH: interaction networks of chemicals and proteins. Nucleic Acids Res (2007) 4.88
Cyclic coordinate descent: A robotics algorithm for protein loop closure. Protein Sci (2003) 4.82
A new measure for functional similarity of gene products based on Gene Ontology. BMC Bioinformatics (2006) 4.82
A robust bulk-solvent correction and anisotropic scaling procedure. Acta Crystallogr D Biol Crystallogr (2005) 4.82
MuSiC: identifying mutational significance in cancer genomes. Genome Res (2012) 4.73
PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites. Genome Biol (2007) 4.66
Natural beta-sheet proteins use negative design to avoid edge-to-edge aggregation. Proc Natl Acad Sci U S A (2002) 4.66
Adding some SPICE to DAS. Bioinformatics (2005) 4.62
TOUCHSTONE II: a new approach to ab initio protein structure prediction. Biophys J (2003) 4.62
Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A (1988) 193.60
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers (1983) 99.69
The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol (1977) 90.57
SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol (1995) 74.88
The interpretation of protein structures: estimation of static accessibility. J Mol Biol (1971) 40.24
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
Surprising similarities in structure comparison. Curr Opin Struct Biol (1996) 22.27
The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids. Biophys J (1992) 21.67
SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model. Acta Crystallogr D Biol Crystallogr (1999) 19.57
Touring protein fold space with Dali/FSSP. Nucleic Acids Res (1998) 18.00
PDBsum: a Web-based database of summaries and analyses of all PDB structures. Trends Biochem Sci (1997) 12.04
Macromolecular Crystallographic Information File. Methods Enzymol (1997) 11.94
A dynamic look at structures: WWW-Entrez and the Molecular Modeling Database. Trends Biochem Sci (1996) 9.95
The HSSP database of protein structure-sequence alignments and family profiles. Nucleic Acids Res (1998) 9.59
Creation of a nuclear magnetic resonance data repository and literature database. Protein Seq Data Anal (1989) 8.61
Protein structural topology: Automated analysis and diagrammatic representation. Protein Sci (1999) 8.24
GRASS: a server for the graphical representation and analysis of structures. Protein Sci (1999) 7.73
IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN). Abbreviations and symbols for the description of conformations of polynucleotide chains. Recommendations 1982. Eur J Biochem (1983) 7.62
Image library of biological macromolecules. Comput Appl Biosci (1996) 7.51
Development of Internet-based multimedia applications. Trends Biochem Sci (1999) 7.34
Developing protein documentaries and other multimedia presentations for molecular biology. Pac Symp Biocomput (1999) 7.33
Macromolecular structure databases: past progress and future challenges. Acta Crystallogr D Biol Crystallogr (1998) 7.26
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng (1998) 28.09
The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids. Biophys J (1992) 21.67
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
Phases of biomarker development for early detection of cancer. J Natl Cancer Inst (2001) 10.37
Development of Internet-based multimedia applications. Trends Biochem Sci (1999) 7.34
Developing protein documentaries and other multimedia presentations for molecular biology. Pac Symp Biocomput (1999) 7.33
Macromolecular structure databases: past progress and future challenges. Acta Crystallogr D Biol Crystallogr (1998) 7.26
Urinary and sexual function after radical prostatectomy for clinically localized prostate cancer: the Prostate Cancer Outcomes Study. JAMA (2000) 6.37
The P53 pathway: what questions remain to be explored? Cell Death Differ (2006) 4.91
Assembly of the cadherin-catenin complex in vitro with recombinant proteins. J Cell Sci (1994) 4.81
The Protein Data Bank and the challenge of structural genomics. Nat Struct Biol (2000) 4.21
The PDB data uniformity project. Nucleic Acids Res (2001) 3.65
Associations of race/ethnicity, education, and dietary intervention with the validity and reliability of a food frequency questionnaire: the Women's Health Trial Feasibility Study in Minority Populations. Am J Epidemiol (1997) 3.57
Structure of tyrosyl-tRNA synthetase refined at 2.3 A resolution. Interaction of the enzyme with the tyrosyl adenylate intermediate. J Mol Biol (1989) 3.16
Selection and analysis of human immunodeficiency virus type 1 variants with increased resistance to ABT-538, a novel protease inhibitor. J Virol (1995) 3.05
Improving crystallographic macromolecular images: the real-space approach. Annu Rev Biophys Biophys Chem (1987) 2.86
Schistosomiasis in the People's Republic of China: prospects and challenges for the 21st century. Clin Microbiol Rev (2001) 2.85
Central melanocortin receptors regulate insulin action. J Clin Invest (2001) 2.83
Optimizing endoscopic biopsy detection of early cancers in Barrett's high-grade dysplasia. Am J Gastroenterol (2000) 2.58
STAR/mmCIF: an ontology for macromolecular structure. Bioinformatics (2000) 2.51
Plakoglobin and beta-catenin: distinct but closely related. Science (1992) 2.40
Overfeeding rapidly induces leptin and insulin resistance. Diabetes (2001) 2.32
To treat or not to treat: the case of tuberculosis. J Math Biol (1997) 1.98
The galactan-binding immunoglobulin Fab J539: an X-ray diffraction study at 2.6-A resolution. Proteins (1986) 1.96
An alternative view of protein fold space. Proteins (2000) 1.95
The protein kinase resource. Trends Biochem Sci (1997) 1.85
Site-specific mutagenesis using asymmetric polymerase chain reaction and a single mutant primer. Nucleic Acids Res (1990) 1.82
Common EF-hand motifs in cholinesterases and neuroligins suggest a role for Ca2+ binding in cell surface associations. Protein Sci (2000) 1.79
Work site-based cancer prevention: primary results from the Working Well Trial. Am J Public Health (1996) 1.74
The link between helminthic infection and atopy. Parasitol Today (2000) 1.72
Crystal structures of native and inhibited forms of human cathepsin D: implications for lysosomal targeting and drug design. Proc Natl Acad Sci U S A (1993) 1.67
Cell of origin determines clinically relevant subtypes of MLL-rearranged AML. Leukemia (2012) 1.64
The CCPN project: an interim report on a data model for the NMR community. Nat Struct Biol (2002) 1.58
MLL-AF9 and FLT3 cooperation in acute myelogenous leukemia: development of a model for rapid therapeutic assessment. Leukemia (2007) 1.57
Crystallographic refinement of the three-dimensional structure of the FabD1.3-lysozyme complex at 2.5-A resolution. J Biol Chem (1991) 1.54
The prosegment-subtilisin BPN' complex: crystal structure of a specific 'foldase'. Structure (1995) 1.53
A dietary intervention in primary care practice: the Eating Patterns Study. Am J Public Health (1997) 1.52
Propofol EC50 for inducing loss of consciousness is lower in the luteal phase of the menstrual cycle. Br J Anaesth (2013) 1.50
A comparison of generalized linear mixed model procedures with estimating equations for variance and covariance parameter estimation in longitudinal studies and group randomized trials. Stat Med (2001) 1.48
Structure of HIV-1 protease with KNI-272, a tight-binding transition-state analog containing allophenylnorstatine. Structure (1995) 1.47
Seattle 5 a Day worksite program to increase fruit and vegetable consumption. Prev Med (2001) 1.47
Occupational risk factors for nasopharyngeal cancer among female textile workers in Shanghai, China. Occup Environ Med (2006) 1.46
A framework for scientific data modeling and automated software development. Bioinformatics (2004) 1.45
Tyrosyl-tRNA synthetase forms a mononucleotide-binding fold. J Mol Biol (1982) 1.44
A new algorithm for the alignment of multiple protein structures using Monte Carlo optimization. Pac Symp Biocomput (2001) 1.43
Are specialist physicians missing out on the e-Health boat? Intern Med J (2009) 1.42
NF-kappa B activation mediates doxorubicin-induced cell death in N-type neuroblastoma cells. J Biol Chem (2001) 1.39
What will be the outcome of the outcomes movement? Aust N Z J Med (1995) 1.39
Baseline fruit and vegetable intake among adults in seven 5 a day study centers located in diverse geographic areas. J Am Diet Assoc (1999) 1.38
Construction of transgenic mice with tissue-specific acceleration of mitochondrial DNA mutagenesis. Genomics (2000) 1.38
Regions of the JAK2 tyrosine kinase required for coupling to the growth hormone receptor. J Biol Chem (1995) 1.38
Control of clonorchiasis by repeated treatments with praziquantel. Korean J Parasitol (2001) 1.35
A database and tools for 3-D protein structure comparison and alignment using the Combinatorial Extension (CE) algorithm. Nucleic Acids Res (2001) 1.34
Pandemic H1N1 influenza: predicting the course of a pandemic and assessing the efficacy of the planned vaccination programme in the United States. Euro Surveill (2009) 1.31
Population mixing, socioeconomic status and incidence of childhood acute lymphoblastic leukaemia in England and Wales: analysis by census ward. Br J Cancer (2008) 1.31
Design and implementation of a collaborative molecular graphics environment. J Mol Graph Model (2001) 1.30
The fern sporangium: a unique catapult. Science (2012) 1.28
Overexpression of the D-alanine racemase gene confers resistance to D-cycloserine in Mycobacterium smegmatis. J Bacteriol (1997) 1.28
The role of cyclooxygenase 2 in ulcerative colitis-associated neoplasia. Am J Pathol (2000) 1.27
Structure and inhibition of plasmepsin II, a hemoglobin-degrading enzyme from Plasmodium falciparum. Proc Natl Acad Sci U S A (1996) 1.26
Structural basis of drug resistance for the V82A mutant of HIV-1 proteinase. Nat Struct Biol (1995) 1.25
Limited human-to-human transmission of avian influenza A(H7N9) virus, Shanghai, China, March to April 2013. Euro Surveill (2014) 1.25
A randomized trial of a tailored, self-help dietary intervention: the Puget Sound Eating Patterns study. Prev Med (2000) 1.24
An analysis of side-chain conformation in proteins. Int J Pept Protein Res (1979) 1.24
Delayed cerebral ischaemia after subarachnoid haemorrhage: looking beyond vasospasm. Br J Anaesth (2012) 1.24
Three-dimensional structure of a heteroclitic antigen-antibody cross-reaction complex. Proc Natl Acad Sci U S A (1993) 1.22
Catalysis of a protein folding reaction: mechanistic implications of the 2.0 A structure of the subtilisin-prodomain complex. Biochemistry (1995) 1.20
Protein data representation and query using optimized data decomposition. Comput Appl Biosci (1997) 1.19
A baseline study on the importance of bovines for human Schistosoma japonicum infection around Poyang Lake, China. Am J Trop Med Hyg (2001) 1.18
Creating an artificial two-dimensional Skyrmion crystal by nanopatterning. Phys Rev Lett (2013) 1.18
Genetic tuning of the novel avian influenza A(H7N9) virus during interspecies transmission, China, 2013. Euro Surveill (2014) 1.16
Why is it difficult for staff to discuss advance directives with chronic dialysis patients? J Am Soc Nephrol (1996) 1.16
Modulation of human glutathione S-transferases by botanically defined vegetable diets. Cancer Epidemiol Biomarkers Prev (2000) 1.15
Brassica vegetables increase and apiaceous vegetables decrease cytochrome P450 1A2 activity in humans: changes in caffeine metabolite ratios in response to controlled vegetable diets. Carcinogenesis (2000) 1.15
hSSB1 binds and protects p21 from ubiquitin-mediated degradation and positively correlates with p21 in human hepatocellular carcinomas. Oncogene (2011) 1.14
The safety and quality of decision support systems. Yearb Med Inform (2006) 1.12
The rate of missed test results in an emergency department: an evaluation using an electronic test order and results viewing system. Methods Inf Med (2009) 1.12
Negative and positive mRNA splicing elements act competitively to regulate human immunodeficiency virus type 1 vif gene expression. J Virol (2008) 1.11
Development of a transposon mutagenesis system for Mycobacterium avium subsp. paratuberculosis. FEMS Microbiol Lett (1999) 1.11
Three-dimensional structures of the free and the antigen-complexed Fab from monoclonal anti-lysozyme antibody D44.1. J Mol Biol (1994) 1.09
Solvent rearrangement in an antigen-antibody interface introduced by site-directed mutagenesis of the antibody combining site. J Mol Biol (1994) 1.08
An algorithm based on graph theory for the assembly of contigs in physical mapping of DNA. Comput Appl Biosci (1994) 1.08
Conserved key amino acid positions (CKAAPs) derived from the analysis of common substructures in proteins. Proteins (2001) 1.06
Energetics of folding subtilisin BPN'. Biochemistry (1992) 1.05