Published in J Struct Funct Genomics on January 01, 2004
Proteome-wide prediction of novel DNA/RNA-binding proteins using amino acid composition and periodicity in the hyperthermophilic archaeon Pyrococcus furiosus. DNA Res (2007) 0.85
Identification of DNA-binding proteins using support vector machine with sequence information. Comput Math Methods Med (2013) 0.79
The Protein Data Bank: unifying the archive. Nucleic Acids Res (2002) 12.37
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
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
The RCSB Protein Data Bank: new resources for research and education. Nucleic Acids Res (2012) 5.73
Remediation of the protein data bank archive. Nucleic Acids Res (2007) 4.89
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
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
Automated and accurate deposition of structures solved by X-ray diffraction to the Protein Data Bank. Acta Crystallogr D Biol Crystallogr (2004) 3.11
Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster. Proc Natl Acad Sci U S A (2006) 3.06
Catabolite activator protein: DNA binding and transcription activation. Curr Opin Struct Biol (2004) 2.91
Structural basis of transcription activation: the CAP-alpha CTD-DNA complex. Science (2002) 2.67
Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins. Nucleic Acids Res (2003) 2.37
Data deposition and annotation at the worldwide protein data bank. Mol Biotechnol (2008) 2.30
Ligand Depot: a data warehouse for ligands bound to macromolecules. Bioinformatics (2004) 2.21
Web 3DNA--a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures. Nucleic Acids Res (2009) 2.08
Outcome of a workshop on applications of protein models in biomedical research. Structure (2009) 2.05
The Protein Model Portal. J Struct Funct Genomics (2008) 2.01
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
Validation of protein structures for protein data bank. Methods Enzymol (2003) 1.73
Recommendations of the wwPDB NMR Validation Task Force. Structure (2013) 1.57
Conformational and quantitative characterization of oritavancin-peptidoglycan complexes in whole cells of Staphylococcus aureus by in vivo 13C and 15N labeling. J Mol Biol (2006) 1.50
Salt bridges: geometrically specific, designable interactions. Proteins (2011) 1.39
Report of the wwPDB Small-Angle Scattering Task Force: data requirements for biomolecular modeling and the PDB. Structure (2013) 1.39
Detecting transcriptionally active regions using genomic tiling arrays. Genome Biol (2006) 1.37
The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods. J Struct Funct Genomics (2011) 1.36
Large macromolecular complexes in the Protein Data Bank: a status report. Structure (2005) 1.36
Generalized fragment picking in Rosetta: design, protocols and applications. PLoS One (2011) 1.35
Design of a switchable eliminase. Proc Natl Acad Sci U S A (2011) 1.34
Consensus motif for integrin transmembrane helix association. Proc Natl Acad Sci U S A (2009) 1.33
Three-dimensional EM structure of an intact activator-dependent transcription initiation complex. Proc Natl Acad Sci U S A (2009) 1.26
The Nucleic Acid Database: new features and capabilities. Nucleic Acids Res (2013) 1.23
Data management challenges in three-dimensional EM. Nat Struct Mol Biol (2012) 1.19
Trendspotting in the Protein Data Bank. FEBS Lett (2013) 1.19
Signatures of protein-DNA recognition in free DNA binding sites. J Mol Biol (2009) 1.17
Bending of DNA by asymmetric charge neutralization: all-atom energy simulations. J Am Chem Soc (2002) 1.16
Small-molecule inhibitors of integrin alpha2beta1 that prevent pathological thrombus formation via an allosteric mechanism. Proc Natl Acad Sci U S A (2009) 1.13
Alteration of the oxygen-dependent reactivity of de novo Due Ferri proteins. Nat Chem (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
Representation of viruses in the remediated PDB archive. Acta Crystallogr D Biol Crystallogr (2008) 1.08
Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: recognition of pyrimidine-purine and purine-purine steps. J Mol Biol (2006) 1.07
Future structural genomics initiatives: an interview with Helen Berman, director of the Protein Data Bank. Interview by Wendy A Warr. J Comput Aided Mol Des (2008) 1.07
Design of a data model for developing laboratory information management and analysis systems for protein production. Proteins (2005) 1.06
Improving the representation of peptide-like inhibitor and antibiotic molecules in the Protein Data Bank. Biopolymers (2014) 1.06
Inferring condition-specific modulation of transcription factor activity in yeast through regulon-based analysis of genomewide expression. PLoS One (2008) 1.05
The 2010 cryo-EM modeling challenge. Biopolymers (2012) 1.02
The Protein Structure Initiative Structural Biology Knowledgebase Technology Portal: a structural biology web resource. J Struct Funct Genomics (2012) 1.00
Data deposition and annotation at the worldwide protein data bank. Methods Mol Biol (2008) 1.00
Nitric oxide synthase domain interfaces regulate electron transfer and calmodulin activation. Proc Natl Acad Sci U S A (2013) 1.00
Chemical annotation of small and peptide-like molecules at the Protein Data Bank. Database (Oxford) (2013) 0.99
Statistical models for discerning protein structures containing the DNA-binding helix-turn-helix motif. J Mol Biol (2003) 0.96
Experimental and computational evaluation of forces directing the association of transmembrane helices. J Am Chem Soc (2009) 0.96
Structural investigation of Borrelia burgdorferi OspB, a bactericidal Fab target. J Biol Chem (2005) 0.95
Linking tumor cell cytotoxicity to mechanism of drug action: an integrated analysis of gene expression, small-molecule screening and structural databases. Proteins (2005) 0.94
3DNALandscapes: a database for exploring the conformational features of DNA. Nucleic Acids Res (2009) 0.90
Realism about PDB. Nat Biotechnol (2007) 0.89
New information content in RNA base pairing deduced from quantitative analysis of high-resolution structures. Methods (2009) 0.89
Conformational effects of Gly-X-Gly interruptions in the collagen triple helix. J Mol Biol (2006) 0.89
Residual brain infection in relapsing-fever borreliosis. J Infect Dis (2006) 0.89
Biophysical characterization of natural and mutant fluorescent proteins cloned from zooxanthellate corals. FEBS Lett (2004) 0.86
Understanding the Sequence Preference of Recurrent RNA Building Blocks using Quantum Chemistry: The Intrastrand RNA Dinucleotide Platform. J Chem Theory Comput (2011) 0.85
A structural similarity analysis of double-helical DNA. J Mol Biol (2004) 0.85
Analyzing and building nucleic acid structures with 3DNA. J Vis Exp (2013) 0.84
Safeguarding the integrity of protein archive. Nature (2010) 0.84
The Protein Data Bank and lessons in data management. Brief Bioinform (2004) 0.84
Weak operator binding enhances simulated lac repressor-mediated DNA looping. Biopolymers (2013) 0.83
Approaches toward the directed design of a vaccine against Borrelia burgdorferi. J Infect Dis (2002) 0.82
E. coli trp repressor forms a domain-swapped array in aqueous alcohol. Structure (2004) 0.82
Workshop on the validation and modeling of electron cryo-microscopy structures of biological nanomachines. Pac Symp Biocomput (2011) 0.81
Feature extraction using molecular planes for fuzzy relational clustering of a flexible dopamine reuptake inhibitor. J Chem Inf Model (2007) 0.81
Revealing structural views of biology. Biopolymers (2013) 0.79
Structure of the Escherichia coli RNA polymerase alpha subunit C-terminal domain. Acta Crystallogr D Biol Crystallogr (2010) 0.79
Quality assurance for the query and distribution systems of the RCSB Protein Data Bank. Database (Oxford) (2011) 0.77
Environment-dependent long-range structural distortion in a temperature-sensitive point mutant. Protein Sci (2011) 0.75
27 Analysis of DNA deformations in transcription factor-DNA complexes. J Biomol Struct Dyn (2015) 0.75
Fundamentals of DNA and RNA structure. Methods Biochem Anal (2003) 0.75
Crystals of trp repressor suitable for high-resolution neutron Laue diffraction studies. Acta Crystallogr D Biol Crystallogr (2002) 0.75
Protein structure annotation resources. Methods Mol Biol (2015) 0.75